Re: [R] x[0]: Can '0' be made an allowed index in R?

[Spencer Graves]

Convert to character:


goofy <- 1:9
names(goofy) <- (-4):4
goofy[as.character(0)]
goofy["-2"]


  sg


On 4/22/24 10:31 AM, Ebert,Timothy Aaron wrote:

You could have negative indices. There are two ways to do this.
1) provide a large offset.
Offset <- 30
for (i in -29 to 120) { print(df[i+Offset])}


2) use absolute values if all indices are negative.
for (i in -200 to -1) {print(df[abs(i)])}

Tim



-Original Message-
From: R-help  On Behalf Of Peter Dalgaard via 
R-help
Sent: Monday, April 22, 2024 10:36 AM
To: Rolf Turner 
Cc: R help project ; Hans W 
Subject: Re: [R] x[0]: Can '0' be made an allowed index in R?

[External Email]

Heh. Did anyone bring up negative indices yet?

-pd


On 22 Apr 2024, at 10:46 , Rolf Turner  wrote:


See fortunes::fortune(36).

cheers,

Rolf Turner

--
Honorary Research Fellow
Department of Statistics
University of Auckland
Stats. Dep't. (secretaries) phone:
 +64-9-373-7599 ext. 89622
Home phone: +64-9-480-4619

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat/
.ethz.ch%2Fmailman%2Flistinfo%2Fr-help=05%7C02%7Ctebert%40ufl.edu
%7C79ca6aadcaee4aa3241308dc62d986f6%7C0d4da0f84a314d76ace60a62331e1b84
%7C0%7C0%7C638493933686698527%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAw
MDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=
wmv9OYcMES0nElT9OAKTdjBk%2BB55bQ7BjxOuaVVkPg4%3D=0
PLEASE do read the posting guide
http://www.r/
-project.org%2Fposting-guide.html=05%7C02%7Ctebert%40ufl.edu%7C79
ca6aadcaee4aa3241308dc62d986f6%7C0d4da0f84a314d76ace60a62331e1b84%7C0%
7C0%7C638493933686711061%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiL
CJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=AP78X
nfKrX6B0YVM0N76ty9v%2Fw%2BchHIytw33X7M9umE%3D=0
and provide commented, minimal, self-contained, reproducible code.


--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 
Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] understanding predict.lm

[Spencer Graves]

Doh! Thanks very much. sg


On 11/6/23 5:17 PM, John Fox wrote:

Dear Spencer,

You need the t distribution with correct df, not the standard-normal 
distribution:


 > pt(-z.confInt/2, df=13)
     1 2 3 4 5 6 7 8 9    10    11
0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025
    12    13
0.025 0.025

 > pt(-z.predInt/2, df=13)
     1 2 3 4 5 6 7 8 9    10    11
0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025 0.025
    12    13
0.025 0.025

I hope this helps,
  John


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] understanding predict.lm

[Spencer Graves]

Hello, All:


	  I am unable to manually replicate predict.lm, specifically comparing 
se.fit with (fit[,3]-fit[,2]): I think their ratio should be 
2*qnorm((1-level)/2), and that's not what I'm getting.



	  Consider the following slight modification of the first example in 
help('predict.lm'):



set.seed(1)
x <- rnorm(15)
y <- x + rnorm(15)
predict(lm(y ~ x))
new <- data.frame(x = seq(-3, 3, 0.5))
predict(lm(y ~ x), new, se.fit = TRUE)
pred.w.plim <- predict(lm(y ~ x), new, interval = "prediction",
   se.fit = TRUE)
pred.w.clim <- predict(lm(y ~ x), new, interval = "confidence",
   se.fit = TRUE)

(z.confInt <- with(pred.w.clim, (fit[,3]-fit[,2])/se.fit))
pnorm(-z.confInt/2)

s.pred <- sqrt(with(pred.w.plim,
se.fit^2+residual.scale^2))
(z.predInt <- with(pred.w.plim, (fit[,3]-fit[,2])/s.pred))
pnorm(-z.predInt/2)


	  ** This gives me 0.01537207. I do not understand why it's not 0.025 
with level = 0.95.



  Can someone help me understand this?
  Thanks,
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] simulating future observations from heteroscedastic fits

[Spencer Graves]

On 8/31/23 1:27 AM, Spencer Graves wrote:

Hello, All:


   I want to simulate future observations from fits to 
heteroscedastic data. A simple example is as follows:



(DF3_2 <- data.frame(y=c(1:3, 10*(1:3)),
  gp=factor(rep(1:2, e=3


# I want to fit 4 models
# and simulate future observations from all 4:


fit11 <- lm(y~1, DF3_2)
fit21 <- lm(y~gp, DF3_2)

library(nlme)
(fit12 <- lme(y~1, data=DF3_2, random=~1|gp))
(fit22 <- lme(y~gp, data=DF3_2, random=~1|gp))
library(lme4)
(fit12r <- lmer(y~1+(1|gp), data=DF3_2, REML=FALSE))
(fit22r <- lmer(y~gp+(1|gp), data=DF3_2, REML=FALSE))

# I can simulate what I want for fit11 and fit21
# as follows:

simPred <- function(object, nSims=2){
   pred <- predict(object, DF3_2[6,], se.fit=TRUE,
   interval='prediction')
   with(pred, fit[1, 'fit'] +
  se.fit*rt(nSims, df))
}
simPred(fit11)
simPred(fit21)


# How can I do the same with either fit12 and fit22
# or fit12r and fit22r?



I think I found it:


simPred4 <- function(object, nSims=2){
# class(object) = lmeeMod
  sim <- simulate(object, nsim=nSims,
  newdata=DF3_2[6,])
  sim
}

simPred4(fit12r)
simPred4(fit22r)



       Thanks,
   Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] simulating future observations from heteroscedastic fits

[Spencer Graves]

Hello, All:


	  I want to simulate future observations from fits to heteroscedastic 
data. A simple example is as follows:



(DF3_2 <- data.frame(y=c(1:3, 10*(1:3)),
 gp=factor(rep(1:2, e=3


# I want to fit 4 models
# and simulate future observations from all 4:


fit11 <- lm(y~1, DF3_2)
fit21 <- lm(y~gp, DF3_2)

library(nlme)
(fit12 <- lme(y~1, data=DF3_2, random=~1|gp))
(fit22 <- lme(y~gp, data=DF3_2, random=~1|gp))
library(lme4)
(fit12r <- lmer(y~1+(1|gp), data=DF3_2, REML=FALSE))
(fit22r <- lmer(y~gp+(1|gp), data=DF3_2, REML=FALSE))

# I can simulate what I want for fit11 and fit21
# as follows:

simPred <- function(object, nSims=2){
  pred <- predict(object, DF3_2[6,], se.fit=TRUE,
  interval='prediction')
  with(pred, fit[1, 'fit'] +
 se.fit*rt(nSims, df))
}
simPred(fit11)
simPred(fit21)


# How can I do the same with either fit12 and fit22
# or fit12r and fit22r?


      Thanks,
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] logLIk(lme(...))?

[Spencer Graves]

I found my problem:


The following function gave llGp1, llGp2 and ll22:


logLik_lm <- function(object){
  res <- resid(object)
  n <- length(res)
  s2MLE <- sum(res^2)/n
  lglk <- (-n/2)*(log(2*pi*s2MLE)+1)
  lglk
}
logLik(fitGp1)
logLik(fitGp1)-logLik_lm(fitGp1)
llGp1 - logLik_lm(fitGp1)


logLik(fitGp2)
logLik(fitGp2)-logLik_lm(fitGp2)
llGp2 - logLik_lm(fitGp2)

logLik(fit22)
logLik(fit22)-logLik_lm(fit22)
ll22 -logLik_lm(fit22)


	  These differences were all 0 to within roundoff error.  That 
confirmed for me that I could safely compare logLik.lm and logLik.lme.



	  What I thought should have been a linear operation wasn't.  Please 
excuse the waste of your time.



  Thanks,
      Spencer Graves


On 8/29/23 11:15 AM, Spencer Graves wrote:

Hello, all:


   I have a dataset with 2 groups.  I want to estimate 2 means and 2 
standard deviations.  I naively think I should be able to use lme to do 
that, e.g., lme(y~gp, random=y~1|gp, method='ML').  I think I should get 
the same answer as from lm(y~1, ...) within each level of group.  I can 
get the same means, but I don't know how to extract the within-gp 
standard deviations, and the sum of logLik for the latter two does not 
equal the former.



TOY EXAMPLE:


library(nlme)


set.seed(1)


lmePblm <- data.frame(y=c(rnorm(5, 1, 2), rnorm(5,3,5)),
   gp=factor(rep(1:2, each=5)))


fit22 <- lme(y~gp, lmePblm, random=~1|gp, method='ML')


fitGp1 <- lm(y~1, lmePblm[lmePblm$gp==1, ])


fitGp2 <- lm(y~1, lmePblm[lmePblm$gp==2, ])


(ll22 <- logLik(fit22))


(llGp1 <- logLik(fitGp1))


(llGp2 <- logLik(fitGp2))


# Why isn't (ll22 = llGp1+llGp2)?


(ll22 - llGp1-llGp2)


# And secondarily, how can I get the residual standard deviations
# within each gp from fit22?


   Thanks,
   Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] logLIk(lme(...))?

[Spencer Graves]

Hello, all:


	  I have a dataset with 2 groups.  I want to estimate 2 means and 2 
standard deviations.  I naively think I should be able to use lme to do 
that, e.g., lme(y~gp, random=y~1|gp, method='ML').  I think I should get 
the same answer as from lm(y~1, ...) within each level of group.  I can 
get the same means, but I don't know how to extract the within-gp 
standard deviations, and the sum of logLik for the latter two does not 
equal the former.



TOY EXAMPLE:


library(nlme)


set.seed(1)


lmePblm <- data.frame(y=c(rnorm(5, 1, 2), rnorm(5,3,5)),
  gp=factor(rep(1:2, each=5)))


fit22 <- lme(y~gp, lmePblm, random=~1|gp, method='ML')


fitGp1 <- lm(y~1, lmePblm[lmePblm$gp==1, ])


fitGp2 <- lm(y~1, lmePblm[lmePblm$gp==2, ])


(ll22 <- logLik(fit22))


(llGp1 <- logLik(fitGp1))


(llGp2 <- logLik(fitGp2))


# Why isn't (ll22 = llGp1+llGp2)?


(ll22 - llGp1-llGp2)


# And secondarily, how can I get the residual standard deviations
# within each gp from fit22?


      Thanks,
      Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Book Recommendation

[Spencer Graves]

library(sos)
(sql <- findFn('SQL'))


# This opened two tabs in the default browser on my computer just now. 
The second tab lists 298 different packages with help pages containing 
"SQL", sorted to put the package with the most matches first.  The first 
tab lists 1900 different help pages, sorted to put the highest ranking 
package first.



installPackages(sql)


# This installs the highest ranking packages, because the 'sos' code 
knows how to get more information about installed packages than about 
ones that are not installed. To get that information, I followed this 
"installPackages(sql)" with:



sqo


# Hadley Wickham is listed as an author on 14 of those packages. The 
RSQL and RSQLite are numbers 22 and 50 on that list.  RMySQL and 
RPostgreSQL are numbers 48 and 31, respectively.



	  If you are looking for course content, I suggest you consider using 
findFn with SQL and applications of greatest interest to your target 
audience.



  Spencer Graves


p.s.  DISCLAIMER:  I'm the lead author and maintainer of the sos package.


On 8/28/23 1:48 PM, Hadley Wickham wrote:

You might find this chapter of R for Data Science helpful:
https://r4ds.hadley.nz/databases

Hadley

On Tue, Aug 29, 2023 at 3:47 AM Stephen H. Dawson, DSL via R-help
 wrote:


Good Morning,


I am doing some research to develop a new course where I teach. I am
looking for a book to use in the course content to teach accomplishing
SQL in R.

Does anyone know of a book on this topic to recommend for consideration?


Thank You,
--
*Stephen Dawson, DSL*
/Executive Strategy Consultant/
Business & Technology
+1 (865) 804-3454
http://www.shdawson.com

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.






__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Book Recommendation

[Spencer Graves]

On 8/28/23 12:47 PM, Bert Gunter wrote:

I presume you are familiar with the RSQL and RSQLite packages and their
vignettes.

Can't offer any help, but a point of clarification:
When you say, "teach accomplishing SQL in R," do you explicitly mean using
SQL syntax in R to manipulate data or do you mean just doing SQL-like types
of data manipulation in R? For the former, I assume you would be using the
above-mentioned packages -- or perhaps others that I don't know about like
them. For the latter, which I think would be subsumed under "data wrangling
in R" there are tons of packages, tutorials, and books out there that one
could search for under that rubric. If neither of the above, further
clarification might help you get a better answer.

Cheers,
Bert

On Mon, Aug 28, 2023 at 8:47 AM Stephen H. Dawson, DSL via R-help <
r-help@r-project.org> wrote:


Good Morning,


I am doing some research to develop a new course where I teach. I am
looking for a book to use in the course content to teach accomplishing
SQL in R.

Does anyone know of a book on this topic to recommend for consideration?


Thank You,
--
*Stephen Dawson, DSL*
/Executive Strategy Consultant/
Business & Technology
+1 (865) 804-3454
http://www.shdawson.com

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Questions about R

[Spencer Graves]

Hi, Shaun:


	  I suggest you also check the Wikipedia article on "R (programming 
language)":



https://en.wikipedia.org/wiki/R_(programming_language)


	  That article has 115 numbered "References" that provide more 
information.  You don't have to believe anything you read anywhere. 
However you many know that almost anyone can change almost anything on 
Wikipedia.  What stays tends to be written from a neutral point of view 
citing credible sources.  Many Wikipedia articles contain sections on 
controveries, etc.  I don't find anything like that in this article, 
with good reason.



  Hope this helps.
  Spencer Graves


On 8/17/23 11:48 AM, Bert Gunter wrote:

Incidentally, you might be interested in the banner shown when R starts up:

"R is free software and comes with ABSOLUTELY NO WARRANTY."

I believe this is standard for open source software (upon which a lot of
organizations depend). In any case, that might be the most definitive and
"official" answer you can get.

Bert

On Thu, Aug 17, 2023 at 9:17 AM Bert Gunter  wrote:


This is a volunteer Help list for users of R, which is open source, so you
can see all its code. I can answer no to your questions, unless you are
using one of R's innumerable packages that interacts with the internet and
to which the user may give personal information to enable the desired
functionality (logins, etc.).  But of course how do you know that I am not
some malevolent agent or organization wishing to mislead you for my own
nefarious purposes?

Cheers,
Bert

On Thu, Aug 17, 2023 at 8:37 AM Shaun Parr 
wrote:




Sent from Outlook for Android<https://aka.ms/AAb9ysg>


Hi there,

My name is Shaun and I work in an organisation where one of our users
wishes to install the R software and our process is to assess the safety of
anyone software prior to authorisation. I can’t seem to locate all the
information that we require on the webpage, so could someone kindly advise
me of the following information please?

1. Please can you confirm what user information the software collects
(E.g. Name, password, e-mail address, any Personally Identifiable
Information etc)?
2. If any is collected, please can you confirm if the information
collected by the software stays locally on the device or if it is
transferred anywhere. If it is transferred, could you please advise where
it is transferred to (E.g. your own servers, or a third party data centre
such as Amazon Web Services or Azure)?
3. Are there any third-party components installed within the software
and, if so, are these also kept up-to-date?

If you could kindly advise this information, it would be really
appreciated, thank you 


Shaun

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.





[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Off-topic: ChatGPT Code Interpreter

[Spencer Graves]

	  I don't know about ChatGPT, but Daniel Kahneman won the 2002 Nobel 
Memorial Prize in Economics,[1] even though he's not an economist, for 
his leadership in creating a new subfield in the intersection of human 
psychology and economics now called "behavioral economics".[2] Then in 
2009 Kahneman and Gary Klein published an article on, "Conditions for 
intuitive expertise: a failure to disagree", which concluded that expert 
intuition is learned from frequent, rapid, high-quality feedback. 
People you do not learn from frequent, rapid, high-quality feedback can 
be beaten by simple heuristics developed by intelligent lay people.[3] 
That includes most professions, which Kahneman Sibony and Sunstein call 
"respect-experts".



	  Kahneman Sibony and Sunstein further report that with a little data, 
a regression model can outperform a simple heuristic, and with massive 
amounts of data, artificial intelligence can outperform regression 
models.[4]



	  An extreme but real example of current reality was describe in an 
article on "Asylum roulette":  With asylum judges in the same 
jurisdiction with cases assigned at random, one judge approved 5 percent 
of cases while another approved 88 percent.[5] However, virtually all 
"respect-experts" are influenced in their judgements by time of day and 
whether their favorite sports team won or lost the previous day.  That 
level of noise can be reduced dramatically by use of appropriate 
artificial intelligence.



  Comments?
  Spencer Graves


[1]


https://en.wikipedia.org/wiki/Daniel_Kahneman


[2]


https://en.wikipedia.org/wiki/Behavioral_economics


[3]


https://www.researchgate.net/publication/26798603_Conditions_for_Intuitive_Expertise_A_Failure_to_Disagree


[4]


Daniel Kahneman; Olivier Sibony; Cass Sunstein (2021). Noise: A Flaw in 
Human Judgment (Little, Brown and Company).



[5]


https://en.wikipedia.org/wiki/Refugee_roulette


On 7/17/23 1:46 PM, Bert Gunter wrote:

This is an **off-topic** post about the subject line, that I thought
might be of interest to the R Community. I hope this does not offend
anyone.

The widely known ChatGPT software now offers what  is called a "Code
Interpreter," that, among other things, purports to do "data
analysis."  (Search for articles with details.) One quote, from the
(online) NY Times, is:

"Arvind Narayanan, a professor of computer science at Princeton
University, cautioned that people should not become overly reliant on
code interpreter for data analysis as A.I. still produces inaccurate
results and misinformation.

'Appropriate data analysis requires just a lot of critical thinking
about the data,” he said.' "

Amen. ... Maybe.

(As this is off-topic, if you wish to reply to me, probably better to
do so privately).

Cheers to all,
Bert

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/31/23 2:12 PM, Viechtbauer, Wolfgang (NP) wrote:

How about using the same 'mar' for all plots, but adding an outer margin?

DAX <- EuStockMarkets[, 'DAX']
DAX. <- cbind(DAX, diff(log(DAX)), diff(diff(log(DAX
colnames(DAX.) <- c("DAX", 'vel (%)', 'accel (%)')
head(DAX.)

par(mfrow=c(3,1), mar=c(1,4.5,0,2), oma=c(3,0,1,0))

plot(DAX.[, 1], log='y', ylab='DAX', axes=FALSE)
axis(2)
box(col='grey')

plot(DAX.[, 2], ylab='vel (%)', axes=FALSE)
axis(2)
box(col='grey')

plot(DAX.[, 3], ylab='accel (%)', axes=FALSE)
axis(2)
box(col='grey')
axis(1)

Best,
Wolfgang



That's exactly what I needed.


Thanks, Spencer





-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Spencer Graves
Sent: Wednesday, 31 May, 2023 17:45
To: Eric Berger
Cc: r-help
Subject: Re: [R] plot level, velocity, acceleration with one x axis

On 5/31/23 9:20 AM, Eric Berger wrote:

I sent you an updated response to deal with the redundant copies of the x-axis.
Re-sending.


par(mfrow=c(3,1))
plot(DAX.[, 1], log='y', ylab='DAX', xaxt="n")
plot(DAX.[, 2], ylab='vel (%)', xaxt="n")
plot(DAX.[, 3], ylab='accel (%)')

  I got that.  The primary problem with that is that most of the
vertical space is reserved for axis labels, whether they are printed or
not.  If I squeeze the vertical dimension of the plot, I get, "figure
margins too large".  To control that, I need to set "mar" separately for
each panel, and then the plot regions for each are not the same size.
Using the "layout" function instead of "mfrow" is better, but I don't
see now to make that work consistently without fixing the aspect ratio.
There may be a way in the tidyverse, but I haven't found it yet.  The
only solution I've found so far that makes sense to me is to modify the
code for plot.ts to accept a vector for the log argument, with the
constraint that length(lot) = either 1 or ncol(x) and returning
invisibly an object that would make it feasible for a user to call
axis(2, ...) once for each vertical axis to handle cases where someone
wanted to a vertical scale different from linear and log.  I'd want to
make sure that lines.ts also works with this, because I want to add fits
and predictions.

  Comments?
  Thanks,
  Spencer Graves

** With either of the following plots, if I adjust the aspect ratio by
enlarging or reducing the vertical dimension of the plot, the relative
sizes of the plot regions change.

DAX <- EuStockMarkets[, 'DAX']
DAX. <- cbind(DAX, diff(log(DAX)), diff(diff(log(DAX
colnames(DAX.) <- c("DAX", 'vel (%)', 'accel (%)')
head(DAX.)

plot(DAX., log='xy')

op <- par(mfrow=c(3,1), mar=c(0, 4.1, 4.1, 2.1))
plot(DAX.[, 1], log='y', ylab='DAX', axes=FALSE)
axis(2)
box(col='grey')
par(mar=c(0, 4.1, 0, 2.1))
plot(DAX.[, 2], ylab='vel (%)', axes=FALSE)
axis(2)
box(col='grey')
par(mar=c(5.1, 4.1, 0, 2.1))
plot(DAX.[, 3], ylab='accel (%)', axes=FALSE)
axis(2)
box(col='grey')
axis(1)
par(op)


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/31/23 9:20 AM, Eric Berger wrote:

I sent you an updated response to deal with the redundant copies of the x-axis.
Re-sending.


par(mfrow=c(3,1))
plot(DAX.[, 1], log='y', ylab='DAX', xaxt="n")
plot(DAX.[, 2], ylab='vel (%)', xaxt="n")
plot(DAX.[, 3], ylab='accel (%)')


	  I got that.  The primary problem with that is that most of the 
vertical space is reserved for axis labels, whether they are printed or 
not.  If I squeeze the vertical dimension of the plot, I get, "figure 
margins too large".  To control that, I need to set "mar" separately for 
each panel, and then the plot regions for each are not the same size. 
Using the "layout" function instead of "mfrow" is better, but I don't 
see now to make that work consistently without fixing the aspect ratio. 
There may be a way in the tidyverse, but I haven't found it yet.  The 
only solution I've found so far that makes sense to me is to modify the 
code for plot.ts to accept a vector for the log argument, with the 
constraint that length(lot) = either 1 or ncol(x) and returning 
invisibly an object that would make it feasible for a user to call 
axis(2, ...) once for each vertical axis to handle cases where someone 
wanted to a vertical scale different from linear and log.  I'd want to 
make sure that lines.ts also works with this, because I want to add fits 
and predictions.



  Comments?
  Thanks,
  Spencer Graves


** With either of the following plots, if I adjust the aspect ratio by 
enlarging or reducing the vertical dimension of the plot, the relative 
sizes of the plot regions change.



DAX <- EuStockMarkets[, 'DAX']
DAX. <- cbind(DAX, diff(log(DAX)), diff(diff(log(DAX
colnames(DAX.) <- c("DAX", 'vel (%)', 'accel (%)')
head(DAX.)

plot(DAX., log='xy')

op <- par(mfrow=c(3,1), mar=c(0, 4.1, 4.1, 2.1))
plot(DAX.[, 1], log='y', ylab='DAX', axes=FALSE)
axis(2)
box(col='grey')
par(mar=c(0, 4.1, 0, 2.1))
plot(DAX.[, 2], ylab='vel (%)', axes=FALSE)
axis(2)
box(col='grey')
par(mar=c(5.1, 4.1, 0, 2.1))
plot(DAX.[, 3], ylab='accel (%)', axes=FALSE)
axis(2)
box(col='grey')
axis(1)
par(op)


> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.7.7

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 

LAPACK: 
/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; 
 LAPACK version 3.11.0


locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Chicago
tzcode source: internal

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.3.0  tools_4.3.0 rstudioapi_0.14



On Wed, May 31, 2023 at 4:27 PM Spencer Graves
 wrote:




On 5/30/23 10:23 AM, Eric Berger wrote:

What if you just precede these commands as follows:

par(mfrow=c(3,1))
plot(DAX.[, 1], log='y', ylab='DAX')
plot(DAX.[, 2], ylab='vel (%)')
plot(DAX.[, 3], ylab='accel (%)')


   Most of the space is consumed with two extraneous copies of the axis.
   We can get around that with three calls to par:


op <- par(mfrow=c(3,1), mar=c(0, 4.1, 4.1, 2.1))
plot(DAX.[, 1], log='y', ylab='DAX')
par(mar=c(0, 4.1, 0, 2.1))
plot(DAX.[, 2], ylab='vel (%)')
par(mar=c(5.1, 4.1, 0, 2.1))
plot(DAX.[, 3], ylab='accel (%)')
par(op)


   However, the three panels are NOT equal in size:  roughly 30% vs. 44%
vs. 26%.  I can get closer using layout, but if I change the aspect
ratio, it changes the relationship between the heights of the three
panels.


   That's the problem I'm trying to solve.  It's also why it makes sense
to me to modify plot.ts to accept a vector for the log argument, with
the constraint that length(lot) = either 1 or ncol(x).


   There may be a way to do it using gglot2 / the tidyverse, but I'm not
facile with that, and my web searches have so far failed to produce
anything better than modifying plot.ts.R (and then submitting such with
compatible changes to plot.ts.Rd), as I suggested earlier.


       ???
   Thanks,
   Spencer



On Tue, May 30, 2023 at 5:45 PM Spencer Graves
 wrote:




On 5/30/23 8:48 AM, Eric Berger wrote:

I am a bit confused as to what you are trying to achieve - and  even
if I could guess it is not clear what the interpretation would be.

head(DAX)

1628.75 1613.63 1606.51 1621.04 1618.16 1610.61

Including the leading NA's, what would be the 6 leading terms of the 3
series that you want to plot,
and what would be the Y labels that you want to appear at those levels
(assuming that there was a
Y label for each of them - just to understand the units you are talking about)



DAX <- EuStockMarkets[, 'DAX']
DAX. <- cbind(DAX, diff(log(DAX)), diff(diff(log(DAX
c

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/30/23 10:23 AM, Eric Berger wrote:

What if you just precede these commands as follows:

par(mfrow=c(3,1))
plot(DAX.[, 1], log='y', ylab='DAX')
plot(DAX.[, 2], ylab='vel (%)')
plot(DAX.[, 3], ylab='accel (%)')


	  Most of the space is consumed with two extraneous copies of the axis. 
 We can get around that with three calls to par:



op <- par(mfrow=c(3,1), mar=c(0, 4.1, 4.1, 2.1))
plot(DAX.[, 1], log='y', ylab='DAX')
par(mar=c(0, 4.1, 0, 2.1))
plot(DAX.[, 2], ylab='vel (%)')
par(mar=c(5.1, 4.1, 0, 2.1))
plot(DAX.[, 3], ylab='accel (%)')
par(op)


	  However, the three panels are NOT equal in size:  roughly 30% vs. 44% 
vs. 26%.  I can get closer using layout, but if I change the aspect 
ratio, it changes the relationship between the heights of the three 
panels.



	  That's the problem I'm trying to solve.  It's also why it makes sense 
to me to modify plot.ts to accept a vector for the log argument, with 
the constraint that length(lot) = either 1 or ncol(x).



	  There may be a way to do it using gglot2 / the tidyverse, but I'm not 
facile with that, and my web searches have so far failed to produce 
anything better than modifying plot.ts.R (and then submitting such with 
compatible changes to plot.ts.Rd), as I suggested earlier.



  ???
  Thanks,
  Spencer



On Tue, May 30, 2023 at 5:45 PM Spencer Graves
 wrote:




On 5/30/23 8:48 AM, Eric Berger wrote:

I am a bit confused as to what you are trying to achieve - and  even
if I could guess it is not clear what the interpretation would be.

head(DAX)

1628.75 1613.63 1606.51 1621.04 1618.16 1610.61

Including the leading NA's, what would be the 6 leading terms of the 3
series that you want to plot,
and what would be the Y labels that you want to appear at those levels
(assuming that there was a
Y label for each of them - just to understand the units you are talking about)



DAX <- EuStockMarkets[, 'DAX']
DAX. <- cbind(DAX, diff(log(DAX)), diff(diff(log(DAX
colnames(DAX.) <- c("DAX", 'vel (%)', 'accel (%)')
head(DAX.)


   DAX exhibits growth that is roughly exponential, so I want to plot it
on a log scale:


plot(DAX.[, 1], log='y', ylab='DAX')
plot(DAX.[, 2], ylab='vel (%)')
plot(DAX.[, 3], ylab='accel (%)')


   This is what I want as three panels of a single plot.


   I think I could get it by modifying the code for plot.ts so it
accepted ylab as a vector, etc., as I previously mentioned.


   What do you think?
   Thanks,
   Spencer Graves



On Tue, May 30, 2023 at 4:06 PM Spencer Graves
 wrote:




On 5/30/23 6:16 AM, Eric Berger wrote:

My code assumes that DAX is a ts object, as in your original post.

On Tue, May 30, 2023 at 2:06 PM Eric Berger  wrote:


Untested but why not

a <- cbind(log(DAX), exp(diff(log(DAX))), exp(diff(diff(log(DAX)
colnames(a) <- c("logDAX", "vel", "accel")
plot(a)



Progress, but we're not there yet.


a <- cbind(DAX, exp(diff(log(DAX))), exp(diff(diff(log(DAX)
colnames(a) <- c("logDAX", "vel", "accel")
plot(a)
plot(a, axes=FALSE, log='y')
axis(1)
axis(2)


How do I get each y axis labeled in its original units?  I can use
pretty to get where I want tick marks, but I don't know where to place
them "at" in calling axis(2, at= ___)?


(axlb1 <- pretty(range(a[, 1])))
(axlb2 <- pretty(range(log(a[, 2]), na.rm=TRUE)))
(axlb3 <- pretty(range(log(a[, 3]), na.rm=TRUE)))


This suggests I write my own modification of plot.ts that accepts 
log
as a character vector of length = ncol of the ts being plotted and
returns invisibly a list with the default "at" and "label" arguments
required to produce the default labeling.  Then a user who wants a log
scale for some but not all variables can get that easily and can further
modify any of those scales further if they don't like the default.


???
Thanks very much.
Spencer Graves



On Tue, May 30, 2023 at 1:46 PM Spencer Graves
 wrote:




On 5/29/23 2:37 AM, Eric Berger wrote:

How about this:

a <- cbind(AirPassengers, diff(log(AirPassengers)),
diff(diff(log(AirPassengers
colnames(a)[2:3] <- c("percent increase", "acceleration")
plot(a, xlab="year", main="AirPassengers")



 My real problem is more difficult:  I'm analyzing CO2 data from Our
World in Data (https://ourworldindata.org/co2-emissions), and I need to
plot the CO2 data on a log scale but velocity and acceleration on linear
scales.  The following is comparable:


str(DAX <- EuStockMarkets[, 'DAX'])
str(DAX. <- cbind(DAX, diff(log(DAX)),
  diff(diff(log(DAX)
colnames(DAX.)[2:3] <- c('vel', 'accel')
plot(DAX.)


 I want the first of the three panels to plot on the log scale, but
the other two on linear scales.  Th

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/30/23 8:48 AM, Eric Berger wrote:

I am a bit confused as to what you are trying to achieve - and  even
if I could guess it is not clear what the interpretation would be.

head(DAX)

1628.75 1613.63 1606.51 1621.04 1618.16 1610.61

Including the leading NA's, what would be the 6 leading terms of the 3
series that you want to plot,
and what would be the Y labels that you want to appear at those levels
(assuming that there was a
Y label for each of them - just to understand the units you are talking about)



DAX <- EuStockMarkets[, 'DAX']
DAX. <- cbind(DAX, diff(log(DAX)), diff(diff(log(DAX
colnames(DAX.) <- c("DAX", 'vel (%)', 'accel (%)')
head(DAX.)


	  DAX exhibits growth that is roughly exponential, so I want to plot it 
on a log scale:



plot(DAX.[, 1], log='y', ylab='DAX')
plot(DAX.[, 2], ylab='vel (%)')
plot(DAX.[, 3], ylab='accel (%)')


  This is what I want as three panels of a single plot.


	  I think I could get it by modifying the code for plot.ts so it 
accepted ylab as a vector, etc., as I previously mentioned.



  What do you think?
  Thanks,
  Spencer Graves



On Tue, May 30, 2023 at 4:06 PM Spencer Graves
 wrote:




On 5/30/23 6:16 AM, Eric Berger wrote:

My code assumes that DAX is a ts object, as in your original post.

On Tue, May 30, 2023 at 2:06 PM Eric Berger  wrote:


Untested but why not

a <- cbind(log(DAX), exp(diff(log(DAX))), exp(diff(diff(log(DAX)
colnames(a) <- c("logDAX", "vel", "accel")
plot(a)



   Progress, but we're not there yet.


a <- cbind(DAX, exp(diff(log(DAX))), exp(diff(diff(log(DAX)
colnames(a) <- c("logDAX", "vel", "accel")
plot(a)
plot(a, axes=FALSE, log='y')
axis(1)
axis(2)


   How do I get each y axis labeled in its original units?  I can use
pretty to get where I want tick marks, but I don't know where to place
them "at" in calling axis(2, at= ___)?


(axlb1 <- pretty(range(a[, 1])))
(axlb2 <- pretty(range(log(a[, 2]), na.rm=TRUE)))
(axlb3 <- pretty(range(log(a[, 3]), na.rm=TRUE)))


   This suggests I write my own modification of plot.ts that accepts log
as a character vector of length = ncol of the ts being plotted and
returns invisibly a list with the default "at" and "label" arguments
required to produce the default labeling.  Then a user who wants a log
scale for some but not all variables can get that easily and can further
modify any of those scales further if they don't like the default.


   ???
   Thanks very much.
   Spencer Graves



On Tue, May 30, 2023 at 1:46 PM Spencer Graves
 wrote:




On 5/29/23 2:37 AM, Eric Berger wrote:

How about this:

a <- cbind(AirPassengers, diff(log(AirPassengers)),
diff(diff(log(AirPassengers
colnames(a)[2:3] <- c("percent increase", "acceleration")
plot(a, xlab="year", main="AirPassengers")



My real problem is more difficult:  I'm analyzing CO2 data from Our
World in Data (https://ourworldindata.org/co2-emissions), and I need to
plot the CO2 data on a log scale but velocity and acceleration on linear
scales.  The following is comparable:


str(DAX <- EuStockMarkets[, 'DAX'])
str(DAX. <- cbind(DAX, diff(log(DAX)),
 diff(diff(log(DAX)
colnames(DAX.)[2:3] <- c('vel', 'accel')
plot(DAX.)


I want the first of the three panels to plot on the log scale, but
the other two on linear scales.  The obvious attempt does not work:


plot(DAX., log=c('y', '', ''))
#Error in length(log) && log != "" :
#  'length = 3' in coercion to 'logical(1)'


Trying to construct my own axes isn't easy, either:


str(logDAX <- cbind(log(DAX), diff(log(DAX)),
 diff(diff(log(DAX)
colnames(logDAX) <- c('logDAX', 'vel', 'accel')
plot(logDAX, axes=FALSE)
axis(1)
axis(2)


I'm thinking of creating my own copy of "plot.ts", and changing it 
so
it accepts the "log" argument as a vector of length equal to ncol of the
ts object to be plotted AND returning an object that would allow a user
to call "axis" ncol times.


Suggestions?


Thanks,
Spencer Graves



HTH,
Eric


On Mon, May 29, 2023 at 7:57 AM Spencer Graves
 wrote:


Hello, All:


 I want to plot level, velocity, and acceleration in three panels 
with
only one x axis.  The code below does this using "layout".  However, I
want the three plot areas to be of equal size, and this won't do that:
If I stretch the plot vertically, the relative sizes of the three panels
changes.  There's probably a way to do this with ggplot2, but I have yet
to find it.


 Suggestions?
 Thanks,
 Spencer Graves


str(AirTime <- as.numeric(time(AirPassengers)))
str(AP <- as.

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/30/23 6:16 AM, Eric Berger wrote:

My code assumes that DAX is a ts object, as in your original post.

On Tue, May 30, 2023 at 2:06 PM Eric Berger  wrote:


Untested but why not

a <- cbind(log(DAX), exp(diff(log(DAX))), exp(diff(diff(log(DAX)
colnames(a) <- c("logDAX", "vel", "accel")
plot(a)



  Progress, but we're not there yet.


a <- cbind(DAX, exp(diff(log(DAX))), exp(diff(diff(log(DAX)
colnames(a) <- c("logDAX", "vel", "accel")
plot(a)
plot(a, axes=FALSE, log='y')
axis(1)
axis(2)


	  How do I get each y axis labeled in its original units?  I can use 
pretty to get where I want tick marks, but I don't know where to place 
them "at" in calling axis(2, at= ___)?



(axlb1 <- pretty(range(a[, 1])))
(axlb2 <- pretty(range(log(a[, 2]), na.rm=TRUE)))
(axlb3 <- pretty(range(log(a[, 3]), na.rm=TRUE)))


	  This suggests I write my own modification of plot.ts that accepts log 
as a character vector of length = ncol of the ts being plotted and 
returns invisibly a list with the default "at" and "label" arguments 
required to produce the default labeling.  Then a user who wants a log 
scale for some but not all variables can get that easily and can further 
modify any of those scales further if they don't like the default.



  ???
  Thanks very much.
  Spencer Graves



On Tue, May 30, 2023 at 1:46 PM Spencer Graves
 wrote:




On 5/29/23 2:37 AM, Eric Berger wrote:

How about this:

a <- cbind(AirPassengers, diff(log(AirPassengers)),
diff(diff(log(AirPassengers
colnames(a)[2:3] <- c("percent increase", "acceleration")
plot(a, xlab="year", main="AirPassengers")



   My real problem is more difficult:  I'm analyzing CO2 data from Our
World in Data (https://ourworldindata.org/co2-emissions), and I need to
plot the CO2 data on a log scale but velocity and acceleration on linear
scales.  The following is comparable:


str(DAX <- EuStockMarkets[, 'DAX'])
str(DAX. <- cbind(DAX, diff(log(DAX)),
diff(diff(log(DAX)
colnames(DAX.)[2:3] <- c('vel', 'accel')
plot(DAX.)


   I want the first of the three panels to plot on the log scale, but
the other two on linear scales.  The obvious attempt does not work:


plot(DAX., log=c('y', '', ''))
#Error in length(log) && log != "" :
#  'length = 3' in coercion to 'logical(1)'


   Trying to construct my own axes isn't easy, either:


str(logDAX <- cbind(log(DAX), diff(log(DAX)),
diff(diff(log(DAX)
colnames(logDAX) <- c('logDAX', 'vel', 'accel')
plot(logDAX, axes=FALSE)
axis(1)
axis(2)


   I'm thinking of creating my own copy of "plot.ts", and changing it so
it accepts the "log" argument as a vector of length equal to ncol of the
ts object to be plotted AND returning an object that would allow a user
to call "axis" ncol times.


   Suggestions?


   Thanks,
   Spencer Graves



HTH,
Eric


On Mon, May 29, 2023 at 7:57 AM Spencer Graves
 wrote:


Hello, All:


I want to plot level, velocity, and acceleration in three panels 
with
only one x axis.  The code below does this using "layout".  However, I
want the three plot areas to be of equal size, and this won't do that:
If I stretch the plot vertically, the relative sizes of the three panels
changes.  There's probably a way to do this with ggplot2, but I have yet
to find it.


Suggestions?
Thanks,
Spencer Graves


str(AirTime <- as.numeric(time(AirPassengers)))
str(AP <- as.numeric(AirPassengers))

def.par <- par(no.readonly = TRUE) # save default, for resetting...
(mat3x1 <- matrix(1:3, 3))
plot3x1 <- layout(mat3x1, heights=c(1.4, 1, 1.5))
layout.show(plot3x1)

par(mar=c(0, 4.1, 4.1, 2.1))
plot(AirTime, AP, log='y', type='l', axes=FALSE,
main='AirPassengers', ylab='AirPassengers')
box(col='grey')
axis(2, las=1)

par(mar=c(0, 4.1, 0, 2.1))
vAP <- diff(log(AP))
plot(tail(AirTime, -1), vAP, type='l',
ylab='percent increase', axes=FALSE)
box(col='grey')
axis(2, las=1)

par(mar=c(5.1, 4.1, 0, 2.1))
plot(tail(AirTime, -2), diff(vAP), type='l',
ylab='acceleration', xlab='year',
las=1)
box(col='grey')

par(def.par)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/29/23 2:37 AM, Eric Berger wrote:

How about this:

a <- cbind(AirPassengers, diff(log(AirPassengers)),
diff(diff(log(AirPassengers
colnames(a)[2:3] <- c("percent increase", "acceleration")
plot(a, xlab="year", main="AirPassengers")



	  My real problem is more difficult:  I'm analyzing CO2 data from Our 
World in Data (https://ourworldindata.org/co2-emissions), and I need to 
plot the CO2 data on a log scale but velocity and acceleration on linear 
scales.  The following is comparable:



str(DAX <- EuStockMarkets[, 'DAX'])
str(DAX. <- cbind(DAX, diff(log(DAX)),
  diff(diff(log(DAX)
colnames(DAX.)[2:3] <- c('vel', 'accel')
plot(DAX.)


	  I want the first of the three panels to plot on the log scale, but 
the other two on linear scales.  The obvious attempt does not work:



plot(DAX., log=c('y', '', ''))
#Error in length(log) && log != "" :
#  'length = 3' in coercion to 'logical(1)'


  Trying to construct my own axes isn't easy, either:


str(logDAX <- cbind(log(DAX), diff(log(DAX)),
  diff(diff(log(DAX)
colnames(logDAX) <- c('logDAX', 'vel', 'accel')
plot(logDAX, axes=FALSE)
axis(1)
axis(2)


	  I'm thinking of creating my own copy of "plot.ts", and changing it so 
it accepts the "log" argument as a vector of length equal to ncol of the 
ts object to be plotted AND returning an object that would allow a user 
to call "axis" ncol times.



  Suggestions?


  Thanks,
  Spencer Graves



HTH,
Eric


On Mon, May 29, 2023 at 7:57 AM Spencer Graves
 wrote:


Hello, All:


   I want to plot level, velocity, and acceleration in three panels with
only one x axis.  The code below does this using "layout".  However, I
want the three plot areas to be of equal size, and this won't do that:
If I stretch the plot vertically, the relative sizes of the three panels
changes.  There's probably a way to do this with ggplot2, but I have yet
to find it.


   Suggestions?
   Thanks,
   Spencer Graves


str(AirTime <- as.numeric(time(AirPassengers)))
str(AP <- as.numeric(AirPassengers))

def.par <- par(no.readonly = TRUE) # save default, for resetting...
(mat3x1 <- matrix(1:3, 3))
plot3x1 <- layout(mat3x1, heights=c(1.4, 1, 1.5))
layout.show(plot3x1)

par(mar=c(0, 4.1, 4.1, 2.1))
plot(AirTime, AP, log='y', type='l', axes=FALSE,
   main='AirPassengers', ylab='AirPassengers')
box(col='grey')
axis(2, las=1)

par(mar=c(0, 4.1, 0, 2.1))
vAP <- diff(log(AP))
plot(tail(AirTime, -1), vAP, type='l',
   ylab='percent increase', axes=FALSE)
box(col='grey')
axis(2, las=1)

par(mar=c(5.1, 4.1, 0, 2.1))
plot(tail(AirTime, -2), diff(vAP), type='l',
   ylab='acceleration', xlab='year',
   las=1)
box(col='grey')

par(def.par)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

On 5/29/23 2:37 AM, Eric Berger wrote:

How about this:

a <- cbind(AirPassengers, diff(log(AirPassengers)),
diff(diff(log(AirPassengers
colnames(a)[2:3] <- c("percent increase", "acceleration")
plot(a, xlab="year", main="AirPassengers")



That's it.  Thanks.  sg



HTH,
Eric


On Mon, May 29, 2023 at 7:57 AM Spencer Graves
 wrote:


Hello, All:


   I want to plot level, velocity, and acceleration in three panels with
only one x axis.  The code below does this using "layout".  However, I
want the three plot areas to be of equal size, and this won't do that:
If I stretch the plot vertically, the relative sizes of the three panels
changes.  There's probably a way to do this with ggplot2, but I have yet
to find it.


   Suggestions?
   Thanks,
   Spencer Graves


str(AirTime <- as.numeric(time(AirPassengers)))
str(AP <- as.numeric(AirPassengers))

def.par <- par(no.readonly = TRUE) # save default, for resetting...
(mat3x1 <- matrix(1:3, 3))
plot3x1 <- layout(mat3x1, heights=c(1.4, 1, 1.5))
layout.show(plot3x1)

par(mar=c(0, 4.1, 4.1, 2.1))
plot(AirTime, AP, log='y', type='l', axes=FALSE,
   main='AirPassengers', ylab='AirPassengers')
box(col='grey')
axis(2, las=1)

par(mar=c(0, 4.1, 0, 2.1))
vAP <- diff(log(AP))
plot(tail(AirTime, -1), vAP, type='l',
   ylab='percent increase', axes=FALSE)
box(col='grey')
axis(2, las=1)

par(mar=c(5.1, 4.1, 0, 2.1))
plot(tail(AirTime, -2), diff(vAP), type='l',
   ylab='acceleration', xlab='year',
   las=1)
box(col='grey')

par(def.par)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] plot level, velocity, acceleration with one x axis

[Spencer Graves]

Hello, All:


	  I want to plot level, velocity, and acceleration in three panels with 
only one x axis.  The code below does this using "layout".  However, I 
want the three plot areas to be of equal size, and this won't do that: 
If I stretch the plot vertically, the relative sizes of the three panels 
changes.  There's probably a way to do this with ggplot2, but I have yet 
to find it.



  Suggestions?
  Thanks,
      Spencer Graves


str(AirTime <- as.numeric(time(AirPassengers)))
str(AP <- as.numeric(AirPassengers))

def.par <- par(no.readonly = TRUE) # save default, for resetting...
(mat3x1 <- matrix(1:3, 3))
plot3x1 <- layout(mat3x1, heights=c(1.4, 1, 1.5))
layout.show(plot3x1)

par(mar=c(0, 4.1, 4.1, 2.1))
plot(AirTime, AP, log='y', type='l', axes=FALSE,
 main='AirPassengers', ylab='AirPassengers')
box(col='grey')
axis(2, las=1)

par(mar=c(0, 4.1, 0, 2.1))
vAP <- diff(log(AP))
plot(tail(AirTime, -1), vAP, type='l',
 ylab='percent increase', axes=FALSE)
box(col='grey')
axis(2, las=1)

par(mar=c(5.1, 4.1, 0, 2.1))
plot(tail(AirTime, -2), diff(vAP), type='l',
 ylab='acceleration', xlab='year',
 las=1)
box(col='grey')

par(def.par)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] identify the distribution of the data

[Spencer Graves]

On 2/8/23 12:06 PM, Ebert,Timothy Aaron wrote:

IMO) The best approach is to develop a good understanding of the individual 
processes that resulted in the observed values. The blend of those processes 
then results in the distribution of the observed values. This is seldom done, 
and often not possible to do. The alternatives depend on why you are doing this.

0) Sometime the nature of the data suggest a distribution. You list integer 
values. If all observations are integer (counts for example) then Poisson may 
be appropriate. With two values then maybe the Binomial distribution. 
Continuous data might be normally distributed (Gaussian distribution). If I 
roll one six-sided die many times I will have a uniform distribution (assuming 
a fair die). I could then try the same task but roll 2 dice and add the result. 
I still have discrete values, but the shape is closer to Gaussian. The 
distribution looks more and more Gaussian as I add more dice together in each 
roll.



	  I concur:  The application will often suggest a distribution, e.g., 
Poisson, binomial or negative binomial for nonnegative integers, Weibull 
for lifetime data, etc.



	  I love normal probability plots -- the qqnorm function.  This can 
identify outliers or multimodality or the need for a transformation. 
Continuous data that are always positive are often log-normal -- or a 
mixture of log-normals.



x <- rnorm(100)
X <- exp(x)
qqnorm(X, datax=TRUE, log='x')


	  The central limit theorem says that the distribution of almost any 
sum of random variables will be more nearly normal than the 
distributions of individual summands.  It also says that almost any 
product of positive random variables will be more nearly log-normal than 
the distributions of individual components of the product.  This 
application to products is less well known and occasionally controversial.



https://en.wikipedia.org/wiki/Gibrat%27s_law


  Spencer Graves

  
1) Try a simulation. Draw 5 values from a normal distribution, make a histogram. Then do it again. Is it easy to see that both samples are from the same distribution? Personally, the answer is no. So increase the sample size until you are happy with a decision that any two draws are from the same distribution. For my part, at 1 million most people would not be able to detect any difference between the two histograms. This helps calibrate the people. How does your sample size compare to your choice in this exercise?


2) Given that you have sufficient data (see above), can you see the 
distribution in your data? Is that good enough?

3) Are you doing this as part of following the assumptions of statistical 
models? In such tests for normality, we tend to assume that a failure to reject 
the null hypothesis is sufficient proof that the null hypothesis is true. 
However, in most other cases we are told that a failure to reject the null 
hypothesis is not sufficient to prove the null hypothesis. You need to work 
this out, but the importance, consequences, and alternatives of testing model 
assumptions is a large body of literature with (sometimes) widely divergent 
viewpoints.

4) There are hundreds of distributions. 
https://cran.r-project.org/web/views/Distributions.html but the common distributions are 
seen in sites like this one:  https://www.stat.umn.edu/geyer/old/5101/rlook.html. Given 
so many choices, you can probably find one that will fit your data reasonably well. 
Depending on how many data points you have will determine the reliability of that answer. 
Is that really informative to the problem you are trying to solve? Answering "what 
distribution do these data follow?" is not usually the goal.

Regards,
Tim
  


-Original Message-
From: R-help  On Behalf Of Bert Gunter
Sent: Wednesday, February 8, 2023 12:00 PM
To: Bogdan Tanasa 
Cc: r-help 
Subject: Re: [R] identify the distribution of the data

[External Email]

1. This is a statistical question, which usually is inappropriate here:
this list is about R language (including packages) programming.

2. IMO (so others may disagree), your question indicates a profound misunderstanding of basic statistical 
issues. While maybe you phrased it poorly or I misunderstand, but "identify the type of 
distribution" is basically a meaningless query. Explaining why this is so and what may be more 
meaningful would require a deep dive into statistics. You might try referencing a basic statistical text 
and/or online tutorials. Try searching on "Goodness of fit", "statistical modeling" or 
the like.

Cheers,
Bert

On Wed, Feb 8, 2023 at 8:35 AM Bogdan Tanasa  wrote:


Dear all,

I do have dataframes with numerical values such as 1,9, 20, 51, 100
etc

Which way do you recommend to use in order to identify the type of the
distribution of the data (normal, poisson, bernoulli, exponential,
log-normal etc ..)

Thanks so much,

Bogda

Re: [R] Plotmath isn't working for special characters

[Spencer Graves]

On 1/24/23 3:33 PM, David Stevens wrote:

Simple expressions on plots, such as parse(text='x >= y') have been
resulting in just a placeholder box (x box y and not the symbol) in my R
plot labels in windows, R v 4.2.2. I haven't down an exhaustive test but
<= and >= have this behavior.

plot(1,1,main=parse(text="x >= y"))

Has anyone else seen this?



  What's your "sessionInfo()"?


  I got the symbol, not problem.  Spencer Graves


sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7.2

Matrix products: default
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib


locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods
[7] base

loaded via a namespace (and not attached):
[1] compiler_4.2.2  tools_4.2.2 rstudioapi_0.14
[4] remotes_2.4.2
> >

best

David



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R Certification

[Spencer Graves]

	  If you go to "https://cran.r-project.org; and click, "Download R for 
macOS", you will find several versions that you can download and that 
have a "digital signature".



	  After downloading, you can "check the integrity of the downloaded 
package by checking the signature: pkgutil --check-signature R-4.2.2.pkg".



	  Beyond that, RStudio and other companies will happily sell you a 
maintenance contract, which will get you more polite answers than from a 
list serve like this ;-)



  Spencer Graves


On 1/2/23 11:24 AM, John Kane wrote:

Hi Mukesh,

Have a look at the blurb that prints at the start-up of R.

"R is free software and comes with ABSOLUTELY NO WARRANTY."

This is a hint that the R-Project is unlikely to be issuing certificates.



On Mon, 2 Jan 2023 at 08:18, Mukesh Ghanshyamdas Lekhrajani via R-help <
r-help@r-project.org> wrote:


Thanks Petr !

I will look at other training bodies as Coursera, or few others... but I
was just wondering if there could be a  certificate from the "originators"
itself, I mean an "R" certificate from "r-project" itself and that would
carry more importance than external / unauthorized certificate bodies.

But, if you suggest there is no such certification provided by
"r-project", then the only option for me is to search else where like -
Coursera or few others.

I now have got my answers, but later the day - if ever "r-project" comes
up with "R Language" certifications, do keep me informed.


Thanks, Mukesh
9819285174.


-Original Message-
From: PIKAL Petr 
Sent: Monday, January 2, 2023 6:13 PM
To: mukesh.lekhraj...@yahoo.com; R-help Mailing List 


Subject: RE: [R] R Certification

Hallo Mukesh

R project is not Microsoft or Oracle AFAIK. But if you need some
certificate you could take courses on Coursera, they are offering
certificates.

Cheers
Petr


-Original Message-
From: R-help  On Behalf Of Mukesh
Ghanshyamdas Lekhrajani via R-help
Sent: Monday, January 2, 2023 1:04 PM
To: 'Jeff Newmiller' ; 'Mukesh Ghanshyamdas
Lekhrajani via R-help' ; r-help@r-project.org
Subject: Re: [R] R Certification

Hello Jeff !

Yes, you are right.. and that’s why I am asking this question - just

like other

governing bodies that issue certification on their respective

technologies, does

"r-project.org" also have a learning path ? and then a certification.

Say - Microsoft issues certificate for C#, .Net, etc..
Then, Oracle issues certificates for Java, DB etc..

These are authentic governing bodies for learning and issuing

certificates


On exactly similar lines -  "r-project.org" would also be having some

learning

path and then let "r-project" take the proctored exam and issue a

certificate...


I am not looking at any external institute for certifying me on "R" -

but, the

governing body itself..

So, the question again is - "does r-project provide a learning path and

issue

certificate after taking exams"

Thanks, Mukesh
9819285174



-Original Message-
From: Jeff Newmiller 
Sent: Monday, January 2, 2023 2:26 PM
To: mukesh.lekhraj...@yahoo.com; Mukesh Ghanshyamdas Lekhrajani via R-
help ; r-help@r-project.org
Subject: Re: [R] R Certification

I think this request is like saying "I want a unicorn." There are many
organizations that will enter your name into a certificate form for a

fee, possibly

with some credibility... but if they put "r-project.org" down as the

name of the

organization granting this "certificate" then you are probably getting

fooled.


On December 30, 2022 8:33:09 AM PST, Mukesh Ghanshyamdas Lekhrajani via
R-help  wrote:

Hello R Support Team,



I want to do R certification, could you help me with the list of
certificates with their prices so it helps me to register.



I want to do the certification directly from the governing body
"r-project.org" and not from any 3rd party.



Please help.







Mukesh

+91 9819285174


 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


--
Sent from my phone. Please excuse my brevity.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide

http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting gu

Re: [R] [External] Amazing AI

[Spencer Graves]

On 12/21/22 7:50 AM, Barry Rowlingson wrote:

Next year one of my R programming assigments will read like this:

"Here is some R code written by a multi-million dollar AI system to
compute [something]. It doesn't work. Fix the bugs, then ask the AI to
write a letter to its creators apologising for how rubbish it is at
coding. Collect one million dollars."



You might want to be careful about such a promise.  Kahneman, Sibony, 
and Sunstein (2021) Noise:  A flaw in human judgment (Little, Brown and 
Company) claim that genuine expertise is acquired by learning from 
frequent, rapid, high-quality feedback on the quality of their 
decisions.  Few people have access to such feedback.  They call leaders 
in fields without such feedback "respect-experts", and note that 
respect-experts have only the illusion of competence.



	  1.  They further say that most respect-experts can be beaten by 
simple heuristics developed by intelligent lay people.



	  2.  Moreover, with a modest amount of data, ordinary least squares 
can beat most such heuristics.



	  3.  And if lots of data are available, AI can beat the simple 
heuristics.



	  They provide substantial quantities of research to support those 
claims.



	  Regarding your million dollars, it should not be hard to write an R 
interface to existing AI code cited by Kahneman et al.



	  Do you really want one of your students initiating a legal procedure 
to try to collect your million dollars?



	  A quarter century ago, my friend Soren Bisgaard told me about a 
colleague who had raved about AI.  Soren thought, "You prefer artificial 
intelligence to real intelligence?"



	  I perceive a role for AI in identifying subtle phenomena missed by 
more understandable modeling techniques.  Let's use the best 
understandable model, and apply AI to the residuals from that.  Then 
identify the variables that make the largest contributions to a useful 
AI model, and see if they can be added to the other model.



  Spencer Graves



On Sun, Dec 18, 2022 at 7:01 PM Boris Steipe  wrote:


This email originated outside the University. Check before clicking links or 
attachments.

Technically not a help question. But crucial to be aware of, especially for 
those of us in academia, or otherwise teaching R. I am not aware of a suitable 
alternate forum. If this does not interest you, please simply ignore - I 
already know that this may be somewhat OT.

Thanks.
--

You very likely have heard of ChatGPT, the conversation interface on top of the 
GPT-3 large language model and that it can generate code. I thought it doesn't 
do R - I was wrong. Here is a little experiment:

MY PROMPT:
==
Please write me some R code that will read a tsv file, remove all rows that have duplicates in the 
column "names", and store the median values of the remaining rows in a variable called 
"Medians". Of course, that calculation should only be done with columns that are numeric. 
Print the last variable in order from largest to smallest.


AI RESPONSE:


Here is some R code that should accomplish what you've described:

(Note: the code is formatted in a little terminal window, complete with a button to 
"copy code" at the top.)


# Read the tsv file
data <- read.table("file.tsv", header = TRUE, sep = "\t")

# Remove rows with duplicates in the "names" column
data <- data[!duplicated(data$names), ]

# Select only the numeric columns
num_columns <- sapply(data, is.numeric)
numeric_data <- data[, num_columns]

# Calculate the medians for each column
Medians <- apply(numeric_data, 1, median)

# Sort Medians in descending order
Medians <- sort(Medians, decreasing = TRUE)

# Print Medians
print(Medians)


This code assumes that the tsv file is called "file.tsv" and is stored in the 
current working directory. It also assumes that the first row of the file contains the 
column names.



MY PROMPT:
==
Can you provide me with a bit of sample data that I can use to test this code?

AI RESPONSE:

Certainly! Here is some sample data that you can use to test the code I 
provided:


nameage height  weight
Alice   23  5.6 120
Bob 32  6.2 180
Charlie 29  5.9 160
Alice   23  5.6 120
David   25  5.8 140
Eve 27  5.5 110


You can save this data as a tsv file and use it to test the code.


--

Notes:
1) The code, as written does not work with the test data. The reason is that the test data 
specifies a column "name", but the code assumes "names" (which I specified in 
the instructions). Once this is fixed in the test data, the code executes.

2) The instructions are not accurately translated: I had asked for row means. 
But changing the marg

Re: [R] cannot print a list with cat

[Spencer Graves]

On 10/24/22 7:39 AM, Steven T. Yen wrote:

I have a "list" containing four elements, as shown below:

 > t(mycontrol)

  tol reltol steptol gradtol
[1,] 0   0  1e-08   1e-12

Printing this in a main program causes no problem (as shown above).
But, using the command t(mycontrol) the line gets ignored. Any idea? 



I'm confused.  I get:


> (mycontrol <- list(tol=0, reltol=0,
+ steptol=1e-8, gradtol=1e-12))
$tol
[1] 0

$reltol
[1] 0

$steptol
[1] 1e-08

$gradtol
[1] 1e-12

>
> t(mycontrol)
 tol reltol steptol gradtol
[1,] 0   0  1e-08   1e-12


	  I don't know what you mean by "main program" vs. "the command 
t(mycontrol)".



  ???
  Spencer Graves


> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.7

Matrix products: default
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib


locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_4.2.1 tools_4.2.1



Thanks.
Steven Yen

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] ggplot2 install.package

[Spencer Graves]

	  From long and unhappy experience, I routinely reboot before reporting 
problems like this, then upgrade all software where feasible ... 
including "update.packages".  Some problems magically disappear after 
doing this.



	  If they persist, then, as it says at the end of each email on this 
thread, "PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html and provide commented, 
minimal, self-contained, reproducible code."  If you do that, it 
increases the chances that the help you get will actually be helpful ;-)



  Spencer


On 10/11/22 1:01 AM, sibylle.stoec...@gmx.ch wrote:

Dear R users

Thanks a lot. I will try again. The error code was below the email, but there 
was some encryption:
- Error in nchar(homeDir:invalid multibyte string, element 1
- I realised that I was able to install ggplot2, but the error is afterwards 
when loading ggplot2 (library()).

Kind regards
Sibylle

install.packages("ggplot2", dependencies = TRUE)
WARNING: Rtools is required to build R packages but is not currently installed. 
Please download and install the appropriate version of Rtools before proceeding:

Installiere Paket nach ‘C:/Users/Sibylle 
Stöckli/AppData/Local/R/win-library/4.2’
(da ‘lib’ nicht spezifiziert)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.2/ggplot2_3.3.6.zip'
Content type 'application/zip' length 4122980 bytes (3.9 MB)
downloaded 3.9 MB

Paket ‘ggplot2’ erfolgreich ausgepackt und MD5 Summen abgeglichen

Die heruntergeladenen Binärpakete sind in
 C:\Users\Sibylle 
Stöckli\AppData\Local\Temp\RtmpcBknba\downloaded_packages
Error in nchar(homeDir) : invalid multibyte string, element 1

-Ursprüngliche Nachricht-
Von: Ebert,Timothy Aaron 
Gesendet: Dienstag, 11. Oktober 2022 02:42
An: sibylle.stoec...@gmx.ch; R-help@r-project.org
Betreff: RE: [R] ggplot2 install.package

Can you please provide us with a copy of the error msg? I have used ggplot2 
with R 4.2.1, and probably R 4.2.0 in RStudio on Windows 11 and not had 
trouble. You might need to update R, or RStudio. R and RStudio need to be 
compatible versions.

Tim

-Original Message-
From: R-help  On Behalf Of sibylle.stoec...@gmx.ch
Sent: Monday, October 10, 2022 9:33 AM
To: R-help@r-project.org
Subject: [R] ggplot2 install.package

[External Email]

Dear R members



I am working with RStudio R 4.2.0 and using ggplot2 and gridExtra.

Since some windows updates I get some error when loading  ggplot2.

*   It seems that I am able to install ggplot2. The problem is when
loading ggplot2 with library().
*   Do you have any ideas to solve the problem?





Kind regards

Sibylle




**

install.packages("ggplot2", dependencies = TRUE)

WARNING: Rtools is required to build R packages but is not currently installed. 
Please download and install the appropriate version of Rtools before proceeding:



https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fwindows%2FRtools%2Fdata=05%7C01%7Ctebert%40ufl.edu%7C05f8820150e648d4f29108daab015484%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638010323276937614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7Csdata=PKqDjS%2FEfL4Mtho3TRywJUuy%2FpGQ9A3seBjgGr6IScM%3Dreserved=0

Installiere Paket nach  C:/Users/Sibylle St ckli/AppData/Local/R/win-library/4.2

(da  lib  nicht spezifiziert)

trying URL
'https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.rstudio.com%2Fbin%2Fwindows%2Fcontrib%2F4.2%2Fggplot2_3.3.6.zipdata=05%7C01%7Ctebert%40ufl.edu%7C05f8820150e648d4f29108daab015484%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638010323276937614%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000%7C%7C%7Csdata=b5dcFImQLYrE850p5SnbOyibj9KV0JrZIvfL8trNI84%3Dreserved=0'

Content type 'application/zip' length 4122980 bytes (3.9 MB)

downloaded 3.9 MB



Paket  ggplot2  erfolgreich ausgepackt und MD5 Summen abgeglichen



Die heruntergeladenen Bin rpakete sind in

 C:\Users\Sibylle
St ckli\AppData\Local\Temp\RtmpcBknba\downloaded_packages

Error in nchar(homeDir) : invalid multibyte string, element 1


 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Parsing XML?

[Spencer Graves]

Hi, Richard et al.:


On 7/28/22 1:50 AM, Richard O'Keefe wrote:

What do you mean by "a list that I can understand"?
A quick tally of the number of XML elements by identifier:
1 echoedSearchRetrieveRequest
1 frbrGrouping
1 maximumRecords
1 nextRecordPosition
1 numberOfRecords
1 query
1 records
1 resultSetIdleTime
1 searchRetrieveResponse
1 servicelevel
1 sortKeys
1 startRecord
1 wskey
2 version
50 leader
50 recordData
51 recordPacking
51 recordSchema
100 record
105 controlfield
923 datafield
1900 subfield



  How did you get that?


	  Please forgive me for being so dense.  I've done several web searches 
and tried to work several tutorials, etc., without so far seeing what I 
might do that could be informative.



	  Even this list of "XML elements by identifiers" STILL does not 
include things like the name of the newspaper and publisher plus start 
and end dates.  I believe these fields are there, but I can't see how to 
parse them.  I earlier parsed a JSON version of essentially the same 
dataset.  However, the JSON version seemed not to distinguish between 
newspapers that were still publishing and those for which the end date 
was unknown.  My contact at the Library of Congress then suggested I 
parse the XML version.



  Thanks,
  Spencer



What of this information do you actually want?
The elements of the list should be what?


On Thu, 28 Jul 2022 at 08:52, Spencer Graves 
<mailto:spencer.gra...@effectivedefense.org>> wrote:


Hello, All:


           What would you suggest I do to parse the following XML
file into a
list that I can understand:


XMLfile <-

"https://chroniclingamerica.loc.gov/data/bib/worldcat_titles/bulk5/ndnp_Alabama_all-yrs_e_0001_0050.xml

<https://chroniclingamerica.loc.gov/data/bib/worldcat_titles/bulk5/ndnp_Alabama_all-yrs_e_0001_0050.xml>"




           This is the first of  XML files containing "U.S.
Newspaper
Directory" maintained by the US Library of Congress discussed in the
thread below.  I've tried various things using the XML and xml2.


XMLdata <- xml2::read_xml(XMLfile)
str(XMLdata)
XMLdat <- XML::xmlParse(XMLdata)
str(XMLdat)
XMLtxt <- xml2::xml_text(XMLdata)
nchar(XMLtxt)
#[1] 29415


           Someplace there's a schema for this.  I don't know if
it's embedded
in this XML file or in a separate file.  If it's in a separate file,
how
could I describe it to my contacts with the Library of Congress so they
would understand what I needed and could help me get it.


           Thanks,
           Spencer Graves


p.s.  All 29415 characters in XMLtext appear in the thread below.


 Forwarded Message 
Subject:        [Newspapers and Current Periodicals] How can I get
counts of
the numbers of newspapers by year in the US, and preferably also
elsewhere? A search of "U.S. Newspaper Directory,
Date:   Wed, 27 Jul 2022 14:59:03 +
    From:   Kerry Huller mailto:seri...@ask.loc.gov>>
To:     Spencer Graves mailto:spencer.gra...@effectivedefense.org>>
CC: t...@loc.gov <mailto:t...@loc.gov>



--# Type your reply above this line #--



Newspapers and Current Periodicals Reference Librarian

Jul 27 2022, 10:59am via System

Hello Spencer,

So, when I view the xml, I'm actually looking at it in XML editor
software, so I can view the tags and it's structured neatly. I've
copied
and pasted the text from the beginning of the file and the first
newspaper title below from my XML editor:




http://www.loc.gov/zing/srw/
<http://www.loc.gov/zing/srw/>"
xmlns:oclcterms="http://purl.org/oclc/terms/
<http://purl.org/oclc/terms/>"
xmlns:dc="http://purl.org/dc/elements/1.1/
<http://purl.org/dc/elements/1.1/>"
xmlns:diag="http://www.loc.gov/zing/srw/diagnostic/
<http://www.loc.gov/zing/srw/diagnostic/>"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance
<http://www.w3.org/2001/XMLSchema-instance>">
1.1
2250


info:srw/schema/1/marcxml
xml

http://www.loc.gov/MARC21/slim
<http://www.loc.gov/MARC21/slim>">
       0nas a2207i 4500
       1030438981
       180404c2015aluwr n       0   a0eng
   
       
           2018200464
       
       
         DLC
         rda
         DLC
         eng
       
       
         1
       
       
         2577-5316
         1
       
       
         021110
         USPS
       
       
         711 Alabama Avenue, Selma, AL
36701
       
       
 

Re: [R] A humble request

[Spencer Graves]

stand it.
   DO ask your supervisor help you to select an alternative,
   and if you can't figure that out between you,
   ASK a more informative question.



On Mon, 4 Jul 2022 at 00:38, John Kane <mailto:jrkrid...@gmail.com>> wrote:


Spenser,
the idea to source the fonction makes sense but since tho OP is a very
new beginner perhaps you could point him towards code showing him how
to do this?  I have never done this AFAIR, and while I suspect a few
minutes googling would show me how, it is likely to be more difficult
for a noobie.

On Sun, 3 Jul 2022 at 07:25, Spencer Graves
mailto:spencer.gra...@effectivedefense.org>> wrote:
 >
 > Muhammad Zubair Chishti:
 >
 >
 >           What specifically have you tried?  What were the results?
 >
 >
 >           Please "provide commented, minimal, self-contained,
reproducible
 > code", per "the posting guide
 > http://www.R-project.org/posting-guide.html
<http://www.R-project.org/posting-guide.html>", as indicated in at
the end
 > of each email in this thread.
 >
 >
 >           And don't overlook the suggestion I made:  Download the
archived
 > package.  Do NOT try to compile it. Instead source only the
function you
 > want, try to run it.  With luck, it will work.  If it doesn't,
you will
 > get a diagnostic that can help you take the next step.
 >
 >
 >           Spencer
 >
 >
 > On 7/3/22 1:28 AM, Andrew Simmons wrote:
 > > It seems like this package was archived because package "ifultools"
 > > was archived. I tried installing "ifultools" from source, but
it has a
 > > seriously large amount of C compilation issues. The main issue
seems
 > > to be that variable PROBLEM was never defined anywhere, and it is
 > > unclear what its definition should be. Unfortunately, as far as
I can
 > > tell, this issue is unfixable. If you want to install "wmtsa",
you'll
 > > have to use an older version of R. Otherwise, you can use one
of the
 > > other wavelet analysis packages that Richard O'Keefe mentioned.
 > >
 > > On Sun, Jul 3, 2022 at 2:01 AM Muhammad Zubair Chishti
 > > mailto:mzchis...@eco.qau.edu.pk>> wrote:
 > >>
 > >> Dear Respected Experts and specifically Professor Richard O'Keefe,
 > >> Thank you so much for your precious time and generous help.
However, the
 > >> problem is still there and I am just unable to resolve it due
to the lack
 > >> of expertise in R. Still, the hope is there. I believe that
this platform
 > >> can help me.
 > >>
 > >> Regards
 > >> Muhammad Zubair Chishti
 > >> School of Business,
 > >> Zhengzhou University, Henan, China
 > >> My Google scholar link:
 > >> https://scholar.google.com/citations?hl=en=YPqNJMwJ
<https://scholar.google.com/citations?hl=en=YPqNJMwJ>
 > >> My ReseachGate Profile:
 > >> https://www.researchgate.net/profile/Muhammad-Chishti
<https://www.researchgate.net/profile/Muhammad-Chishti>
 > >>
 > >>
 > >> On Sun, Jul 3, 2022 at 9:11 AM Richard O'Keefe
mailto:rao...@gmail.com>> wrote:
 > >>
 > >>> A postscript to my previous comment.
 > >>> I used to supervise PhD students.
 > >>> Let me advise you to write this issue up as a draft section
for your
 > >>> thesis.
 > >>> 1. Why I wanted to use the wmtsa package.
 > >>> 2. Why I didn't.
 > >>> 3. How I went about selecting a replacement.
 > >>> 4. What I chose and why that's the right choice.
 > >>> 5. How the analyses I wanted to do are done in
 > >>>     package X and what difference it makes.
 > >>>
 > >>> Off the top of my head, the only reasons for struggling to
use an old
 > >>> package are to try to replicate someone else's results and/or
to try to use
 > >>> their software (built atop the dead package) with new data. 
Well, if you

 > >>> get different results, that's interesting too, and then it's
time to work
 > >>> harder to resurrect the dead package.
 > >>>
 > >>> Speaking of which, an easier route might be to set up a separate
 > >>> environment running an old version of R that *can* run the
old code and the
 > >>> old co

Re: [R] A humble request

[Spencer Graves]

On 7/2/22 12:30 PM, David Winsemius wrote:




On Jul 2, 2022, at 9:32 AM, Muhammad Zubair Chishti  
wrote:

Dear Respected Sir,
Thank you for the quick response. However, the link your shared provides
the old version of wmtsa that is not working in R 4.2.0.
Can you please tell me any other solution for this issue?


Your response suggests that you do not understand how one installs a source 
package for R. You probably need to educate yourself about how to compile 
packages from source. Since the process is different for Linux, MacOS, and 
Windows, you would need to pay attention to the specific requirements of your 
unnamed OS.



BUT you do not need to compile the entire package to use a function in 
it:  You only need to source that particular function ... and any others 
it calls that you don't already have ;-)  That simplifies the task 
greatly.  With luck, Muhammad Zubair Chishti can source only the desired 
functions, and they will run and do what is desired with no further 
effort.  If not, Muhammad can be guided by the error message(s):  If 
they complain that a certain function is not available, Muhammad can 
find it and source it.  If the problem is more subtle, Muhammad can use 
"debug", as I earlier suggested.  Spencer Graves




You might find as I did that the wmtsa package has some dependencies that are 
also archived, namely pkg:splus2R (provided generously by Insightful for many 
years but apparently no longer) and pkg:ifultools. They both have 
incompatibilities that prevent compilation from source with my Mac setup. I did 
find a mirror that has a binary version of splus2R that did install and load.

install.packages("splus2R", repo="https://mirrors.vcea.wsu.edu/r-cran/;, 
type="binary", dependencies=TRUE)

So maybe part of your PhD training should be learning how to compile packages 
and address changes in the compilers being used as R evolves. That is beyond my 
capabilities for offering assistance. Alternately you might find a forum or a 
consultant with similar interests to yours. Again, I can offer no assistance 
because I have never used pkg:wmtsa and don't know what it provided when it was 
compatible with the CRAN universe.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] A humble request

[Spencer Graves]

  Are you familiar with the "debug" function?


	  You can download the package, source the function you want to use. 
If it doesn't run or doesn't seem to give a sensible answer, debug(fun) 
followed by fun(arg1, arg2, arg3) will start the function then stop and 
invite you to walk through the function line by line.  You can look at 
what it does, and change it as you like.  Doing so should help you learn 
R while also making it easier for you to figure out how to make the 
function do what you want.



  Hope this helps.
      Spencer Graves


On 7/2/22 11:39 AM, Muhammad Zubair Chishti wrote:

Dear Respected Professor,
You are right. However, a student like me who doesn't know much R 
requires specific helping packages to install. Therefore, I requested 
here to experts to give the solution for my issue.


I hope that I will get the solution from this platform.

Regards
Muhammad Zubair Chishti

On Sat, 2 Jul 2022, 21:34 Spencer Graves, 
<mailto:spencer.gra...@effectivedefense.org>> wrote:


If I understand correctly the rules for "archived" packages, anyone is
free to download them, compile them locally -- AND resubmit any such
package with themselves as the maintainer:  They were archived, because
they would no longer pass CRAN checks, and the designated maintainer
failed to respond to the notice of problems with newer versions of R.
If anything I've said here is wrong or poorly nuanced, I trust someone
knowledgeable will correct me.  Spencer Graves


On 7/2/22 11:24 AM, Rainer Hurling wrote:
 > Hi Muhammad,
 >
 > Am 02.07.22 um 18:11 schrieb Muhammad Zubair Chishti:
 >> Dear Experts,
 >> I cannot find a package "wmtsa" for my R version "R 4.2.0". Kindly
 >> help me
 >> to find it or share the link with me.
 >> Although I tried the old version of "wmtsa" but failed.
 >> Thank you for your precious time.
 >>
 >> Regards
 >> Muhammad Zubair Chishti
 >>
 >> [[alternative HTML version deleted]]
 >
 > AFAIK there is no package wmtsa anymore. It has been archived on
 > 2020-06-09 [1], the latest version was wmtsa_2.0-3.tar.gz from
2017-12-06.
 >
 > [1] https://cran.r-project.org/src/contrib/Archive/wmtsa/
<https://cran.r-project.org/src/contrib/Archive/wmtsa/>
 >
 > HTH,
 > Rainer
 >
 > __
 > R-help@r-project.org <mailto:R-help@r-project.org> mailing list
-- To UNSUBSCRIBE and more, see
 > https://stat.ethz.ch/mailman/listinfo/r-help
<https://stat.ethz.ch/mailman/listinfo/r-help>
 > PLEASE do read the posting guide
 > http://www.R-project.org/posting-guide.html
<http://www.R-project.org/posting-guide.html>
 > and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org <mailto:R-help@r-project.org> mailing list --
To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
<https://stat.ethz.ch/mailman/listinfo/r-help>
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
<http://www.R-project.org/posting-guide.html>
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Is it possible to set a default working directory for all R consoles?

[Spencer Graves]

	  I use the free version of RStudio, and I routinely work with 
"Projects".  For new projects, I first I create a new project directory 
in Finder (in a Mac) or Windows Explorer if it does not already exist. 
Then in RStudio, I do File > "New Project..." > in "Existing Directory".



	  Then when I want to work on an existing project, I can do File > 
"Recent Projects" in RStudio.  Or I can double click on the appropriate 
*.Rproj file in Finder or Windows Explorer.



  Hope this helps.
  Spencer Graves


On 6/17/22 10:46 AM, Bill Dunlap wrote:

Is there an environment variable containing that IP address?

  as.list(grep(value=TRUE, "172", Sys.getenv())) # as.list to make
printing nicer

If you know which variable is causing the problem you may be able to
override it by setting an R-specific one.

-Bill

On Fri, Jun 17, 2022 at 8:28 AM IAGO GINÉ VÁZQUEZ  wrote:


Hi all,

Is there some way to set a default working directory each time R.exe is
opened? I ask this because Always that I open R 4.2.o in Windows 10 I get
the next warning messages

Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
   path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
   path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
   path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
   path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is denied

Even from cmd.exe in a  C: location

C:\Users\me>R
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :


  path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access
is denied
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is
denied
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is
denied
Warning message:
In normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="\\172.19.2.44\profiles\profiles\me\Documents": Access is
denied

Reading
https://cran.r-project.org/bin/windows/base/rw-FAQ.html#What-are-HOME-and-working-directories_003f,
first I cannot apply the suggested solution (I cannot see such "shortcut’s
properties"), and second, I am not interested just in Rgui, or even
RStudio, but other terminals running R (like VSCode-radian or
SublimeText-Terminus)

Thanks in advance.

Best wishes,

Iago



 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Exact 95% CI around the mean for LogNormal distribution

[Spencer Graves]

	  The mean of a log-Cauchy (aka log-Student's t with 1 degree of 
freedom) is infinite ;-)  The median and other quantiles are not 
affected by transformations, though the mean is.



	  If you really want anything other than a confidence interval about 
the mean of the logs, assuming a log-normal distribution, I think you 
need to think very carefully about the problem you are trying to solve, 
and how that might be impacted by different assumptions about the 
distribution of the data.



	  And for that, I recommend normal probability plotting, i.e., qqnorm 
of log(X):  If that looks plausibly like a straight line, you are fine 
with a log-normal assumption.  If not, my favorite reference is



Titterington, Smith and Makov (1985) Statistical Analysis of Finite 
Mixture Distributions (Wiley).



  Hope this helps.
  Spencer Graves


On 3/16/22 5:44 PM, Bert Gunter wrote:

This is largely a statistics question, so somewhat off topic here (see
the posting guide linked below). Ergo the lack of a response yet.

Therefore you *might* do better posting on the r-sig-ecology list.

And now for a couple of statistics comments, which you are free to
ignore of course, and which you may already be well aware of. Assuming
the rv X is approximately lognormally distributed means that log(x) is
~ normally distributed which means that a (symmetric) CI for the mean
of the log(X) (=: meanlog of X) is also approximately a CI for the
median of log(X). Hence the back transform (exp()) of the meanlog CI
is an approx CI for the **median** of the lognormal distribution. The
median of a lognormal is **not** the same as the mean, but it
generally makes more sense, as the mean of a skew distribution like
the lognormal has no clear interpretation, while the median (or any
quantile) still does.

Your mileage may vary, of course.

Cheers,
Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Mar 16, 2022 at 1:10 PM varin sacha via R-help
 wrote:


Dear R-experts,

I have used the EnvStats package and the elnorm function (p. 248).
I would like to calculate the exact 95% confidence intervals around the mean, 
not around the meanlog.
Here below my R code, how can I get the exact 95% CIs around the mean ?
Many thanks.


library(EnvStats)
x=rlnorm(10,0,1)
mean(x)
elnorm(x,method="mvue",ci=TRUE,ci.type="two-sided",ci.method="exact",conf.level=0.95)

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Is there a Truth Table Generator in R?

[Spencer Graves]

library(sos)
tt <- findFn("{truth table}")
installPackages(tt)
tt


	  This just now opened two sheets in my default browser.  The first 
listed all the help pages in contributed packages with the phrase "truth 
table", sorted to put first the ones in packages with the most matches. 
 The second is a summary by package.



  Hope this helps.
  Spencer Graves


On 3/12/22 10:42 AM, Paul Bernal wrote:

Dear friends,

Hope you are doing great. I have been searching for a truth table generator
in R, but everything I find has a Python implementation instead.

Maybe there is in fact a truth table generator in R, but I am not searching
in the right places?

Any help and/or guidance will be greatly appreciated.

Best regards,
Paul

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Searching for packages

[Spencer Graves]

	  There is also sos::findFn, discussed in a vignette included in that 
package.  When I created that package, I felt it was the fastest 
literature search for anything statistical:  It will identify all help 
pages that match a search string and sort them by package.  It creates 
an object so related searches can be combined by union or intersection. 
 And the print method by default creates two pages in your default 
browser, one listing the help pages and the second giving the package 
summary.



  See also:


https://en.wikiversity.org/wiki/Searching_R_Packages


https://journal.r-project.org/archive/2018/RJ-2018-058/RJ-2018-058.pdf


  sg


On 2/28/22 1:47 PM, Ebert,Timothy Aaron wrote:

Thank you for the list.

-Original Message-
From: Bert Gunter 
Sent: Monday, February 28, 2022 10:47 AM
To: Rui Barradas 
Cc: Ebert,Timothy Aaron ; serv...@shdawson.com; 
r-help@r-project.org
Subject: Re: [R] Searching for packages

[External Email]

Other places beside google to look for R info:

https://urldefense.proofpoint.com/v2/url?u=https-3A__rdrr.io_=DwIFaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRzsn7AkP-g=NX0Xg1Ds2e1R_R7VKRbwJ9Nj-9mEmj5NnaA8zGWLlX904sfhElg1hwTnFBnnDpaM=oi6J8PKSQJp4dd82zs3hlWnFQWnHaXrfDLawV-2gDkg=
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rdocumentation.org_=DwIFaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRzsn7AkP-g=NX0Xg1Ds2e1R_R7VKRbwJ9Nj-9mEmj5NnaA8zGWLlX904sfhElg1hwTnFBnnDpaM=WlC49B04XegAvmAosdabM_1CYDvQ3QHC6bzZ_-cVU00=
https://urldefense.proofpoint.com/v2/url?u=https-3A__rseek.org_=DwIFaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRzsn7AkP-g=NX0Xg1Ds2e1R_R7VKRbwJ9Nj-9mEmj5NnaA8zGWLlX904sfhElg1hwTnFBnnDpaM=3H-rSYG6BgbLVYLsFTZAOZBvPc43aw16HtLgcX4S2_o=

Bert Gunter

"The trouble with having an open mind is that people keep coming along and sticking 
things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, Feb 28, 2022 at 5:44 AM Rui Barradas  wrote:


Hello,

Actually, I only found it at the second try. The RSiteSearch webpage
has a search bar, I've used it search binGroup* and found it on screen 3.

Rui Barradas

Às 13:32 de 28/02/2022, Ebert,Timothy Aaron escreveu:

binGroup2 (version 1.02) was released 2020-04-07. There was one update on 2021-03-17 
(according to available.versions("binGroup2").
My last system update was (I assume) recent. My system is governed by my 
University. I get monthly updates, rarely more often. My version of R is 4.1.
I tried Rui's suggestion (thank you) of searching using R. I read through the 
list several times but did not find binGroup2, though it is possible that it 
was there as binGroup and I need to open all the documents to find it.

Tim


-Original Message-
From: Stephen H. Dawson, DSL 
Sent: Monday, February 28, 2022 7:46 AM
To: Ebert,Timothy Aaron ; r-help@r-project.org
Subject: Re: [R] Searching for packages

[External Email]

When was binGroup2 released?

When is your last system update?

*Stephen Dawson, DSL*
/Executive Strategy Consultant/
Business & Technology
+1 (865) 804-3454
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.shdawson.com
=DwICaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kVeAsRzsn7AkP-g=WEV48V
_ui8Oz-EeQtPAqqF1cRT83c11S15V05P3diVQoJspuLdN1R04nGi2PSLKn=J6gEolZ
qXpDtRFdEzUW6R1ySBhZw3FgsLL2GoKQ1vg0=


On 2/28/22 07:36, Ebert,Timothy Aaron wrote:

If I want help on a package I can usually go to google and type "package.name in 
r" and I get what I need in the first few hits. Google typically offers suggestions 
if my spelling is a bit off, and I get hits that are close. I searched for the binGroup 
package in the usual way and found that it is no longer supported. I asked the authors 
only to discover that there is a binGroup2 package.

If I search for "tidyv in R" I get tidyverse.

Any idea why I did not get binGroup2 in the binGroup search?

Regards,
Tim

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_m
ail
man_listinfo_r-2Dhelp=DwICaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2kV
eAs
Rzsn7AkP-g=WEV48V_ui8Oz-EeQtPAqqF1cRT83c11S15V05P3diVQoJspuLdN1R0
4nG i2PSLKn=1lwcSxFoUFNj5-s-czuFCrPlhteONuK8xl-a2CkpnVA=
PLEASE do read the posting guide
https://urldefense.proofpoint.com/v2/url?u=http-3A__www.R-2Dproject
.or
g_posting-2Dguide.html=DwICaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2k
VeA
sRzsn7AkP-g=WEV48V_ui8Oz-EeQtPAqqF1cRT83c11S15V05P3diVQoJspuLdN1R
04n Gi2PSLKn=rVBDL-rnzLnz-rie3bN1-pU8DPfnVxnJMTfbsKzW3nw=
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_ma
ilman_listinfo_r-2Dhelp=DwIFaQ=sJ6xIWYx-zLMB3EPkvcnVg=9PEhQh2k
VeAsRzsn7AkP-g=NX0Xg1Ds2e1R_R7VKRbwJ9Nj-9mEmj5NnaA8zGWLlX904sfhElg

Re: [R] nlme::lme sigma parameter standard deviation or variance?

[Spencer Graves]

  Modifying the first example in help('lme', pac='nlme'):


library(nlme)


fm1 <- lme(distance ~ age, data = Orthodont) # random is ~ age


fm1$sigma


fm1.2 <- lme(2*distance ~ age, data = Orthodont) # random is ~ age


fm1.2$sigma


  Conclusion:  Standard deviation, as indicated in help('lmeObject').


  Hope this helps.
  Spencer Graves


On 12/18/21 4:00 AM, Eric Berger wrote:

You can run a test. Multiply all your data by a scalar, say 2.
If this changes the result lme_mod$sigma by a factor of 2, then it is
a std deviation.
If it changes the result by a factor of 4, then it is a variance.

HTH,
Eric

On Sat, Dec 18, 2021 at 11:26 AM Courtney Van Den elzen
 wrote:


Hi R-help,

I am a researcher fitting linear mixed models using the package nlme. I am
wondering whether the sigma value that is outputted as part of the model
object is standard deviation or variance? for example, I might fit a model

lme_mod <- nlme::lme(response ~ predictor1 + predictor2, random =
(~1|grouping1))

I am wondering whether lme_mod$sigma is actually a standard deviation or if
it's a variance.

Thanks so much,
Courtney

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Date read correctly from CSV, then reformatted incorrectly by R

[Spencer Graves]

	  I've written Ecfun::asNumericDF to overcome some of the common 
problems with read.data, read.csv, etc.:



https://www.rdocumentation.org/packages/Ecfun/versions/0.2-5/topics/asNumericDF


	  I use it routinely to help parse numbers, dates, etc., that are read 
as character. I'm sure it can be improved.  It's on GitHub in case 
anyone would like to take the time to suggest improvements:



https://github.com/sbgraves237/Ecfun


  Hope this helps.
  Spencer Graves


On 11/20/21 4:13 PM, Avi Gross via R-help wrote:

This seems to be a topic that comes up periodically. The various ways in R
and other packages for reading in data often come with methods that simply
guess wrong or encounter one or more data items in a column that really do
not fit so fields may just by default become a more common denominator of
character or perhaps floating point.

There are ways that some such programs can be given a hint of what you
expect or even be supplied with a way to coerce them into what you want
while being read in. But realistically, often a more practical  method might
be to take the data.frame variety you read in and before using it for other
purposes, check it for validity and make any needed changes. Simplistic ones
might be to see how many columns were read in to see if it matches
expectations or generate an error. Or you may trim columns (or rows) that
are not wanted.

In that vein, are there existing functions available that will accept what
types you want one or more columns to be in and that validate if the current
type is something else and then convert if needed? I mean we have functions
like as.integer(df$x ) or more flexibly as(df$x, "integer") and you may
simply build on a set of those and create others to suit any special needs.

Of course a good method carefully checks the results before over-writing as
sometimes the result may not be the same length (as shown below) or may
violate some other ideas or rules:


as(c(NULL, NA, 3, 3.1, "3.1", list(1,2,"a")), "character")

[1] "NA"  "3"   "3.1" "3.1" "1"   "2"   "a"

So if you have dates in some format, or sometimes an unknown format, there
are ways, including some others have shown, to make them into some other
date format or even make multiple columns that together embody the format.

What people sometimes do is assume software is perfect and should do
anything they want. It is the other way around and the programmer or data
creator has some responsibilities to use the right software on the right
data and that may also mean sanity checks along the way to  see if the data
is what you expect or alter it to be what you need.


-Original Message-
From: R-help  On Behalf Of Philip Monk
Sent: Saturday, November 20, 2021 3:28 PM
To: Jeff Newmiller 
Cc: R-help Mailing List 
Subject: Re: [R] Date read correctly from CSV, then reformatted incorrectly
by R

Thanks, Jeff.

I follow what you're doing below, but know I need to read up on Date /
POSIXct.  Helpful direction!  :)

On Sat, 20 Nov 2021 at 18:41, Jeff Newmiller 
wrote:


Beat me to it! But it is also worth noting that once converted to Date or

POSIXct, timestamps should be treated as data without regard to how that
data is displayed. When you choose to output that data you will have options
as to the display format associated with the function you are using for
output.


My take:

dta <- read.table( text=
"Buffer28/10/201619/11/2016  31/12/201616/01/2017

05/03/2017

1002.437110889-8.696748953.2392998162.443183304

2.346743827

2002.524329899-7.6888620683.3868117342.680347706

2.253885237

3002.100784256-8.0598558353.1437865072.615152896

2.015645973

4001.985608385-10.67072062.8945727912.591925038

2.057913137

5001.824982163-9.1225197362.5603507272.372226799

1.995863839

", header=TRUE, check.names=FALSE, as.is=TRUE)

dta

library(dplyr)
library(tidyr)

dt_fmt <- "%d/%m/%Y"

dta_long <- (   dta
 %>% pivot_longer( cols = -Buffer
 , names_to = "dt_chr"
 , values_to = "LST"
 )
 %>% mutate( dt_date = as.Date( dt_chr, format = dt_fmt )
   , dt_POSIXct = as.POSIXct( dt_chr, format = dt_fmt,

tz = "Etc/GMT+8" )

   )
 )

dta_long

On November 20, 2021 10:01:56 AM PST, Andrew Simmons 

wrote:

The as.Date function for a character class argument will try reading
in two formats (%Y-%m-%d and %Y/%m/%d).


This does not look like the format you have provided, which is why it
doesn't work. Try something like:


x <- c("28/10/2016", "19/11/2016", "31/12/2016", "16/01/2016",
"05/03/2017") as.Date(x, format = "%

Re: [R] Date

[Spencer Graves]

	  My speculation is that Microsoft Excel recognized that as a date and 
saved it in the "mm/dd/" format you saw when reading it into R with 
dat=read.csv("myfile.csv").



	  "str" told you the format.  You can convert that from character to 
Date using as.Date(dat$mydate, '%m/%d/%Y'), as documented in 
help('as.Date').



NOTE: The error message, "character string is not in a standard 
unambiguous format" is almost appropriate:  In this case, it's clear 
that "09/16/2019" refers to month 09, day 16, and year 2019.  However, 
if it were "09/06/2019", we would not know if it were September 6 or 9 
June of 2019.  If it were  "09/06/08", we would have the added 
possibility with the year first, followed by month and day:  June 8, 
2009.  This ambiguity is resolved most forcefully by ISO 8601.



  Hope this helps.
  Spencer Graves


On 11/4/21 5:30 PM, PIKAL Petr wrote:

Hi

Not sure why the date format was changed but if I am correct R do not read 
dates as dates but as character vector. You need to transfer such columns to 
dates by asDate. The error is probably from your use two asDate commands.

Cheers
Petr
-Original Message-
From: R-help  On Behalf Of Val
Sent: Thursday, November 4, 2021 10:43 PM
To: r-help@R-project.org (r-help@r-project.org) 
Subject: [R] Date

IHi All, l,

I am  reading a csv file  and one of the columns is named as  "mydate"
  with this form, 2019-09-16.

I am reading this file as

dat=read.csv("myfile.csv")
  the structure of the data looks like as follow

str(dat)
mydate : chr  "09/16/2019" "02/21/2021" "02/22/2021" "10/11/2017" ...

Please note the format  has  changed from -mm-dd  to mm/dd/
When I tried to change this   as a Date using

as.Date(as.Date(mydate, format="%m/%d/%Y" )
I am getting this error message
 Error in charToDate(x) :
   characte string is not in a standard unambiguous format

My question is,
1. how can I read the file as it is (i.e., without changing the date format) ?
2. why does R change the date format?

Thank you,

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních 
partnerů PRECHEZA a.s. jsou zveřejněny na: 
https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about 
processing and protection of business partner’s personal data are available on 
website: https://www.precheza.cz/en/personal-data-protection-principles/
Důvěrnost: Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a 
podléhají tomuto právně závaznému prohláąení o vyloučení odpovědnosti: 
https://www.precheza.cz/01-dovetek/ | This email and any documents attached to 
it may be confidential and are subject to the legally binding disclaimer: 
https://www.precheza.cz/en/01-disclaimer/

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] about L-BFGS-B

[Spencer Graves]

Hello 최병권 :


	  Are you familiar with the "debug" function?  "debug(glm.cmp)" 
followed by the problem command will put you into the environment of 
"glm.cmp", and you can walk through that function line by line looking 
at each variable.



	  If you need more help, "PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html and provide commented, 
minimal, self-contained, reproducible code."



	  Also, am I correct that this glm.cmp function is in the COMPoissonReg 
package?  If yes, have you tried contacting the maintainer of that 
package (Andrew Raim ?)?  If you can't solve 
your problem using "debug(glm.cmp)" AND you have NOT yet asked the 
package maintainer with "commented, minimal, self-contained, 
reproducible code."  They might like to have that example to make the 
code easier to use, e.g., by giving a more informative error message.



  Hope this helps,
  Spencer Graves


On 8/15/21 7:26 AM, J C Nash wrote:

You have the answer in the error message: the objective function has
been calculated as +/-Inf somehow. You are going to have to figure
out where the function is computed and why it is not finite.

JN

On 2021-08-15 12:41 a.m., 최병권 wrote:

Hello Dear,

I am Choy from Seoul.
I have a question about R

Is it possible to answer the error that occurred while executing R?
I am currently doing zero inflated regression because the data follows a
poisson distribution.


However, for glm.c <http://glm.cm>mp (rndclass ~ CR4), the results are
normally displayed, but when an independent variable is added, the
following error message is displayed:

#Error in optim(par.init, loglik, method = optim.method, control =
optim.control,  :
   L-BFGS-B needs finite values of 'fn'


I can't solve it, but I'd appreciate it if you could help.

For reference, the estimated regression equation is attached below.

# A CMP example with offset terms
  cmp.m3 = glm.cmp(rndclass ~ CR4 + offset(CR4), data=dta)  -(1)
  print(cmp.m3)

  # A ZICMP example with offset terms.

  zicmp.m4 = glm.cmp(rndclass ~ CR4+offset(CR4),
 formula.nu = ~ offset(CR4),
   formula.p = ~ CR4+offset(CR4), data=dta)  -(2)

# dependent variable:

  summary(dta$rndc)
 0 1 2 3
12398  1290 11341   109

Thank you

Best
Choy

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] SOS package: findFn does not work

[Spencer Graves]

Thanks for the question.  Two things:


** 1.  TRY THE DEVELOPMENT VERSION OBTAINABLE AS FOLLOWS:


install.packages('devtools') # if it's not installed


library(devtools)


install_github("sbgraves237/sos")


library(sos)


 z <- findFn("spline", maxPages = 2)


# This should work.


** 2.  PLEASE PROVIDE:


sessionInfo()


	  "findFn('spline')" just worked for me using both the CRAN and 
development versions of sos.  (2.1-0 from CRAN under Windows 10; 2.1- 
from GitHub under macOS 11.4; both with R 4.1.0).



	  I need to push the GitHub version to CRAN.  However, it would help me 
if I understood your configuration and if the GitHub version fixes the 
problem for you.



  Thanks for the report.  I apologize for the inconvenience.


  Spencer Graves


On 8/7/21 2:57 AM, hp wan wrote:

Dear All,

Recently, I found that the SOS package (very helpful package) does not
work.  When I used the "findFn" function to search something, it always
said "found 0 matches" (see below). My desktop system is Win 10 and R
version is R-4.1.0. Any suggestion was greatly appreciated.

HP



z <- findFn("spline", maxPages = 2)

found 0 matches
Warning message:
In findFn("spline", maxPages = 2) :
   HIT not found in HTML;  processing one page only.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Sin curve question

[Spencer Graves]

plot(sin, to=pi) # also works but with x labeled in radians.


# With x axis labeled in degrees
plot(sin, to=pi, axes=FALSE)
axis(2)
lbls <- seq(0, 180, 30)
axis(1, pi*lbls/180, lbls)


	  This can probably be done in ggplot2, but I don't know how off the 
top of my head.



  Hope this helps.
  Spencer


On 7/24/21 2:04 PM, Eric Berger wrote:

Alternatively with base graphics

N <- 500 ## number of points (arbitrary)
degrees <- seq(from=0,to=180,length=N)
degreesToRadians <- function(d) { pi * d / 180.0}  ## vectorIzed!
plot(x=degrees,y=sin(degreesToRadians(degrees)),type='l',
  xlab="x",ylab="sin(x)",main="sin(x) vs x\nx is in degrees")


On Sat, Jul 24, 2021 at 9:52 PM Sorkin, John 
wrote:


Try something like the following

copdat$degrees <- c(1:180)

John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and
Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior
to faxing)

On Jul 24, 2021, at 2:41 PM, Thomas Subia via R-help 
wrote:

Colleagues,

Here is my code which plots sin(x) vs x, for angles between 0 and 180
degrees.

library(ggplot2)
library(REdaS)
copdat$degrees <- c(0,45,90,135,180)
copdat$radians <- deg2rad(copdat$degrees)
copdat$sin_x <- sin(copdat$radians)

ggplot(copdat,aes(x=degrees,y=sin_x))+
  geom_point(size = 2)+ geom_line()+
  theme_cowplot()+xlab("x")+
  ylab("sin(x)")+
  scale_x_continuous(breaks=seq(0,180,30))+
  ggtitle("sin(x) vs x\nx is in degrees")

My trig students would prefer a curved line plot similar to what can be
plotted with Excel smooth line functionality.
I wanted to provide a relatively simple R script using ggplot to do this
without having to resort to fitting a sine curve to these points.

Some guidance would be appreciated.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see

https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-helpdata=04%7C01%7CJSorkin%40som.umaryland.edu%7C1ffa4922f2ba41588da908d94ed2a982%7C717009a620de461a88940312a395cac9%7C0%7C0%7C637627488997910453%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=90qApIoS6rwqkQuKPzy3x2AUPntuJ2W%2FtJgPGfiddEI%3Dreserved=0
PLEASE do read the posting guide
https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.htmldata=04%7C01%7CJSorkin%40som.umaryland.edu%7C1ffa4922f2ba41588da908d94ed2a982%7C717009a620de461a88940312a395cac9%7C0%7C0%7C637627488997910453%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=s9YIcjlEo4MvI6hcX%2FkV4gwJJKa172QrPEnHsqTiRa8%3Dreserved=0
and provide commented, minimal, self-contained, reproducible code.

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] MAC version 10

[Spencer Graves]

  What web site did you go to?  Have you tried:


https://cran.r-project.org/bin/macosx/


	  Then click on "R-4.1.0.pkg".  That should download as normal.  Then 
double click on that, etc.



      Spencer Graves


On 7/6/21 3:52 PM, Farrah T wrote:

Hello,

I have Mac Version 10 Catalina and I would like to download R on this device 
for my summer class. I have difficulty to find a right option when I go to the 
website. May you please kindly share the step by step guidance with me. The 
screenshot with be great. I downloaded few zip files and yet didn’t know how to 
follow after that step neither. Looking forward to hearing from your side.

Best,
Fararh
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] input string ... cannot be translated to UTF-8, is it valid in 'ANSI_X3.4-1968'?

[Spencer Graves]

Hello:


	  What if anything should I do regarding notes from either "load" or 
"attach" that, "input string ... cannot be translated to UTF-8, is it 
valid in 'ANSI_X3.4-1968'?"?



	  I'm running R 4.0.5 under macOS 11.2.3;  see "sessionInfo()" and 
detailed instructions below on the precise file I dowloaded from the web 
and tried to read.



	  I may be able to get what I want just ignoring this.  However, I'd 
like to know how to fix this.



  Thanks,
  Spencer Graves


sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib


locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

loaded via a namespace (and not attached):
 [1] compiler_4.0.5htmltools_0.5.1.1 tools_4.0.5   yaml_2.2.1 

 [5] tinytex_0.31  rmarkdown_2.7 knitr_1.31 
digest_0.6.27

 [9] xfun_0.22 rlang_0.4.10  evaluate_0.14
> search()
 [1] ".GlobalEnv""file:NAVCO 1.3 List.RData"
 [3] "file:NAVCO 1.3 List.RData" "tools:rstudio"
 [5] "package:stats" "package:graphics"
 [7] "package:grDevices" "package:utils"
 [9] "package:datasets"  "package:methods"
[11] "Autoloads" "package:base"


*** To get the file I used for this, I went to 
"https://www.ericachenoweth.com/research;.  From there I clicked 
"Version 1.3".  This took me to



https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/ON9XND


I then clicked the "Download" icon to the right of "NAVCO 1.3 List.tab". 
 This gave me 5 "Download Options", one of which was "RData Format";  I 
selected that.  This downloaded "NAVCO 1.3 List.RData", which I moved to 
getwd().  Then I did 'load("NAVCO 1.3 List.RData")' and 'attach("NAVCO 
1.3 List.RData")'.  Both of those gave me 8 repetitions of a message 
like "input string ... cannot be translated to UTF-8, is it valid in 
'ANSI_X3.4-1968'?" with different values substituted for "...".


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] about a p-value < 2.2e-16

[Spencer Graves]

On 2021-3-19 9:52 AM, Jiefei Wang wrote:

After digging into the R source, it turns out that the argument `exact` has
nothing to do with the numeric precision. It only affects the statistic
model used to compute the p-value. When `exact=TRUE` the true distribution
of the statistic will be used. Otherwise, a normal approximation will be
used.

I think the documentation needs to be improved here, you can compute the
exact p-value *only* when you do not have any ties in your data. If you
have ties in your data you will get the p-value from the normal
approximation no matter what value you put in `exact`. This behavior should
be documented or a warning should be given when `exact=TRUE` and ties
present.

FYI, if the exact p-value is required, `pwilcox` function will be used to
compute the p-value. There are no details on how it computes the pvalue but
its C code seems to compute the probability table, so I assume it computes
the exact p-value from the true distribution of the statistic, not a
permutation or MC p-value.



  My example shows that it does NOT use Monte Carlo, because 
otherwise it uses some distribution.  I believe the term "exact" means 
that it uses the permutation distribution, though I could be mistaken.  
If it's NOT a permutation distribution, I don't know what it is.



  Spencer


Best,
Jiefei



On Fri, Mar 19, 2021 at 10:01 PM Jiefei Wang  wrote:


Hey,

I just want to point out that the word "exact" has two meanings. It can
mean the numerically accurate p-value as Bogdan asked in his first email,
or it could mean the p-value calculated from the exact distribution of the
statistic(In this case, U stat). These two are actually not related, even
though they all called "exact".

Best,
Jiefei

On Fri, Mar 19, 2021 at 9:31 PM Spencer Graves <
spencer.gra...@effectivedefense.org> wrote:



On 2021-3-19 12:54 AM, Bogdan Tanasa wrote:

thanks a lot, Vivek ! in other words, assuming that we work with 1000

data

points,

shall we use EXACT = TRUE, it uses the normal approximation,

while if EXACT=FALSE (for these large samples), it does not ?


As David Winsemius noted, the documentation is not clear.
Consider the following:


set.seed(1)  > x <- rnorm(100) > y <- rnorm(100, 2) > > wilcox.test(x,

y)$p.value
[1] 1.172189e-25 > wilcox.test(x, y)$p.value [1] 1.172189e-25 > >
wilcox.test(x, y, EXACT=TRUE)$p.value [1] 1.172189e-25 > wilcox.test(x,
y, EXACT=TRUE)$p.value [1] 1.172189e-25 > wilcox.test(x, y,
exact=TRUE)$p.value [1] 4.123875e-32 > wilcox.test(x, y,
exact=TRUE)$p.value [1] 4.123875e-32 > > wilcox.test(x, y,
EXACT=FALSE)$p.value [1] 1.172189e-25 > wilcox.test(x, y,
EXACT=FALSE)$p.value [1] 1.172189e-25 > wilcox.test(x, y,
exact=FALSE)$p.value [1] 1.172189e-25 > wilcox.test(x, y,
exact=FALSE)$p.value [1] 1.172189e-25 > We get two values here:
1.172189e-25 and 4.123875e-32. The first one, I think, is the normal
approximation, which is the same as exact=FALSE. I think that with
exact=FALSE, you get a permutation distribution, though I'm not sure.
You might try looking at "wilcox_test in package coin for exact,
asymptotic and Monte Carlo conditional p-values, including in the
presence of ties" to see if it is clearer. NOTE: R is case sensitive, so
"EXACT" is a different variable from "exact". It is interpreted as an
optional argument, which is not recognized and therefore ignored in this
context.
   Hope this helps.
   Spencer



On Thu, Mar 18, 2021 at 10:47 PM Vivek Das  wrote:


Hi Bogdan,

You can also get the information from the link of the Wilcox.test

function

page.

“By default (if exact is not specified), an exact p-value is computed

if

the samples contain less than 50 finite values and there are no ties.
Otherwise, a normal approximation is used.”

For more:



https://stat.ethz.ch/R-manual/R-devel/library/stats/html/wilcox.test.html

Hope this helps!

Best,

VD


On Thu, Mar 18, 2021 at 10:36 PM Bogdan Tanasa 

wrote:

Dear Peter, thanks a lot. yes, we can see a very precise p-value, and

that

was the request from the journal.

if I may ask another question please : what is the meaning of

"exact=TRUE"

or "exact=FALSE" in wilcox.test ?

i can see that the "numerically precise" p-values are different.

thanks a

lot !

tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
tst$p.value
[1] 8.535524e-25

tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=FALSE)
tst$p.value
[1] 3.448211e-25

On Thu, Mar 18, 2021 at 10:15 PM Peter Langfelder <
peter.langfel...@gmail.com> wrote:


I thinnk the answer is much simpler. The print method for hypothesis
tests (class htest) truncates the p-values. In the above example,
instead of using

wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)

and copying the output, just print the p-value:

tst = wilcox.test(rnorm(100), rnorm(100, 2), exact

Re: [R] about a p-value < 2.2e-16

[Spencer Graves]

On 2021-3-19 12:54 AM, Bogdan Tanasa wrote:
> thanks a lot, Vivek ! in other words, assuming that we work with 1000 data
> points,
>
> shall we use EXACT = TRUE, it uses the normal approximation,
>
> while if EXACT=FALSE (for these large samples), it does not ?


   As David Winsemius noted, the documentation is not clear. 
Consider the following:

> set.seed(1)  > x <- rnorm(100) > y <- rnorm(100, 2) > > wilcox.test(x, 
> y)$p.value 
[1] 1.172189e-25 > wilcox.test(x, y)$p.value [1] 1.172189e-25 > > 
wilcox.test(x, y, EXACT=TRUE)$p.value [1] 1.172189e-25 > wilcox.test(x, 
y, EXACT=TRUE)$p.value [1] 1.172189e-25 > wilcox.test(x, y, 
exact=TRUE)$p.value [1] 4.123875e-32 > wilcox.test(x, y, 
exact=TRUE)$p.value [1] 4.123875e-32 > > wilcox.test(x, y, 
EXACT=FALSE)$p.value [1] 1.172189e-25 > wilcox.test(x, y, 
EXACT=FALSE)$p.value [1] 1.172189e-25 > wilcox.test(x, y, 
exact=FALSE)$p.value [1] 1.172189e-25 > wilcox.test(x, y, 
exact=FALSE)$p.value [1] 1.172189e-25 > We get two values here: 
1.172189e-25 and 4.123875e-32. The first one, I think, is the normal 
approximation, which is the same as exact=FALSE. I think that with 
exact=FALSE, you get a permutation distribution, though I'm not sure. 
You might try looking at "wilcox_test in package coin for exact, 
asymptotic and Monte Carlo conditional p-values, including in the 
presence of ties" to see if it is clearer. NOTE: R is case sensitive, so 
"EXACT" is a different variable from "exact". It is interpreted as an 
optional argument, which is not recognized and therefore ignored in this 
context.
  Hope this helps.
  Spencer


> On Thu, Mar 18, 2021 at 10:47 PM Vivek Das  wrote:
>
>> Hi Bogdan,
>>
>> You can also get the information from the link of the Wilcox.test function
>> page.
>>
>> “By default (if exact is not specified), an exact p-value is computed if
>> the samples contain less than 50 finite values and there are no ties.
>> Otherwise, a normal approximation is used.”
>>
>> For more:
>>
>> https://stat.ethz.ch/R-manual/R-devel/library/stats/html/wilcox.test.html
>>
>> Hope this helps!
>>
>> Best,
>>
>> VD
>>
>>
>> On Thu, Mar 18, 2021 at 10:36 PM Bogdan Tanasa  wrote:
>>
>>> Dear Peter, thanks a lot. yes, we can see a very precise p-value, and that
>>> was the request from the journal.
>>>
>>> if I may ask another question please : what is the meaning of "exact=TRUE"
>>> or "exact=FALSE" in wilcox.test ?
>>>
>>> i can see that the "numerically precise" p-values are different. thanks a
>>> lot !
>>>
>>> tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
>>> tst$p.value
>>> [1] 8.535524e-25
>>>
>>> tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=FALSE)
>>> tst$p.value
>>> [1] 3.448211e-25
>>>
>>> On Thu, Mar 18, 2021 at 10:15 PM Peter Langfelder <
>>> peter.langfel...@gmail.com> wrote:
>>>
>>>> I thinnk the answer is much simpler. The print method for hypothesis
>>>> tests (class htest) truncates the p-values. In the above example,
>>>> instead of using
>>>>
>>>> wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
>>>>
>>>> and copying the output, just print the p-value:
>>>>
>>>> tst = wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
>>>> tst$p.value
>>>>
>>>> [1] 2.988368e-32
>>>>
>>>>
>>>> I think this value is what the journal asks for.
>>>>
>>>> HTH,
>>>>
>>>> Peter
>>>>
>>>> On Thu, Mar 18, 2021 at 10:05 PM Spencer Graves
>>>>  wrote:
>>>>> I would push back on that from two perspectives:
>>>>>
>>>>>
>>>>>   1.  I would study exactly what the journal said very
>>>>> carefully.  If they mandated "wilcox.test", that function has an
>>>>> argument called "exact".  If that's what they are asking, then using
>>>>> that argument gives the exact p-value, e.g.:
>>>>>
>>>>>
>>>>>   > wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)
>>>>>
>>>>>   Wilcoxon rank sum exact test
>>>>>
>>>>> data:  rnorm(100) and rnorm(100, 2)
>>>>> W = 691, p-value < 2.2e-16
>>>>>
>>>>>
>>>>>   2.

Re: [R] about a p-value < 2.2e-16

[Spencer Graves]

  I would push back on that from two perspectives:


        1.  I would study exactly what the journal said very 
carefully.  If they mandated "wilcox.test", that function has an 
argument called "exact".  If that's what they are asking, then using 
that argument gives the exact p-value, e.g.:



> wilcox.test(rnorm(100), rnorm(100, 2), exact=TRUE)

    Wilcoxon rank sum exact test

data:  rnorm(100) and rnorm(100, 2)
W = 691, p-value < 2.2e-16


        2.  If that's NOT what they are asking, then I'm not 
convinced what they are asking makes sense:  There is is no such thing 
as an "exact p value" except to the extent that certain assumptions 
hold, and all models are wrong (but some are useful), as George Box 
famously said years ago.[1]  Truth only exists in mathematics, and 
that's because it's a fiction to start with ;-)



  Hope this helps.
  Spencer Graves


[1]
https://en.wikipedia.org/wiki/All_models_are_wrong


On 2021-3-18 11:12 PM, Bogdan Tanasa wrote:

  <https://meta.stackexchange.com/questions/362285/about-a-p-value-2-2e-16>
Dear all,

i would appreciate having your advice on the following please :

in R, the wilcox.test() provides "a p-value < 2.2e-16", when we compare
sets of 1000 genes expression (in the genomics field).

however, the journal asks us to provide the exact p value ...

would it be legitimate to write : "p-value = 0" ? thanks a lot,

-- bogdan

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Very slow optim()

[Spencer Graves]

Hi, Deepayan:


On 2021-03-13 01:27, Deepayan Sarkar wrote:

On Sat, Mar 13, 2021 at 10:08 AM Spencer Graves
 wrote:


TWO COMMENTS:


1.  DID YOU ASSIGN THE OUTPUT OF "optim" to an object, like "est <-
optim(...)"?  If yes and if "optim" terminated normally, the 60,000+
paramters should be there as est$par.  See the documentation on "optim".


2.  WHAT PROBLEM ARE YOU TRYING TO SOLVE?


   I hope you will forgive me for being blunt (or perhaps bigoted), but
I'm skeptical about anyone wanting to use optim to estimate 60,000+
parameters.  With a situation like that, I think you would be wise to
recast the problem as one in which those 60,000+ parameters are sampled
from some hyperdistribution characterized by a small number of
hyperparameters.  Then write a model where your observations are sampled
from distribution(s) controlled by these random parameters.  Then
multiply the likelihood of the observations by the likelihood of the
hyperdistribution and integrate out the 60,000+ parameters, leaving only
a small number hyperparameters.


Just a comment on this comment: I think it's perfectly reasonable to
optimize 60k+ parameters with conjugate gradient. CG was originally
developed to solve linear equations of the form Ax=b. If x was not
large in size, one would just use solve(A, b) instead of an iterative
method.

Use of CG is quite common in image processing. A relatively small
300x300 image will give you 90k parameters.

-Deepayan



  Thanks for this.


  If both A and b are 300x300, then x will also be 300x300.


  What do you do in this case if A is not square or even ill 
conditioned?


	  Do you care if you get only one of many possible or approximate 
solutions, and the algorithm spends most of its time making adjustments 
in a singular subspace that would have best been avoided?



  Spencer

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Very slow optim()

[Spencer Graves]

TWO COMMENTS:


1.  DID YOU ASSIGN THE OUTPUT OF "optim" to an object, like "est <- 
optim(...)"?  If yes and if "optim" terminated normally, the 60,000+ 
paramters should be there as est$par.  See the documentation on "optim".



2.  WHAT PROBLEM ARE YOU TRYING TO SOLVE?


	  I hope you will forgive me for being blunt (or perhaps bigoted), but 
I'm skeptical about anyone wanting to use optim to estimate 60,000+ 
parameters.  With a situation like that, I think you would be wise to 
recast the problem as one in which those 60,000+ parameters are sampled 
from some hyperdistribution characterized by a small number of 
hyperparameters.  Then write a model where your observations are sampled 
from distribution(s) controlled by these random parameters.  Then 
multiply the likelihood of the observations by the likelihood of the 
hyperdistribution and integrate out the 60,000+ parameters, leaving only 
a small number hyperparameters.



	  When everything is linear and all the random variables / random 
effects and observation errors follow normal distributions, this is the 
classic linear, mixed-effects situation that is routinely handled well 
for most such situations by the nlme package, documented with in 
companion book Pinhiero and Bates (2000) Mixed-Effects Models in S and 
S-PLUS (Springer).  If the models are nonlinear but with curvature that 
is reasonably well behaved and the random variables / random effects and 
observation errors are still normal, the nlme package and Pinhiero and 
Bates still provide a great approach to most such situations, as far as 
I know.  When the observations are non-normally distributed, then the 
best software I know is the lme4 package.  I have not used it recently, 
but it was written and being maintained by some of the leading experts 
in this area as far as I know.



CONCLUSION:


	  If you are short on time and "1" will work for you, do that. 
Obviously, you will need to do some further analysis to understand the 
60,000+ parameters you estimated -- which implies by itself that you 
really should be using approach "2".  However, if I'm short on time and 
need an answer, then I'd ignore "2" and hope to get something by 
plotting and doing other things with the 60,000+ parameters that should 
be in "est$par" if "optim" actually ended normally.



	  However, if the problem is sufficiently important to justify more 
work, then I'd want to cast it as some kind if mixed-effects model, per 
"2" -- perhaps using an analysis of "1" as a first step towards "2".



  Hope this helps.
  Spencer


On 2021-03-12 20:53, J C Nash wrote:

optim() has no method really suitable for very large numbers of parameters.

- CG as set up has never worked very well in any of its implementations
   (I wrote it, so am allowed to say so!). Rcgmin in optimx package works
   better, as does Rtnmin. Neither are really intended for 60K parameters
   however.

- optim::L-BFGS-B is reasonable, but my experience is that it still is not
   intended for more than a couple of hundred parameters.

JN



On 2021-03-12 9:31 p.m., Jeff Newmiller wrote:

Calculate fewer of them?

If you don't setup your code to save intermediate results, then you cannot see 
intermediate results.

On March 11, 2021 8:32:17 PM PST, "毕芳妮 via R-help"  wrote:

Dear list,
I am using optim() to estimate over 60 thousans of parameters, and use
the server to run the program.But it took me 5 hours and there was just
no result coming out.How could I do to show some results that have been
calculated by optim()?
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.




__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] forecast accuracy

[Spencer Graves]

Hello, Faheem:


	  1.  You might get a better response if you "PLEASE do read the 
posting guide http://www.R-project.org/posting-guide.html and provide 
commented, minimal, self-contained, reproducible code", as it says at 
the bottom of each email in this list.  That would make it easier for 
people to understand the problem you are trying to solve.



	  2.  Are you familiar with the "fda" package?  I assume you are, but 
if not, I suggest you look at it.



	  3.  If you are familiar with the "fda" package, have you reviewed the 
Wikipedia article on "Functional data analysis" and Ramsay, Hooker and 
Graves (2009) Functional data analysis with R and Matlab (Springer)? 
The latter provides more extensive documentation for the "fda" package.



	  4.  Have you written directly to the maintainer of the "fda" package? 
 You can get his email from help("fda").



  Hope this helps.
  Spencer Graves


On 2021-02-17 06:02, Faheem Jan via R-help wrote:

I am new in the functional time series,  my question may be stupid as  I am 
new, I am  functional forecasting one year a head, Know I want to check the 
forecast accuracy by calculating the mean absolute percentage error, but I am 
unable to due this R, please help me or suggest me any link which help me  to 
solve my problem, Regard


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Is there anyone who uses both R and Python here? How do you debug? Perhaps in RStudio?

[Spencer Graves]

You can mix R and Python code in the same R Markdown vignette.  See:


https://bookdown.org/yihui/rmarkdown/language-engines.html


```{r "RcodeChunk"}
# R code
```

```{python "PythonCodeChunk"}
# Python code
```

	  I did this a couple of years ago.  I haven't used Python since. 
However, this is described in the book Xie, Allaire, and Grolemund 
(2020) R Markdown: The Definitive Guide (Chapman & Hall and available 
for free at the above link).



  Spencer Graves


On 2021-01-27 10:31, Robert Knight wrote:

An iterative process works well. Python to get the data desired and then
Rscript script.r from a command line.   My process involves building a
script in R using, using Rstudio, Pycharm, VS Code, Kate, or some other
editor.  Then using data input built with Python as input to Rscript. The R
scripts produce excel files or CSV data for other use   RStudio is amazing
for some slow pace academic work.  The "expected a numeric but got a char"
error appeared to often for my needs and so the workflows wound up with
Python building data that's already cleaned for use in R to avoid data
import troubles.  My code use a functional paradigm rather than object
oriented paradigm.  Python does more than just munge my data since it
handled many mathematic operations on it, but it's ultimate purpose is to
clean large amounts of data to avoid import errors in R.

On Wed, Jan 27, 2021, 1:49 AM C W  wrote:


Hello all,

I'm a long time R user, but recently also using Python. I noticed that
RStudio rolled out Python through reticulate. It's great so far!

My question is, how do you debug in Python?

In R, I simply step through the code script in my console with cmd+enter.
But you can't do that with Python, some of them are objects.

Here's my example.
class person:
  def __init__(self, id, created_at, name, attend_date, distance):
   """Create a new `person`.
   """
   self._id = id
   self.created_at = created_at
   self.name = name
   self.attend_date = attend_date
   self.distance = distance

  @classmethod
   def get_person(self, employee):
   """Find and return a person by.
   """
   return person(employee['created_at'],
employee['id'],
employee['name'],
employee['attend_date'],
employee['distance']
)

The error message says self._id was 'str', but expecting an 'int'. I can't
do:

self._id = 5

I guess it's "hidden". Can't really assign and test like that.

It seems hardcore Python programmers just use a debugger, and do not
understand the greatness of interactive IDE and console. I'd still like to
stay in IDE, hopefully.

So, how are the R users coping with object classes? Do you just instantiate
every time? What if you got 10 of these class person objects to debug?

I know this may be a Python question. But, I really wanted to see from a R
user's working experience.

Thanks a lot,

Mike

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] merging multiple .csv files

[Spencer Graves]

	  Did you work the examples in help("merge")?  Also, have you looked at 
the "dplyr" package?  It has 9 different vignettes.  The lead author is 
Hadley Wickham, who won the 2019 COPSS Presidents' Award for work like 
this.



	  Alternatively, you could manually read all 10 files, then figure out 
from that what the merged object should look like with what rows and 
what columns.



  I might start with something like:


PosAll <- unique(c(table1$Pos, table2$Pos, ... ))


Combined <- data.frame(Pos=PosAll, col1=NA, col2=NA, ...)


	  Then create the object you want that contains a column "Pos" = 
PosAll.  Then:



rownames(table1) <- table1$Pos
rownames(table2) <- table2$Pos
...

sel1 <- PosAll %in% table1$Pos
...

Combined[sel1, names(table1)] <- table1[PosAll[sel1], ]


	  CAVEAT:  I haven't tried this exact code.  It may not work as 
written.  However, I've done things like this in the past.  "merge" and 
"dplyr" have seemed too much like black magic for me.



  Spencer


On 2020-12-15 16:13, pooja sinha wrote:

I know that but I do not want to merge them sequentially because I may lose
some rows which are present in one file while the other doesn't have. I
googled and found something called multmerge but the code is not working
for me. I used the following:

path <-"P:/Documents/Puja Desktop items/Documents/RESULTS/est meth
results/Final_est_meth_data_rn6/WGBS_exon_sort_CHG/merge_csv"


filenames <- list.files(path = path)

View(filenames)
multmerge = function(path){
   filenames=list.files(path=path, full.names=TRUE)
   datalist = lapply(filenames, function(x){read.csv(file=x,header=T)})
   Reduce(function(x,y) {merge(x,y)}, datalist)
}

full_data = multmerge("~/P:/Documents/Puja Desktop
items/Documents/RESULTS/est meth
results/Final_est_meth_data_rn6/WGBS_exon_sort_CHG/merge_csv")

But after running the full_data, the folder is empty.

Thanks,
Puja

On Tue, Dec 15, 2020 at 4:51 PM Bert Gunter  wrote:


?read.csv to read your csv files in data frames
?merge to merge them (sequentially).


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Tue, Dec 15, 2020 at 1:36 PM pooja sinha  wrote:


Hi All,

I have 10 .csv files containing 12 to 15 columns but have some columns in
common. I need to join all of my .csv files into one using one common
column ‘Pos’. The header portion of my .csv files looks as shown below:

Chrom Pos Avg Stdev  A15_3509.C A31_3799.C A32_3800.C A35_3804.C Gene ID
Class ExNum

  Can anyone help me in getting the code for the above problem. Any help
will be highly appreciated.


Thanks,

Puja

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.





[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Google Summer of Code 2021

[Spencer Graves]

Hello, Aarnob Guha:


	  I'm not sure, but r-de...@r-project.org might be a better list for 
this question.



	  Over two years ago, I responded to a "Call For Proposals" from the R 
Consortium suggesting a project to improve the capabilities for 
searching R packages.  That proposal was not funded, but documentation 
of the basic idea is still available:



https://en.wikiversity.org/wiki/Draft_Proposal_for_improving_the_ability_of_R_users_to_search_R_packages


  See also:


https://en.wikiversity.org/wiki/Searching_R_Packages


  Hope this helps.
      Spencer Graves


On 2020-12-08 03:09, Aarnob Guha wrote:

Dear R Project for Statistical Computing,
My name is Aarnob Guha and I am very enthusiastic about participating in
Google Summer of Code in 2021. I've been going through past projects in the
Google Summer of Code archives for this organisation and I was curious as
to whether R Project for Statistical Computing has any projects planned for
2021? If so, I was curious as to what these projects might be so that I can
get an idea of what I need to learn in order to adequately do well in the
project if I end up doing it. If you are ok with disclosing it that is.
Otherwise, it is also fine. Thank you.

Also, I wasn't particularly sure which mailing list to send this email to,
so I just sent it to the general 'help' mailing list. I apologise for any
inconvenience caused by this.
Kind Regards,
Aarnob Guha.

<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
Virus-free.
www.avast.com
<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] How to save Results in svg format

[Spencer Graves]

	  I often have trouble with font sizes in the svg files, because they 
rarely are the same as what I see on the screen.  I then have to read 
the documentation for "par" and play with the cex, cex.axis, cex.lab, 
cex.main, and cex.sub parameters until I get what I want in the svg 
file.  I may also need to play with the "mar" argument in "par". 
Occasionally, I may also have to research some of the other plot 
parameters.



	  In some cases, I may also need a png file.  I can use "png" in the 
same way as "svg", but the cex, etc., parameters must be set 
differently.  I've recently learned how to open an svg file in the free 
open-source software GIMP and adjust the "Resolution" from the 90 
pixels/in default to something more like 300 to get what I want.  I 
couldn't import an svg file recently into a Google Doc.  The 90 pixels 
per inch default conversion didn't look very clean and sharp after 
imported into a Google Doc.  I tried 600 pixels/in and found that Google 
Doc looked like it accepted it at first.  However, when I went back 
later, I found that it had subsequently malfunctioned.  I tried 300 
pixels/in, and I think that worked, though I'm not 100% certain.



  hope this helps.
  Spencer Graves


On 2020-12-03 23:21, David Carlson wrote:

If you look at the examples on the manual pages for the upgma() and NJ()
functions you will see that the results are generally sent to the plot()
function. To save that graph as an .svg file you need to open a graphics
device using the svg() function, plot the data, and close the graphics
device. You probably need something like the following:

svg("UPGMA_5x5.svg")
plot(UPGMA_5x5)
dev.off()

or

svg("NJ_119x119.svg")
plot(NJ_119x119)
dev.off()

There are numerous arguments that set various details for the plot that you
should look at (?svg).

David L Carlson
Texas A University


On Thu, Dec 3, 2020 at 10:24 PM Anas Jamshed 
wrote:


#Loading the required libraries
library(ape)
library(phangorn)
library(seqinr)
#Importing the required file
align_5 <- read.alignment("C:/Users/VAMSI/align 5.fasta", format = "fast")
align_119 <- read.alignment("C:/Users/VAMSI/align 119.fasta", format =
"fasta")
Computing the distance matrix for both UPGMA and NJ algorithms
implementation.
  matrix_5x5 <- dist.alignment(align_5, matrix = "identity")
summary(matrix_5x5)

matrix_119x119 <- dist.alignment(align_119, matrix = "identity")
summary(matrix_119x119)
#Implementation of UPGMA algorithm for a small matrix (5x5) and entire
matrix (119x119)
UPGMA_5x5 <- upgma(matrix_5x5)
UPGMA_119x119 <- upgma(matrix_119x119)
summary(UPGMA_5x5)

summary(UPGMA_119x119)
#Implementation of NJ algorithm for a small matrix (5x5) and entire
matrix (119x119)
NJ_5x5 <- NJ(matrix_5x5)
NJ_119x119 <- NJ(matrix_119x119)
summary(NJ_5x5)

summary(NJ_119x119)


I have done this whole analysis but don't know how can I  the save my
tree file in svg or some other image format . In the avove script , I
am applying the phylogenetic algorithm on the distance matrix which I
have created through fasta file

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see

https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-help__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_QDpGMCc$
PLEASE do read the posting guide
https://urldefense.com/v3/__http://www.R-project.org/posting-guide.html__;!!KwNVnqRv!T-8PRCLc041aD-rW1ehtb14tfQAVpWdpBddf_q6Raeho0RbG9wDodEK_1H9sJRs$
and provide commented, minimal, self-contained, reproducible code.



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Inappropriate color name

[Spencer Graves]

	  Might it be appropriate to raise that question on the Talk page 
associated with the Wikipedia article on "Indian red (color)":



https://en.wikipedia.org/wiki/Indian_red_(color)


  Many Wikimedian are generally sympathetic to discussions of
political correctness and similar topics.  If the name of that article 
were changed, then it should be a lot easier to pursue a similar name 
change elsewhere.



      Spencer Graves


On 2020-11-17 15:25, Mitchell Maltenfort wrote:

What about just amputating the final "n?"

"Indian" might mean one of two things, but "India" is pretty distinct.



On Tue, Nov 17, 2020 at 4:10 PM T. A. Milne via R-help 
wrote:



Apologies to the list for continuing a thread which is clearly off-topic.
However, contacting the maintainer of an R package to complain about this
specific color name seems ill-considered.

1)  The name "indian red" is a part of widely-used color schemes
everywhere, not just in R.  It's the color defined as:

"The color indianred / Indian red with hexadecimal color code #cd5c5c is a
shade of red. In the RGB color model #cd5c5c is comprised of 80.39% red,
36.08% green and 36.08% blue. In the HSL color space #cd5c5c has a hue of
0° (degrees), 53% saturation and 58% lightness. This color has an
approximate wavelength of 611.37 nm."

https://encycolorpedia.com/cd5c5c


2)  The "indian" in the color name refers to ferric oxide, historically
sourced from India.  Per Wikipedia:

"The name Indian red derives from the red laterite soil found in India,
which is composed of naturally occurring iron oxides.[citation needed] The
first recorded use of Indian red as a color term in English was in 1672.[3"

https://en.wikipedia.org/wiki/Indian_red_(color)


Given the name refers to the locus of the ferric oxide source, It isn't
obvious that any particular group should be offended by the name.


--  T. Arthur Milne



On Nov 16, 2020, at 5:46 PM, Rolf Turner 

wrote:


On Tue, 17 Nov 2020 07:54:01 +1100
Jim Lemon  wrote:



Hi Elaine,
There seems to be a popular contest to discover offence everywhere. I
don't think that it does anything against racism, sexism or
antidisestablishmentarianism. Words are plucked from our vast lexicon
to comfort or insult our fellows depending upon the intent of the
user. It is the intent that matters, not the poor word. Chasing the
words wastes your time, blames those who use the words harmlessly,
and gives the real offender time to find another epithet.


Jim:  This is superbly expressed.  I wish that I could have said
that! Your posting should go down in the annals of brilliant rhetoric,
alongside Dr. Johnson's "Letter to Lord Chesterfield".

cheers,

Rolf


You know, I wouldn’t have continued this thread (which has now wandered
off topic from the original somewhat-more-technical question), but I feel
now like it’s necessary to do so (and only fair, if anyone is considering
moderating me after letting these posts by):

That is a view commonly held by white people, and even more overwhelmingly
by white men. Our field is already not as diverse as it should be for a
variety of reasons, and this “pretending no one else on earth exists” kind
of stuff is at least some part of the reason. The question at issue here
aside, white men complaining about people finding racism or sexism
everywhere they look doesn’t pass the sniff test. Most or all of these
things that people are reporting as offensive are being reported by people
you’re clearly not listening to.

Further, impact is what matters. If I step on your foot, I apologize,
regardless of whether or not it was intentional, because it’s the right
thing to do. If someone tells you “that thing you’re saying is offensive or
is hurting me” and you say “I didn’t mean it,” and then keep right on doing
it, what does it say to the person on the receiving end of it? All anyone
that is being “blamed,” as you put it, is being asked to do is to try to do
better next time.

--
#BlackLivesMatter

|| \\UTGERS, |---*O*---
||_// the State  | Ryan Novosielski - novos...@rutgers.edu
|| \\ University | Sr. Technologist - 973/972.0922 (2x0922) ~*~ RBHS Campus
||  \\of NJ  | Office of Advanced Research Computing - MSB C630, Newark
  `'

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



[

Re: [R] WG: Packages for mathematics

[Spencer Graves]

	  Several resources for "Searching R Packages" are discussed in a 
Wikiversity article by that title:



https://en.wikiversity.org/wiki/Searching_R_Packages


	  I've found the "sos" package on CRAN (which has a vignette describing 
use) and "https://www.rdocumentation.org; to be most useful.



	  Many functions are included in base R.  Many more are provided in 
contributed packages.



  Spencer Graves


On 2020-11-16 04:02, ELLENBERGER Mihaela via R-help wrote:





Von: ELLENBERGER Mihaela
Gesendet: Montag, 16. November 2020 10:24
An: cran-submissi...@r-project.org
Betreff: Packegs for mathematics


Hello


I'm undergraduated student of Biomedical Sciences in Switzerland and learning 
how to work with R.

Currently I'm using R-Studio.


I would like to now, which packeges sholud I install please for mathematics ( 
analysis)?

My collegeues don't use all the same maths software ( some of them are using 
Excel, SPSS, Mathematica, etc.)


-Funktionen,Serien, Folgen,Grenzwerte, Stetigkeiten

-Integralrechnungen

-Differentialrechnungen

-Analysis multivariant


Could you sent me an advice please, because there are so many packeges in R.


Kind regards


Mihaela Ellenberger




[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] analyzing results from Tuesday's US elections

[Spencer Graves]

On 2020-11-07 23:39, Abby Spurdle wrote:

What can you tell me about plans to analyze data from this year's
general election, especially to detect possible fraud?


I was wondering if there's any R packages with out-of-the-box
functions for this sort of thing.
Can you please let us know, if you find any.


I might be able to help with such an effort.  I have NOT done
much with election data, but I have developed tools for data analysis,
including web scraping, and included them in R packages available on the
Comprehensive R Archive Network (CRAN) and GitHub.[1]


Do you have a URL for detailed election results?
Or even better, a nice R-friendly CSV file...

I recognize that the results aren't complete.
And that such a file may need to be updated later.
But that doesn't necessarily prevent modelling now.



	  I asked, because I don't know of any such.  With the increasingly 
vicious, widespread and systematic attacks on the integrity of elections 
in the US, I think it would be good to have a central database of 
election results with tools regularly scraping websites of local and 
state election authorities.  Whenever new data were posted, the software 
would update the central repository and send emails to anyone 
interested.  That could simplify data acquisition, because historical 
data could already be available there.  And it would be one standard 
format for the entire US and maybe the world.



	  This could be extremely valuable in exposing electoral fraud, thereby 
reducing its magnitude and effectiveness.  This is a global problem, but 
it seems to have gotten dramatically worse in the US in recent years.[2]



	  I'd like to join -- or organize -- a team of people working on this. 
If we can create the database and data analysis tools in a package like 
Ecfun on CRAN, I think we can interest college profs, especially those 
teaching statistics to political science students, who would love to 
involve their students in something like this.  They could access data 
real time in classes, analyze it using standard tools that we could 
develop, and involve their students in discussing what it means and what 
it doesn't.  They could discuss Bayesian sequential updating and quality 
control concepts using data that are real and relevant to the lives of 
their students.  It could help get students excited about both 
statistics and elections.



	  Such a project may already exist.  I know there are projects at some 
major universities that sound like they might support this.  However 
with the limited time I've invested in this so far, I didn't find any 
that seemed to provide easy access to such data and an easy way to join 
such a project.  Ballotpedia has such data but don't want help in 
analyzing it and asked for a few hundred dollars for data for one 
election cycle in Missouri, which is what I requested.  I can get that 
for free from the web site of the Missouri Secretary of State.



	  I thought I might next ask the Carter Center about this.  However, 
but I'm totally consumed with other priorities right now.  I don't plan 
to do anything on this in the short term -- unless I can find 
collaborators.



	  If such a central database doesn't exist -- and maybe even if it does 
-- I thought it might be good to make all the data available in a 
standard format in Wikidata, which is a project of the Wikimedia 
Foundation, which is also the parent organization of Wikipedia.  Then I 
could help create software and documentation on how to scrape data from 
the web sites of different election organizations that have it and 
automatically update Wikidata while also sending emails to people who 
express interest in those election results.  Then we could create 
software for analyzing such data and make that available, e.g., on 
Wikiversity, which is another project of the Wikimedia Foundation -- 
with the R code in Ecfun or some other CRAN package.



	  If we start now, I think we could have something mediocre in time for 
various local elections that occur next year with improvements for the 
2022 US Congressional elections and something even better for the 2024 
US presidential elections.



  Thanks for asking.
  Spencer Graves


[1]
https://github.com/sbgraves237


[2]
https://en.wikiversity.org/wiki/Electoral_integrity_in_the_United_States

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] analyzing results from Tuesday's US elections

[Spencer Graves]

Hello:


  What can you tell me about plans to analyze data from this year's 
general election, especially to detect possible fraud?



  I might be able to help with such an effort.  I have NOT done 
much with election data, but I have developed tools for data analysis, 
including web scraping, and included them in R packages available on the 
Comprehensive R Archive Network (CRAN) and GitHub.[1]



  Penny Abernathy, who holds the Knight Chair in Journalism and 
Digital Media Economics at UNC-Chapel Hill, told me that the electoral 
fraud that disqualified the official winner from NC-09 to the US House 
in 2018 was detected by a college prof, who accessed the data two weeks 
after the election.[2]



  Spencer Graves


[1]
https://github.com/sbgraves237


[2]
https://en.wikiversity.org/wiki/Local_Journalism_Sustainability_Act

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] CRAN R For Windows 3.6.3

[Spencer Graves]

	  If you have production code written in R that make it expensive to 
even consider upgrading to the latest R, it may be worth paying the 
support fees of an organization like RStudio.



	  Otherwise, I think it make sense to upgrade to the latest version and 
hope for the best.  If you encounter problems, you can ask someplace on 
StackExchange or one of the R email lists like this or a package 
maintainer, as Duncan said.



  Spencer


On 2020-09-19 12:44, Duncan Murdoch wrote:

On 18/09/2020 1:39 p.m., Shapira, Leeor via R-help wrote:
Can you please let me know the End of Life and End of Vendor Support 
dates for CRAN R for Windows 3.6.3? Thank you.


R doesn't have either of those.  There is no vendor support ever.  It is 
free software; it is up to its users to support it.  On the other hand, 
it is free software, so you can use it forever.


In practice, there is de facto support from its authors in that they are 
very responsive to bug reports.  That ends with the next release, so 
3.6.3 support ended in April, 2020 when R 4.0.0 was released.


Another way to think of support and end of life equivalents is to ask 
how long CRAN will provide the source code to packages for it.  There 
are no time limits on that, though it can be some work to find a set and 
tools to build them if you are using older releases.


And finally, you might want to know how long CRAN will keep updating 
binary packages for R 3.6.3.  I think that should continue until the 
release of R 4.1.0, sometime around April 2021.


Duncan Murdoch

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] [External] Re: help with web scraping

[Spencer Graves]

Dear Rasmus Liland et al.:


On 2020-07-25 11:30, Rasmus Liland wrote:

On 2020-07-25 09:56 -0500, Spencer Graves wrote:

Dear Rasmus et al.:


It is LILAND et al., is it not?  ... else it's customary to
put a comma in there, isn't it? ...



The APA Style recommends "Sharp et al., 2007":


https://blog.apastyle.org/apastyle/2011/11/the-proper-use-of-et-al-in-apa-style.html


  Regarding Confucius, I'm confused.




right, moving on:

On 2020-07-25 04:10, Rasmus Liland wrote:








Please research using Thunderbird, Claws
mail, or some other sane e-mail client;
they are great, I promise.



Thanks.  I researched it and turned of HTML.  Please excuse:  I noticed 
it was a problem, but hadn't prioritized time to research and fix it 
until your comment.  Thanks.





Please excuse:? Before my last post, I
had written code to do all that.?


Good!


In brief, the political offices are
"h3" tags.?


Yes, some type of header element at
least, in-between the various tables,
everything children of the div in the
element tree.


I used "strsplit" to split the string
at "".? I then wrote a
function to find "", extract the
political office and pass the rest to
"XML::readHTMLTable", adding columns
for party and political office.


Yes, doing that for the political office
is also possible, but the party is
inside the table's caption tag, which
end up as the name of the table in the
XML::readHTMLTable list ...


However, this suppressed ""
everywhere.?


Why is that, please explain.



	  I don't know why the Missouri Secretary of State's web site includes 
"" to signal a new line, but it does.  I also don't know why 
XML::readHTMLTable suppressed "" everywhere it occurred, but it did 
that.  After I used gsub to replace "" with "\n", I found that 
XML::readHTMLTable did not replace "\n", so I got what I wanted.




I thought there should be
an option with something like
"XML::readHTMLTable" that would not
delete "" everywhere, but I
couldn't find it.?


No, there is not, AFAIK.  Please, if
anyone else knows, please say so *echoes
in the forest*


If you aren't aware of one, I can
gsub("", "\n", ...) on the string
for each political office before
passing it to "XML::readHTMLTable".? I
just tested this:? It works.


Such a great hack!  IMHO, this is much
more flexible than using
xml2::read_html, rvest::read_table,
dplyr::mutate like here[1]


I have other web scraping problems in
my work plan for the few days.?


Maybe, idk ...


I will definitely try
XML::htmlTreeParse, etc., as you
suggest.


I wish you good luck,
Rasmus

[1] 
https://stackoverflow.com/questions/38707669/how-to-read-an-html-table-and-account-for-line-breaks-within-cells



  And I added my solution to this problem to this Stackoverflow thread.


  Thanks again,
  Spencer



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] [External] Re: help with web scraping

[Spencer Graves]

Dear Rasmus et al.:


On 2020-07-25 04:10, Rasmus Liland wrote:
> On 2020-07-24 10:28 -0500, Spencer Graves wrote:
>> Dear Rasmus:
>>
>>> Dear Spencer,
>>>
>>> I unified the party tables after the
>>> first summary table like this:
>>>
>>> url <- 
>>> "https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;
>>> M_sos <- RCurl::getURL(url)
>>> saveRDS(object=M_sos, file="dcp.rds")
>>> dat <- XML::readHTMLTable(M_sos)
>>> idx <- 2:length(dat)
>>> cn <- unique(unlist(lapply(dat[idx], colnames)))
>> This is useful for this application.
>>
>>> dat <- do.call(rbind,
>>>   sapply(idx, function(i, dat, cn) {
>>> x <- dat[[i]]
>>> x[,cn[!(cn %in% colnames(x))]] <- NA
>>> x <- x[,cn]
>>> x$Party <- names(dat)[i]
>>> return(list(x))
>>>   }, dat=dat, cn=cn))
>>> dat[,"Date Filed"] <-
>>>   as.Date(x=dat[,"Date Filed"],
>>>   format="%m/%d/%Y")
>> This misses something extremely
>> important for this application:?  The
>> political office.? That's buried in
>> the HTML or whatever it is.? I'm using
>> something like the following to find
>> that:
>>
>> str(LtGov <- gregexpr('Lieutenant Governor', M_sos)[[1]])
> Dear Spencer,
>
> I came up with a solution, but it is not
> very elegant.  Instead of showing you
> the solution, hoping you understand
> everything in it, I istead want to give
> you some emphatic hints to see if you
> can come up with a solution on you own.
>
> - XML::htmlTreeParse(M_sos)
>- *Gandalf voice*: climb the tree
>  until you find the content you are
>  looking for flat out at the level of
>  �The Children of the Div�, *uuuUUU*
>- you only want to keep the table and
>  header tags at this level
> - Use XML::xmlValue to extract the
>values of all the headers (the
>political positions)
> - Observe that all the tables on the
>page you were able to extract
>previously using XML::readHTMLTable,
>are at this level, shuffled between
>the political position header tags,
>this means you extract the political
>position and party affiliation by
>using a for loop, if statements,
>typeof, names, and [] and [[]] to grab
>different things from the list
>(content or the bag itself).
>XML::readHTMLTable strips away the
>line break tags from the Mailing
>address, so if you find a better way
>of extracting the tables, tell me,
>e.g. you get
>
>   8805 HUNTER AVEKANSAS CITY MO 64138
>
>and not
>
>   8805 HUNTER AVEKANSAS CITY MO 64138
>
> When you've completed this �programming
> quest�, you're back at the level of the
> previous email, i.e.  you have have the
> same tables, but with political position
> and party affiliation added to them.


 � Please excuse:� Before my last post, I had written code to do all 
that.� In brief, the political offices are "h3" tags.� I used "strsplit" 
to split the string at "".� I then wrote a function to find "", 
extract the political office and pass the rest to "XML::readHTMLTable", 
adding columns for party and political office.


 � However, this suppressed "" everywhere.� I thought there 
should be an option with something like "XML::readHTMLTable" that would 
not delete "" everywhere, but I couldn't find it.� If you aren't 
aware of one, I can gsub("", "\n", ...) on the string for each 
political office before passing it to "XML::readHTMLTable".� I just 
tested this:� It works.


 � I have other web scraping problems in my work plan for the few 
days.� I will definitely try XML::htmlTreeParse, etc., as you suggest.


 � Thanks again.
 � Spencer Graves
>
> Best,
> Rasmus
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] prevent XML::readHTMLTable from suppressing

[Spencer Graves]

Hello, All:


  Thanks to Rasmus Liland, William Michels, and Luke Tierney with 
my earlier web scraping question.  With their help, I've made progress.  
Sadly, I still have a problem:  One field has "", which gets 
suppressed by XML::readHTMLTable:



sosURL <- 
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;

sosChars <- RCurl::getURL(sosURL)
MOcan <- XML::readHTMLTable(sosChars)
MOcan[[2]][1, 2]
[1] "4476 FIVE MILE RDSENECA MO 64865"


(Seneca <- regexpr('SENECA', sosChars))
substring(sosChars, Seneca-22, Seneca+14)


[1] "4476 FIVE MILE RDSENECA MO 64865"


  How can I get essentially the same result but without having 
XML::readHTMLTable suppress ""?



NOTE:  I get something very similar with xml2::read_html and 
rvest::html_table:



sosPointers <- xml2::read_html(sosChars)
MOcan2 <- rvest::html_table(sosPointers)
MOcan2[[2]][1, 2]
[1] "4476 FIVE MILE RDSENECA MO 64865"


  MOcan2 does not have names, and some of the fields are 
automatically converted to integers, which I think is not smart in this 
application.



  Thanks,
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] [External] Re: help with web scraping

[Spencer Graves]

Dear Rasmus:


On 2020-07-24 09:16, Rasmus Liland wrote:
> On 2020-07-24 08:20 -0500, luke-tier...@uiowa.edu wrote:
>> On Fri, 24 Jul 2020, Spencer Graves wrote:
>>> On 2020-07-23 17:46, William Michels wrote:
>>>> On Thu, Jul 23, 2020 at 2:55 PM Spencer Graves
>>>>  wrote:
>>>>> Hello, All:
>>>>>
>>>>> I've failed with multiple
>>>>> attempts to scrape the table of
>>>>> candidates from the website of
>>>>> the Missouri Secretary of
>>>>> State:
>>>>>
>>>>> https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975
>>>> Hi Spencer,
>>>>
>>>> I tried the code below on an older
>>>> R-installation, and it works fine.
>>>> Not a full solution, but it's a
>>>> start:
>>>>
>>>>> library(RCurl)
>>>> Loading required package: bitops
>>>>> url <- 
>>>>> "https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;
>>>>> M_sos <- getURL(url)
>>> Hi Bill et al.:
>>>
>>> That broke the dam:� It gave me a
>>> character vector of length 1
>>> consisting of 218 KB.� I fed that to
>>> XML::readHTMLTable and
>>> purrr::map_chr, both of which
>>> returned lists of 337 data.frames.
>>> The former retained names for all
>>> the tables, absent from the latter.
>>> The columns of the former are all
>>> character;� that's not true for the
>>> latter.
>>>
>>> Sadly, it's not quite what I want:
>>> It's one table for each office-party
>>> combination, but it's lost the
>>> office designation. However, I'm
>>> confident I can figure out how to
>>> hack that.
>> Maybe try something like this:
>>
>> url <- 
>> "https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;
>> h <- xml2::read_html(url)
>> tbl <- rvest::html_table(h)
> Dear Spencer,
>
> I unified the party tables after the
> first summary table like this:
>
>   url <- 
> "https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;
>   M_sos <- RCurl::getURL(url)
>   saveRDS(object=M_sos, file="dcp.rds")
>   dat <- XML::readHTMLTable(M_sos)
>   idx <- 2:length(dat)
>   cn <- unique(unlist(lapply(dat[idx], colnames)))


 � This is useful for this application.

>   dat <- do.call(rbind,
> sapply(idx, function(i, dat, cn) {
>   x <- dat[[i]]
>   x[,cn[!(cn %in% colnames(x))]] <- NA
>   x <- x[,cn]
>   x$Party <- names(dat)[i]
>   return(list(x))
> }, dat=dat, cn=cn))
>   dat[,"Date Filed"] <-
> as.Date(x=dat[,"Date Filed"],
>     format="%m/%d/%Y")


 � This misses something extremely important for this application:� 
The political office.� That's buried in the HTML or whatever it is.� I'm 
using something like the following to find that:


str(LtGov <- gregexpr('Lieutenant Governor', M_sos)[[1]])


 � After I figure this out, I will use something like your code to 
combine it all into separate tables for each office, and then probably 
combine those into one table for the offices I'm interested in.� For my 
present purposes, I don't want all the offices in Missouri, only the 
executive positions and those representing parts of the Kansas City 
metro area in the Missouri legislature.


 � Thanks again,
 � Spencer Graves

>   write.table(dat, file="dcp.tsv", sep="\t",
>   row.names=FALSE,
>   quote=TRUE, na="N/A")
>
> Best,
> Rasmus
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] [External] Re: help with web scraping

[Spencer Graves]

On 2020-07-24 08:20, luke-tier...@uiowa.edu wrote:

Maybe try something like this:

url <- 
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;

h <- xml2::read_html(url)



Error in open.connection(x, "rb") : HTTP error 404.


  Thanks for the suggestion, but this failed for me on the platform 
described in "sessionInfo" below.




tbl <- rvest::html_table(h)



  As I previously noted, RCurl::getURL returned a single character 
string of roughly 218 KB, from which I've so far gotten most but not all 
of what I want.  Unfortunately, when I fed that character vector to 
rvest::html_table, I got:



Error in UseMethod("html_table") :
  no applicable method for 'html_table' applied to an object of class 
"character"



  I don't know for sure yet, but I believe I'll be able to get what 
I want from the single character string using, e.g., gregexpr and other 
functions.



  Thanks again,
  Spencer Graves



Best,

luke

On Fri, 24 Jul 2020, Spencer Graves wrote:


Hi Bill et al.:


  That broke the dam:  It gave me a character vector of length 1 
consisting of 218 KB.  I fed that to XML::readHTMLTable and 
purrr::map_chr, both of which returned lists of 337 data.frames. The 
former retained names for all the tables, absent from the latter.  
The columns of the former are all character;  that's not true for the 
latter.



  Sadly, it's not quite what I want:  It's one table for each 
office-party combination, but it's lost the office designation. 
However, I'm confident I can figure out how to hack that.



  Thanks,
  Spencer Graves


On 2020-07-23 17:46, William Michels wrote:

Hi Spencer,

I tried the code below on an older R-installation, and it works fine.
Not a full solution, but it's a start:


library(RCurl)

Loading required package: bitops
url <- 
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;

M_sos <- getURL(url)
print(M_sos)

[1] "\r\n\r\n\r\n\r\n\r\n\tSOS, Missouri - Elections:
Offices Filed in Candidate Filing\r\n wrote:

Hello, All:


    I've failed with multiple attempts to scrape the table of
candidates from the website of the Missouri Secretary of State:


https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975 




    I've tried base::url, base::readLines, xml2::read_html, and
XML::readHTMLTable; see summary below.


    Suggestions?
    Thanks,
    Spencer Graves


sosURL <-
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975; 



str(baseURL <- base::url(sosURL))
# this might give me something, but I don't know what

sosRead <- base::readLines(sosURL) # 404 Not Found
sosRb <- base::readLines(baseURL) # 404 Not Found

sosXml2 <- xml2::read_html(sosURL) # HTTP error 404.

sosXML <- XML::readHTMLTable(sosURL)
# List of 0;  does not seem to be XML

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 


LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib 



locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2    curl_4.3
[4] xml2_1.3.2 XML_3.99-0.3

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.





__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] help with web scraping

[Spencer Graves]

Hi Bill et al.:


  That broke the dam:  It gave me a character vector of length 1 
consisting of 218 KB.  I fed that to XML::readHTMLTable and 
purrr::map_chr, both of which returned lists of 337 data.frames. The 
former retained names for all the tables, absent from the latter.  The 
columns of the former are all character;  that's not true for the latter.



  Sadly, it's not quite what I want:  It's one table for each 
office-party combination, but it's lost the office designation. However, 
I'm confident I can figure out how to hack that.



  Thanks,
  Spencer Graves


On 2020-07-23 17:46, William Michels wrote:

Hi Spencer,

I tried the code below on an older R-installation, and it works fine.
Not a full solution, but it's a start:


library(RCurl)

Loading required package: bitops

url <- 
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;
M_sos <- getURL(url)
print(M_sos)

[1] "\r\n\r\n\r\n\r\n\r\n\tSOS, Missouri - Elections:
Offices Filed in Candidate Filing\r\n wrote:

Hello, All:


I've failed with multiple attempts to scrape the table of
candidates from the website of the Missouri Secretary of State:


https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975


I've tried base::url, base::readLines, xml2::read_html, and
XML::readHTMLTable; see summary below.


Suggestions?
Thanks,
    Spencer Graves


sosURL <-
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;

str(baseURL <- base::url(sosURL))
# this might give me something, but I don't know what

sosRead <- base::readLines(sosURL) # 404 Not Found
sosRb <- base::readLines(baseURL) # 404 Not Found

sosXml2 <- xml2::read_html(sosURL) # HTTP error 404.

sosXML <- XML::readHTMLTable(sosURL)
# List of 0;  does not seem to be XML

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK:
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2curl_4.3
[4] xml2_1.3.2 XML_3.99-0.3

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] help with web scraping

[Spencer Graves]

Hello, All:


  I've failed with multiple attempts to scrape the table of 
candidates from the website of the Missouri Secretary of State:



https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975


      I've tried base::url, base::readLines, xml2::read_html, and 
XML::readHTMLTable; see summary below.



  Suggestions?
  Thanks,
  Spencer Graves


sosURL <- 
"https://s1.sos.mo.gov/CandidatesOnWeb/DisplayCandidatesPlacement.aspx?ElectionCode=750004975;


str(baseURL <- base::url(sosURL))
# this might give me something, but I don't know what

sosRead <- base::readLines(sosURL) # 404 Not Found
sosRb <- base::readLines(baseURL) # 404 Not Found

sosXml2 <- xml2::read_html(sosURL) # HTTP error 404.

sosXML <- XML::readHTMLTable(sosURL)
# List of 0;  does not seem to be XML

sessionInfo()

R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib


locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets
[6] methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.2 tools_4.0.2    curl_4.3
[4] xml2_1.3.2 XML_3.99-0.3

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R 4.0.2 is released

[Spencer Graves]

Thank you and all the core R team.  Spencer Graves


On 2020-06-22 03:21, Peter Dalgaard via R-help wrote:

The build system rolled up R-4.0.2.tar.gz (codename "Taking Off Again") this 
morning.

The list below details the changes in this release.

You can get the source code from

http://cran.r-project.org/src/base/R-4/R-4.0.2.tar.gz

or wait for it to be mirrored at a CRAN site nearer to you.

Binaries for various platforms will appear in due course.


For the R Core Team,

Peter Dalgaard

These are the checksums (md5 and SHA-256) for the freshly created files, in 
case you wish
to check that they are uncorrupted:

MD5 (AUTHORS) = b9c44f9f78cab3184ad9898bebc854b4
MD5 (COPYING) = eb723b61539feef013de476e68b5c50a
MD5 (COPYING.LIB) = a6f89e2100d9b6cdffcea4f398e37343
MD5 (FAQ) = 4afa171cd982aaa60f0ba92e2e7bc5d6
MD5 (INSTALL) = 7893f754308ca31f1ccf62055090ad7b
MD5 (NEWS) = 566a6bb3642e28e6bf01cf98db31137c
MD5 (NEWS.0) = bfcd7c147251b5474d96848c6f57e5a8
MD5 (NEWS.1) = eb78c4d053ec9c32b815cf0c2ebea801
MD5 (NEWS.2) = 496062c138e2def06cebccddfb814ac6
MD5 (NEWS.3) = 012e7f4a80cc8ec947bf3f0ff6117ec8
MD5 (R-latest.tar.gz) = 1eac7293d5fe313a56ddabfda02b437e
MD5 (README) = f468f281c919665e276a1b691decbbe6
MD5 (RESOURCES) = 529223fd3ffef95731d0a87353108435
MD5 (THANKS) = 251d20510bfc3cc93b82c5a99f7efcc6
MD5 (VERSION-INFO.dcf) = 62496d3a0fd8cc2ed644ea518c052371
MD5 (R-4/R-4.0.2.tar.gz) = 1eac7293d5fe313a56ddabfda02b437e

2cde824a7b18958e5f06b391c801c8288be0f84fa8934b7ddefef23c67e60c09  AUTHORS
e6d6a009505e345fe949e1310334fcb0747f28dae2856759de102ab66b722cb4  COPYING
6095e9ffa777dd22839f7801aa845b31c9ed07f3d6bf8a26dc5d2dec8ccc0ef3  COPYING.LIB
eddf87b12197c7b3b19cbc9b11c1beab95b14e3dcd715bf37d2f6a8b2a72c2a1  FAQ
f87461be6cbaecc4dce44ac58e5bd52364b0491ccdadaf846cb9b452e9550f31  INSTALL
ec05bba338358410fae6b34fed061605989ab3601aba1b3fcb45a610d5dd2eb9  NEWS
4e21b62f515b749f80997063fceab626d7258c7d650e81a662ba8e0640f12f62  NEWS.0
12b30c724117b1b2b11484673906a6dcd48a361f69fc420b36194f9218692d01  NEWS.1
e80de410c77f05ff2012fa70051b89119845f734a7fa5c55857e61e4ed7d5f6e  NEWS.2
7201d139947afa52b5e09d26dc01445edf444506264355b2185122bc1ed3dce0  NEWS.3
d3bceab364da0876625e4097808b42512395fdf41292f4915ab1fd257c1bbe75  
R-latest.tar.gz
2fdd3e90f23f32692d4b3a0c0452f2c219a10882033d1774f8cadf25886c3ddc  README
408737572ecc6e1135fdb2cf7a9dbb1a6cb27967c757f1771b8c39d1fd2f1ab9  RESOURCES
c9c7cb32308b4e560a22c858819ade9de524a602abd4e92d1c328c89f8037d73  THANKS
10cc5f566a4a5ce49147e7dcfbe9180dba09ccb9efb17298b067309eb799e92e  
VERSION-INFO.dcf
d3bceab364da0876625e4097808b42512395fdf41292f4915ab1fd257c1bbe75  
R-4/R-4.0.2.tar.gz

This is the relevant part of the NEWS file

CHANGES IN R 4.0.2:

   UTILITIES:

 * R CMD check skips vignette re-building (with a warning) if the
   VignetteBuilder package(s) are not available.

   BUG FIXES:

 * Paths with non-ASCII characters caused problems for package
   loading on Windows PR#17833.

 * Using tcltk widgets no longer crashes R on Windows.

 * source(*, echo=TRUE) no longer fails in some cases with empty
   lines; reported by Bill Dunlap in PR#17769.

 * on.exit() now correctly matches named arguments, thanks to
   PR#17815 (including patch) by Brodie Gaslam.

 * regexpr(*, perl=TRUE) no longer returns incorrect positions into
   text containing characters outside of the Unicode Basic
   Multilingual Plane on Windows.



__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Rtools required

[Spencer Graves]

  I just encountered something that looks exactly like that with R 
4.0.0 and the latest RStudio AND with Rtools40 installed under Windows 
10 (AND some manual adjustment of the path to delete references to old 
versions of Rtools and make sure Rtools40 was there).



  I got around it by have Rtools40 installed AND running 
"install.packages('xmlw')" inside R 4.0.0 inside a CMD prompt.  That 
worked, even though the same command inside RStudio failed with:



WARNING:  Rtools is required to build an R package but no version of 
Rtools compatible with the currently running version of R was found.  
Note that the following incompatible version(s) of Rtools were found:


  - Rtools 3.5 (installed at C:\Rtools).


  I got this message after deleting references to C:\Rtools from 
the path and rebooting.



*** I BELIEVE YOU NEED Rtools40 installed, because binaries for some 
packages are not (yet) available for R 4.0.0.



  Hope this helps.
      Spencer Graves


On 2020-04-29 21:02, Bert Gunter wrote:

Wouldn't packages that have to be built from source on installation
require Rtools?

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Wed, Apr 29, 2020 at 6:48 PM Steven  wrote:

Thanks to all - very helpful. I search from c:\ and now find file
.Renviron located in C:\Users\USER\Documents. That does it.

I would like to pose an additional question, since it would also fall
under the same subject line. This is an RStudio question but since I am
using the free version the RStudio folks would not help me.

My students simply need to install packages and are not building any
packages so they have no reason to install Rtools.

When they install (not build) packages (from CRAN or file archive) they
received the same warning message saying

"Rtools required to build a package".

This is nonsense of course as they are, as I said, simply installing. I
tell them to user an older RStudio version, specifically 1.1.463 that's
free of that warning. Any idea?

Steven Yen

On 2020/4/30 上午 06:30, Fox, John wrote:

Dear Steven,

It's possible that Windows will hide .Renviron, but it's generally a good idea, in my opinion, in 
Folder Options > View to click "Show hidden files" and uncheck "hide 
extensions". Then .Renviron should show up (once you've created it).

Best,
   John


-Original Message-
From: Bert Gunter 
Sent: Wednesday, April 29, 2020 5:50 PM
To: Steven 
Cc: Fox, John ; R-help Mailing List 
Subject: Re: [R] Rtools required

Type
?.Renviron
?R.home
?"environment variables"

at the R prompt to get what I think should be the info you need (or at
least useful info).


Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Wed, Apr 29, 2020 at 2:37 PM Steven  wrote:

Thanks John. Where is file .Renviron located? It must be a hidden file.
I cannot find it.

On 2020/4/28 下午 08:29, Fox, John wrote:

Dear Steven,

Did you follow the instruction on the Rtools webpage to add

PATH="${RTOOLS40_HOME}\usr\bin;${PATH}"

to your .Renviron file?

I hope this helps,
John

 -
 John Fox, Professor Emeritus
 McMaster University
 Hamilton, Ontario, Canada
 Web: http::/socserv.mcmaster.ca/jfox


On Apr 28, 2020, at 4:38 AM, Steven  wrote:

Dear All

I updated to R-4.0.0. and also installed the latest Rtools 4.0 (to
now the new default folder c:\rtools40). While compiling a package
(binary) I received the follow marning message saying Rtools is
required. Any clues? Thanks.

Steven Yen

WARNING: Rtools is required to build R packages but is not
currently installed. Please download and install the appropriate
version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/


   [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented

Re: [R] R 3.6.2 is released

[Spencer Graves]

Ditto.  Spencer Graves


On 2019-12-12 07:54, Rich Shepard wrote:

On Thu, 12 Dec 2019, Peter Dalgaard via R-help wrote:


The build system rolled up R-3.6.2.tar.gz (codename "Dark and Stormy
Night") this morning.


Peter,

My thanks to all of you on the R core team.

Regards,

Rich

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] transforming dates

[Spencer Graves]

On 2019-11-03 17:04, Peter Dalgaard wrote:



On 3 Nov 2019, at 21:22 , David Winsemius  wrote:


On 11/3/19 11:51 AM, Bert Gunter wrote:

===

Hey, that's my birthday! Err, no it isn't... ;-)



  Is that November 3 of 2019 or March 19 of 2011 or 11 March 2019?  
[please excuse the typo in the earlier response]



  The English still use stones as a unit of mass, and most of the 
US still steadfastly refuses to seriously consider metrication or  ISO 
8601.  I know an architect in the US, who has worked on several 
different projects every year for the past 40 years only one of which 
has been in metric units.



   Binary, octal or hex is superior to decimal, except for the fact 
that most humans have 10 digits on hands and feet.  And decimal is 
vastly superior to arithmetic in mixed bases, e.g., adding miles, rods, 
yards, feet, inches, and 64ths.



  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] transforming dates

[Spencer Graves]

On 2019-11-03 17:04, Peter Dalgaard wrote:



On 3 Nov 2019, at 21:22 , David Winsemius  wrote:


On 11/3/19 11:51 AM, Bert Gunter wrote:

===

Hey, that's my birthday! Err, no it isn't... ;-)



  Is that November 11 of 2019 or March 19 of 2011 or 11 March 2019?


  The English still use stones as a unit of mass, and most of the 
US still steadfastly refuses to seriously consider metrication or  ISO 
8601.  I know an architect in the US, who has worked on several 
different projects every year for the past 40 years only one of which 
has been in metric units.



   Binary, octal or hex is superior to decimal, except for the fact 
that most humans have 10 digits on hands and feet.  And decimal is 
vastly superior to arithmetic in mixed bases, e.g., adding miles, rods, 
yards, feet, inches, and 64ths.



  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] R 3.6.1

[Spencer Graves]

  What might be the likely outcomes of an attempt to reinstall 3.6.1?


  And might that depend on whether the current 3.6.1 was 
uninstalled first?



  Spencer


On 2019-07-17 07:17, Jeff Newmiller wrote:
It would never make sense for such messages to reflect normal and 
expected operation, so hypothesizing about intentionally changing 
stack behavior doesn't make sense.


The default format for saveRDS changed in 3.6.0. There may be bugs 
associated with that, but rolling back to 3.6.0 would just trade bugs.


https://cran.r-project.org/doc/manuals/r-devel/NEWS.html

On July 16, 2019 8:56:28 PM CDT, Jan Galkowski 
 wrote:

Did something seriously change in R 3.6.1 at least for Windows in terms
of stack impacts?

I'm encountering many problems with the 00UNLOCK, needing to disable
locking during installations.

And I'm encountering


Error: C stack usage 63737888 is too close to the limit

for cases I did not before, even when all I'm doing is serializing an
object to be saved with *saveRDS* or even *save.image(.)*.

Yes, I know, I did not append a minimally complete example. Just wanted
to see if it was just me, or if anyone else was seeing this.

It's on Windows 7 HE and I've run *R* here for years.

My inclination is to drop back to 3.6.0 if it is just me or if no one
knows about this problem.

Thanks,

- Jan Galkowski.


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] random truncation

[Spencer Graves]

PLEASE EXCUSE:  This discussion has diverged from R into discussing the 
precise assumptions seemingly descriptive of an application that drove 
the initial post to this thread.  A reply by Abby Spurdle seemed to  me 
to raise questions, whose answers may not be intelligible without 
material snipped from Spurdle's reply.  I wish to thank Spurdle from the 
reply and apologize to those who feel this is an abuse of this list.  I 
trust that those in the latter category will please not bother to read 
further.  For anyone still interested in this problem, below please find 
my earlier analysis with corrections that attempt to respond to 
Spurdle's most recent concerns.  Thanks, Spencer Graves



On 2019-07-12 22:31, Abby Spurdle wrote:

> The distribution of the randomly truncated variable has thus four
> parameters: a, b, mu and sigma.  I was able to write down the likelihood
> and attempted to maximise it

I read the Wikipedia article more carefully.
The formula is relatively simple, and is based on the application of 
Bayes Theorem.
If one doesn't want to work out the integral, numerical methods can be 
used.


However, the problem needs to be defined *precisely* first.



Correct:  In my case, I confess I hadn't thought this through completely 
before posting.  I tried Rseek, as Bert Gunter suggested.  That led me 
to the "truncreg" and "DTDA" packages, neither of which seemed to be 
what I wanted;  thanks to Bert, Rolf, and Abby for your comments.



  I'm observing a random variable Y[i] = (x[i]'b+e[i]) given 
Y[i]>(z[i]'c+f[i]) where the tick mark (') denotes transpose of a 
vector, and e and f are normally distributed with mean 0 and standard 
deviations s and t, respectively, i = 1:n.  Thus, Y[i] follows a 
truncated normal distribution with mean x[i]'b and standard deviation s, 
with the truncation condition being that Y[i]>(z[i]'c+f[i]).



  I want the total of all the Y's from the untruncated 
distribution, i.e., including those truncated (and not observed).



  I think the likelihood is the product of the density of Y[i] 
given x[i] and given that Y[i] is actually observed.  By substituting 
Y[i] = (x[i]'b+e[i]) into the truncation condition Y[i]>(z[i]'c+f[i]), 
we get the following:



        (x[i]'b+e)>(z[i]c+f).


This occurs if and only if:


        (x[i]'b-z[i]'c)>(f-e),


Therefore, the probability that Y[i] is observed (and not truncated) is


        Pr{Y[i] observed} = Phi((x[i]'b-z[i]'c)/sqrt(s^2+t^2))


where Phi is the cdf of the standard normal.


  And then the likelihood for observation i can be written as follows:


        f(y[i]|x[i], z[i], b, c, s, t) = phi((y[i]-x[i]'b)/s) / 
Phi((x[i]'b-z[i]'c)/sqrt(s^2+t^2)).



  We may not be able to estimate "c" in this, because if one of the 
z[i]'s is nonzero, we can pick "c" so z[i]'c is Inf.  That makes the 
denominator 0 and the likelihood Inf.  (If all the z[i]'s are zero, we 
still cannot estimate "c".)  However, if "b" is estimable, ignoring the 
truncation, then we can estimate "b", "s" and "t" given "c".



  And then the desired total of all the Y's, observed and 
unobserved, would be the sum of y[i] divided by Pr{Y[i] observed}.



  This likelihood is simple enough, it can be easily programmed in 
R and maximized over variations in "b", "s" and "t" given "c".  I can 
get starting values for "b" and "s" from "lm", ignoring the truncation.  
And I can first fit the model assuming t = s, then test whether it's 
different using likelihood ratio.  And I can try to estimate "c", but I 
should probably use values I can estimate from other sources until I'm 
comfortable with the estimates I get for "b", "s" and "t" given an 
assumed value for "c".



  Comments?
  Thanks so much.
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] random truncation

[Spencer Graves]

On 2019-07-12 22:31, Abby Spurdle wrote:

> The distribution of the randomly truncated variable has thus four
> parameters: a, b, mu and sigma.  I was able to write down the likelihood
> and attempted to maximise it

I read the Wikipedia article more carefully.
The formula is relatively simple, and is based on the application of 
Bayes Theorem.
If one doesn't want to work out the integral, numerical methods can be 
used.


However, the problem needs to be defined *precisely* first.



Correct:  In my case, I confess I hadn't thought this through completely 
before posting.  I tried Rseek, as Bert Gunter suggested.  That led me 
to the "truncreg" and "DTDA" packages, neither of which seemed to be 
what I wanted;  thanks to Bert, Rolf, and Abby for your comments.



  I'm observing Y[i] = (X[i]'b+e) given Y[i]>(z[i]'c+f) where e and 
f are normally distributed with standard deviations s and t, 
respectively, i = 1:n.  I want the total of all the Y's, including those 
truncated (and not observed).



  I think the likelihood is the product of the density of Y[i] 
given x[i] and given that Y[i] is actually observed.  The latter can be 
further written as follows:



        (x[i]'b+e)>(z[i]c+f)
iff
        (x[i]'b-z[i]'c)>(f-e),


Therefore, the probability that Y[i] is observed is


        Pr{Y[i] observed} = Phi((x[i]'b-z[i]'c)/sqrt(s^2+t^2))


where Phi is the cdf of the standard normal.


  And then the likelihood for observation i can be written as follows:


        f(y[i]|x[i], z[i], b, c, s, t) = phi((y[i]-x[i]'b)/s) / 
Phi((x[i]'b-z[i]'c)/sqrt(s^2+t^2).



  We may not be able to estimate "c" in this, because if one of the 
z[i]'s is nonzero, we can pick "c" so z[i]'c is Inf.  That makes the 
denominator 0 and the likelihood Inf.  (If all the z[i]'s are zero, we 
still cannot estimate "c".)  However, if "b" is estimable, ignoring the 
truncation, then we can estimate "b", "s" and "t" given "c".



  And then the desired total of all the Y's, observed and 
unobserved, would be the sum of y[i] divided by Pr{Y[i] observed}.



  This likelihood is simple enough, it can be easily programmed in 
R and maximized over variations in "b", "s" and "t" given "c".  I can 
get starting values for "b" and "s" from "lm", ignoring the truncation.  
And I can first fit the model assuming t = s, then test whether it's 
different using likelihood ratio.  And I can try to estimate "c", but I 
should probably use values I can estimate from other sources until I'm 
comfortable with the estimates I get for "b", "s" and "t" given an 
assumed value for "c".



  Comments?
  Thanks so much.
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] random truncation

[Spencer Graves]

Hello:


  What do you suggest I do about modeling random truncation?


   I have data on a variable Y in strata S[0], S[1], ..., S[n], 
where Y is always observed in S[0] but is less often observed in the 
other strata.  I assume that the probability of observing Y is a 
monotonically increasing function of Y and a monotonically decreasing 
function of d[i] = the distance from S[0] to S[i].



  There is a section on "random truncation" in the Wikipedia 
article on "Truncated distribution".[1]  It would be nice if I had an R 
package that would make it relatively easy to model the truncation as a 
function of "d" and / or publication that described someone doing it in 
R.  (I also have a couple of other variables that influence the 
distribution of Y.)



  Thanks,
  Spencer Graves


[1] https://en.wikipedia.org/wiki/Truncated_distribution#Random_truncation

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] density vs. mass for discrete probability functions

[Spencer Graves]

On 2019-03-15 08:37, peter dalgaard wrote:

Mathematically, you can bring discrete and continuous distributions on a common 
footing by defining probability functions as densities wrt. counting measure. 
You don't really need Radon-Nikodym derivatives to understand the idea, just 
the fact that sums can be interpreted as integrals wrt counting measure, hence 
sum_{x in A} f(x) and int_A f(x) dx are essentially the same concept.



  Correct.  That's for clearing up my "mud".  sg

-pd


On 15 Mar 2019, at 01:43 , Stefan Schreiber  wrote:

Dear R users,

While experimenting with the dbinom() function and reading its
documentation (?dbinom) it reads that "dbinom gives the density" but
shouldn't it be called "mass" instead of "density"? I assume that it
has something to do with keeping the function for "density" consistent
across discrete and continuous probability functions - but I am not
sure and was hoping someone could clarify?

Furthermore the help file for dbinom() function references a link
(http://www.herine.net/stat/software/dbinom.html) but it doesn't seem
to land where it should. Maybe this could be updated?

Thank you,
Stefan

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] 3.5.3

[Spencer Graves]

On 2019-03-15 08:54, Jeff Newmiller wrote:

You really need to get into better touch with your feelings, man... how are we 
supposed to know what you want? ;-)

In general you should be using the main release unless you know there is a bug 
in it that affects you and has specifically been addressed in the patched 
version. The patched version may have also introduced new bugs and has in 
general been tested less than the main release version.

But hey... pick your own poison... maybe you want to contribute more bug 
reports per week... patched would be just your thing!



  A "fortune"?  sg


On March 15, 2019 6:29:52 AM PDT, Bill Poling  wrote:

Good morning.

This may have already been asked, if so my appologies.

I want to upgrade to 3.5.3 however there is an alternative called
patched.

Do I want it or the basic 3.5.3?

Thank you.

https://www.google.com/search?safe=strict=1C1GCEB_enUS821US821=naWLXLuuAoOb5wKp6K_oBA=difference+between+r+3.5.3+and+3.5.3+patched=difference+between+r+3.5.3+and+3.5.3+patched_l=psy-ab.3...3568.18782..19030...1.0..0.133.3101.34j4..01..gws-wiz...0i7i30j33i10j33i299j33i22i29i30j33i160.nyMRzRN9ebw

WHP



Confidentiality Notice This message is sent from Zelis.
...{{dropped:13}}

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] density vs. mass for discrete probability functions

[Spencer Graves]

On 2019-03-14 19:43, Stefan Schreiber wrote:

Dear R users,

While experimenting with the dbinom() function and reading its
documentation (?dbinom) it reads that "dbinom gives the density" but
shouldn't it be called "mass" instead of "density"? I assume that it
has something to do with keeping the function for "density" consistent
across discrete and continuous probability functions - but I am not
sure and was hoping someone could clarify?



  The Wikipedia article on "Probability density function" gives the 
"Formal definition" that, "the density of [a random variable] with 
respect to a reference measure ... is the Radon–Nikodym derivative".



  This sounds bazaar to people who haven't studied 
measure-theoretic probability, but it allows a unified treatment of 
continuous and discrete probabilities and to others that are 
combinations and neither.  The "reference measure" for a discrete 
probability distribution is the "counting measure", which supports the 
use of the word "density" in this context being equivalent to "mass".  
For continuous distributions, the "reference measure" is routinely taken 
to be the "improper prior" that assigns measure 1 to any unit interval 
on the real line.



  Does that make it clear as mud?


  Spencer Graves


https://en.wikipedia.org/wiki/Probability_density_function


Furthermore the help file for dbinom() function references a link
(http://www.herine.net/stat/software/dbinom.html) but it doesn't seem
to land where it should. Maybe this could be updated?

Thank you,
Stefan

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] RMarkdown vignettes v. Jupyter notebooks?

[Spencer Graves]

Hello:


  What are the differences between Jupyter notebooks and RMarkdown 
vignettes?



  I'm trying to do real time monitoring of the broadcast quality of 
a radio station, and it seems to me that it may be easier to do that in 
Python than in R.[1]  This led me to a recent post to 
"python-l...@python.org" that mentioned "Jupyter, Mathematica, and the 
Future of the Research Paper"[2] by Paul Romer, who won the 2018 Nobel 
Memorial Prize in Economics only a few days ago.  In brief, this article 
suggests that Jupyter notebooks may replace publication in refereed 
scientific journals as the primary vehicle for sharing scientific 
research, because they make it so easy for readers to follow both the 
scientific and computational logic and test their own modifications.



  A "Jupyter Notebook Tutorial: The Definitive Guide"[3] suggested 
I first install Anaconda Navigator.  I got version 1.9.2 of that.  It 
opens with options for eight different "applications" including 
JupyterLab 0.34.9, Jupyter Notebook 5.6.0, Spyder 3.3.1 (an IDE for 
Python), and RStudio 1.1.456.



  This leads to several questions:


        1.  In general, what experiences have people had with 
Jupyter Notebooks, Anaconda Navigator, and RMarkdown vignettes in 
RStudio, and the similarities and differences?  Do you know any 
references that discuss this?



        2.  More specifically, does it make sense to try to use 
RStudio from within Anaconda Navigator, or is one better off using 
RStudio as a separate, stand alone application -- or should one even 
abandon RStudio and run R instead from within a Jupyter Notebook? [I'm 
new to this topic, so it's possible that this question doesn't even make 
sense.]



  Thanks,
  Spencer Graves


[1] If you have ideas for how best to do real time monitoring of 
broadcast quality of a radio station, I'd love to hear them.  I need 
software that will do that, preferably something that's free, open 
source.  The commercial software I've seen for this is not adequate for 
my purposes, so I'm trying to write my own.  I have a sample script in 
Python that will read a live stream from a radio tuner and output a 
*.wav of whatever length I want, and I wrote Python eight years ago for 
a similar real time application.  I'd prefer to use R, but I don't know 
how to get started.



[2] 2018-04-13: 
"https://paulromer.net/jupyter-mathematica-and-the-future-of-the-research-paper;. 
This further cites a similar article in The Atlantic from 2018-04-05: 
"www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676".


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] using S4 objects in "with"?

[Spencer Graves]

On 2018-09-26 15:34, Duncan Murdoch wrote:

On 26/09/2018 4:16 PM, Spencer Graves wrote:

    Is there anything comparable to "with" for S4 objects?


EXAMPLE:


    A "Wave" object in the tuneR package has slots "left" and
"right", plus others.  I'd like to be able to do something like the
following:


library(tuneR)
x <- seq(0, 2*pi, length = 6)
all.equal(x, rev(x))
channel <- round(32000 * sin(440 * x))
Wobj <- Wave(left = channel, right=rev(channel))

with(Wobj, quantile(left-right))


    ** This last statement throws "Error ... object 'left' not 
found".



    Is there something comparable to "with" that can do this?


I don't know of anything that is "officially sanctioned".  A couple of 
ideas:


1.  Slots in S4 are stored in attributes.  So

  with(attributes(Wobj), quantile(left - right))

works.  BUT:  as far as I recall, this is an undocumented 
implementation detail, and you aren't supposed to count on it.


2.  You could write an as.list() method for the Wave class, then

  with(as.list(Wobj),

would work.  This may be the "right" way to do this.



  Thanks.  I'd prefer to have as.list.default convert every S4 
object to a list.  And have with(S4_object, ...) interpret it equivalent 
to with(as.list(S4_object), ...).



  I think I'll do it other ways for the time being.


  Best Wishes,
  Spencer



Duncan Murdoch


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] using S4 objects in "with"?

[Spencer Graves]

  Is there anything comparable to "with" for S4 objects?


EXAMPLE:


  A "Wave" object in the tuneR package has slots "left" and 
"right", plus others.  I'd like to be able to do something like the 
following:



library(tuneR)
x <- seq(0, 2*pi, length = 6)
all.equal(x, rev(x))
channel <- round(32000 * sin(440 * x))
Wobj <- Wave(left = channel, right=rev(channel))

with(Wobj, quantile(left-right))


  ** This last statement throws "Error ... object 'left' not found".


  Is there something comparable to "with" that can do this?


  Thanks,
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Summarizing R script

[Spencer Graves]

  It depends on what you want, but I've found it very useful to 
create packages and submitting them to CRAN.  See "Creating R Packages" 
for how to do that.[1]  Part of this involves creating vignettes using 
Rmarkdown within RStudio.  Creating R packages and routinely running "R 
CMD check" sounds like it would take extra time.  My experience has been 
very much the opposite, because it dramatically reduces the bugs in my 
software and makes it vastly easier to find the bugs that still exist.  
AND I have something I can just hand to others, and they can use it.  
That would be exceedingly difficult otherwise.



  And there are publications like "R Journal" that are looking for 
descriptions of what you've done.  I have a paper in "R Journal" 
describing the "sos" package;  that article is a vignette in that 
package.  This process has worked for me.[2]



   Spencer


[1] Available from help.start().  See also 
"https://cran.r-project.org/doc/manuals/r-release/R-exts.html;.



[2] The "sos" package is the fastest literature search I know for 
anything statistical.  It's availability on CRAN combined with the R 
Journal article got me invited to help organize a plenary session on 
"Navigating the R Package Universe" at the useR!2017 conference in 
Brussels last year.  This is an example of how creating an R package 
with a vignette has helped me find an audience.



On 2018-09-26 09:06, Roger Koenker wrote:

I use R CMD BATCH foo which produces a file called foo.Rout and provided the 
script includes
sessionInfo() constitutes a quite sufficient summary for my purposes, it isn’t 
exactly pretty, but it
is informative.


On Sep 26, 2018, at 3:00 PM, Spencer Brackett  
wrote:

R users,

  Is anyone aware of the proper procedure for summarizing a script(your
complete list of functions, arguments , and error codes within your R
console for say a formal report or publication?

Many thanks,

Best wishes,

Spencer Brackett

-- Forwarded message -
From: CHATTON Anne via R-help 
Date: Wed, Sep 26, 2018 at 6:03 AM
Subject: [R] Problems to obtain standardized betas in multiply-imputed data
To: r-help@r-project.org 


Dear all,

I am having problems in obtaining standardized betas on a multiply-imputed
data set. Here are the codes I used :
imp = mice(data, 5, maxit=10, seed=42, print=FALSE)
FitImp <- with(imp,lm(y ~ x1 + x2 + x3))
Up to here everything is fine. But when I ask for the standardized
coefficients of the multiply-imputed regressions using this command :
sdBeta <- lm.beta(FitImp)
I get the following error message:
Error in b * sx : argument non numérique pour un opérateur binaire

Can anyone help me with this please?

Anne

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] [FORGED] Question on Binom.Confint

[Spencer Graves]

On 2018-09-14 08:52, Guo, Fang (Associate) wrote:

It's method="lrt" and I used the "binom" package.



  The ultimate answer can be obtained as follows:


> debug(binom.confint)
> binom.confint(x = 0, n = 100, tol = 1e-8, method='lrt')


  Then walk through the code line by line.


  Reading the code, I find the following:


  if (any(method == "lrt") || all.methods) {
    res.lrt <- binom.lrt(x, n, conf.level = conf.level, ...)
    res <- if (is.null(res))
    res.lrt
    else rbind(res, res.lrt)
    }


  Then check the help page for "binom.lrt".  That includes the 
following:



Confidence intervals are based on profiling the binomial deviance in the 
neighbourhood of the MLE. If x == 0 or x == n and bayes is TRUE, then a 
Bayesian adjustment is made to move the log-likelihood function away 
from Inf. Specifically, these values are replaced by (x + 0.5)/(n + 1), 
which is the posterier mode of f(p|x) using Jeffrey's prior on p. 
Furthermore, if conf.adj is TRUE, then the upper (or lower) bound uses a 
1 - alpha confidence level. Typically, the observed mean will not be 
inside the estimated confidence interval. If bayes is FALSE, then the 
Clopper-Pearson exact method is used on the endpoints. This tends to 
make confidence intervals at the end too conservative, though the 
observed mean is guaranteed to be within the estimated confidence limits.



  Spencer


-Original Message-
From: Rolf Turner [mailto:r.tur...@auckland.ac.nz]
Sent: Thursday, September 13, 2018 10:02 PM
To: Guo, Fang (Associate) 
Cc: r-help@R-project.org
Subject: Re: [FORGED] [R] Question on Binom.Confint


On 09/14/2018 08:15 AM, Guo, Fang (Associate) wrote:


Hi,

I have a question with the function Binom.Confint(x,n,"method"=lrt).
For likelihood ratio test, I'd like to ask how you define the upper
limit when the frequency of successes is zero. Thanks!

Point 1:  This question is inappropriate for this list, since it is about 
statistical theory and not about R syntax and programming.

Point 2: Where did you find the function Binom.Confint()?  I can find no such 
function anywhere.  I did manage to locate a function
binom.confint() (note the lower case "b" and "c") but it does not have an argument 
"method".  Please do not expect those whom you are addressing to be telepathic.

Point 3:  Having "method"=lrt in the call is decidedly weird.  Perhaps you meant 
method="lrt"; this is entirely different.

cheers,

Rolf Turner

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
***
Warning: This email may contain confidential or privileged information
intended only for the use of the individual or entity to whom it is
addressed. If you are not the intended recipient, please understand
that any disclosure, copying, distribution, or use of the contents
of this email is strictly prohibited.
***
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Question on Binom.Confint

[Spencer Graves]

On 2018-09-13 20:58, David Winsemius wrote:

On Sep 13, 2018, at 1:15 PM, Guo, Fang (Associate)  
wrote:

Hi,

I have a question with the function Binom.Confint(x,n,"method"=lrt). For 
likelihood ratio test, I'd like to ask how you define the upper limit when the frequency 
of successes is zero. Thanks!

First you need to tell use where you are getting Binom.Confint.

Error: object 'Binom.Confint' not found



  sos::findFn('Binom.Confint') found NO function named 
"Binom.Confint", but it did find two named "binom.confint", one in the 
"binom" package and the other in the "NNTbiomarker" package. The same 
search in "rdocumentation.org" returned the same results. The indicated 
command would not work in either.



  Spencer

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] real time monitoring of streaming audio with R?

[Spencer Graves]

Hello, All:


  Is it feasible to do real time monitoring of streaming audio with 
R, writing a compressed copy of what's read to 1-hour long MP3 files?



  I'm a volunteer with a community radio station (kkfi.org).  My 
minimum requirements at the moment are to create MP3 files from what we 
broadcast.  I have a tuner hooked to the audio input of a computer.  I 
can listen to it in real time using the computer audio output jack, and 
I can record it manually using Audacity.  If I have MP3 versions of both 
what we send to the tower and what is actually broadcasted, I can read 
the two into R, compare them, identify substantive differences, write 
appropriate descriptions to files, send emails, etc.  I don't know how 
to sample the live stream.



   I know it can be done in Python, but I don't know how, and I'd 
prefer to use R.  I suspect it can be done with ffplay, part of ffmpeg, 
but again I don't know how.



  Thanks,
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Converting chr to num

[Spencer Graves]

  Have you considered "Ecfun::asNumericChar" (and 
"Ecfun::asNumericDF")?



DF <- data.frame(variable = c("12.6% ", "30.9%", "61.4%", "1"))
Ecfun::asNumericChar(DF$variable)
[1] 0.126 0.309 0.614 1.000


  If you read the documentation including the examples, you will 
see that many of these issues and others are handled automatically in 
the way that I thought was the most sensible.  If you disagree, we can 
discuss other examples and perhaps modify the code for those functions.



  Spencer Graves


On 2018-08-20 00:26, Rui Barradas wrote:

Hello,

Inline.

On 20/08/2018 01:08, Daniel Nordlund wrote:

See comment inline below:

On 8/18/2018 10:06 PM, Rui Barradas wrote:

Hello,

It also works with class "factor":

df <- data.frame(variable = c("12.6%", "30.9%", "61.4%"))
class(df$variable)
#[1] "factor"

as.numeric(gsub(pattern = "%", "", df$variable))
#[1] 12.6 30.9 61.4


This is because sub() and gsub() return a character vector and the 
instruction becomes an equivalent of what the help page ?factor 
documents in section Warning:


To transform a factor f to approximately its original numeric 
values, as.numeric(levels(f))[f] is recommended and slightly more 
efficient than as.numeric(as.character(f)).



Also, I would still prefer

as.numeric(sub(pattern = "%$","",df$variable))
#[1] 12.6 30.9 61.4

The pattern is more strict and there is no need to search 
multiple occurrences of '%'.


The pattern is more strict, and that could cause the conversion to 
fail if the process that created the strings resulted in trailing 
spaces. 


That's true, and I had thought of that but it wasn't in the OP's 
problem description.

The '$' could still be used with something like "%\\s*$":

as.numeric(sub('%\\s*$', '', df$variable))
#[1] 12.6 30.9 61.4


Rui Barradas



Without the '$' the conversion succeeds.

df <- data.frame(variable = c("12.6% ", "30.9%", "61.4%"))
as.numeric(sub('%$', '', df$variable))
[1]   NA 30.9 61.4
Warning message:
NAs introduced by coercion


<<>>


Dan



---
This email has been checked for viruses by AVG.
https://www.avg.com

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Fwd: Quadratic programming, for loop

[Spencer Graves]

  sos::findFn('{quadratic programming}') just identified 156 help 
pages in 68 packages containing the term "quadratic programming".  The 
function mentioned by Berwin Turlach, "solve.QP", is in package 
"quadprog", which has not been updated since 2016-12-20.  I've used 
qudprod successfully, but you might wish to consider some of the other 
options in package(s) more actively maintained.



  The "print" method for sos::findFn('{quadratic programming}') 
produced two sheets in my default browser.  The first of these contained 
156 rows for the 156 help pages in 68 packages, sorted by default by 
c('Count', 'MaxScore', 'TotalScore', 'Package', 'Score', 'Function').  
The second sheet listed only the 68 packages sorted by c('Count', 
'MaxScore', 'TotalScore', 'Package').  You can click on the column 
headers to get them sorted in different orders, if you want.



  "sos::findFn" is for me the fastest literature search for 
anything statistical.  I often write the list of help pages and the 
package summary to an Excel file using the "writeFindFn2xls" function, 
then annotate the package summary with other information to help me 
decide which package(s) and function(s) to try.



  Hope this helps.
  Spencer Graves, lead author of "sos"


On 2018-06-26 07:01, Berwin A Turlach wrote:

G'day all,

On Tue, 26 Jun 2018 11:16:55 +0300
Maija Sirkjärvi  wrote:


It seems that my Amat and dvec are incompatible. Amat is a matrix of
zeros size: *2*J-3,J* and dvec is a vector of length *J*. There
should be no problem, but apparently there is. [...]

solve.QP solves the quadratic program:
 min(-d^T b + 1/2 b^T D b)
where A^T b >= b_0.

Note the transpose. :)
If dvec is of length *J*, then b will be of length J too, and Amat
should be Jx(2J-3) so that its transpose is (2j-3)xJ, making it
compatible for matrix multiplication with b.

Cheers,

Berwin

---
This email has been checked for viruses by Avast antivirus software.
https://www.avast.com/antivirus

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Systemfit Question

[Spencer Graves]

  I got an error when I tried to source the "structure" below 
beginning with "Empdata <- structure(list(country = structure(c(1L, 1L, 
1L, 1L, 1L, 1L,":  The source ended with " "98", "983", "991", "995", 
"997"),

+
+
+
+
+
+  ))
+"


  I supplied ")" and got another "+".  When I supplied a second 
")", I got, "Error in structure(c(15L, 487L, 397L, 323L, 233L, 315L, 
370L, 309L, 268L,  :

  argument is missing, with no default".


  Please excuse if I missed something obvious that I might have 
seen if I had read this entire thread, but it looked to me like this 
example was intended to be self contained and does not seem to be so.



  Spencer


On 2018-05-16 17:21, Ngwinui Azenui wrote:

I can't get my simultaneous equations to work using system fit. Please help.

#Reproducible script
Empdata<- read.csv("/Users/ngwinuiazenui/Documents/UPLOADemp.csv")
View(Empdata)
str(Empdata)
Empdata$gnipc<-as.numeric(Empdata$gnipc)
install.packages("systemfit")
library("systemfit")
pdata <- plm.data(Empdata, index=c("country","year"))
install.packages("plm")
library("plm")

#Simultaneous equation 1
eqprd<- prd ~ in_emp +gnipc
eqemp<- in_emp ~ prd
inst <- ~ gnipc
system<- list(productivity = eqprd, industrialemp = eqemp)
fit2sls<- systemfit(system, "2SLS", inst = inst, data = Empdata)
#I get an error code when I run the last line

#Simultaneous equation 2
eqprd2<- prd ~  in_emp + lag(prd, -1) + gnipc
eqemp2<- in_emp ~ prd + lag(prd, -1) + conflict
system2<- list(productivity = eqprd2, industrialemp = eqemp2)
inst <- ~ lag(prd, -1) + gnipc + conflict
fit2sls<- systemfit(system2, "2SLS", inst = inst, data = Empdata)
#I also wanted to include year and country fix effects(string
variables) to the model in "Simultaneous equation 2)

EmpSur<- systemfit(prd ~ in_emp + ag_emp, method = "SUR", data = pdata)
#When I run the code below, I get a table with reults by country
print(EmpSur)
#An except of the output from running 

Re: [R] Package for Molecular Properties

[Spencer Graves]

library(sos)


(mp <- findFn('{molecular properties}'))


  ** found 7 matches in 4 packages and opened two web pages in my 
default browser with (a) the 7 matches and (b) the 4 packages. The first 
function was something for amino acids, like you suggested.  Two others 
returned compound and substance information from PubChem.



  Does this help?
  Spencer


On 2018-05-02 19:17, bbb_...@verizon.net wrote:

All

Is there a package or library that will, given a nucleotide sequence

1. calculate the extinction coefficient at 260 nm for (Beer-Lambert's law)
2. calculate molecular weight
3. return it's complementary sequence

I was able to find several packages that can do similar calculations for an 
amino acid sequence for proteins but none for nucleic acids.

Any pointers, etc. would be great.

thank you in advance
Indr

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Learning advanced R

[Spencer Graves]

On 2018-03-14 11:52, Rich Shepard wrote:

On Wed, 14 Mar 2018, Duncan Murdoch wrote:

I'm all for learning more languages and using the one that's best for 
each
job, but for people who don't know Python, it would be helpful to 
list the

aspects in which it excels. When should an R user choose to write
something in Python instead?


Duncan,

  "Best" is subjective, but my view is the language most comfortable and
familiar to the developer/analyst should be the one used.

  In my environmental consulting business I use both R and Python. While
Python has support for many statistical models I'm more comfortable 
with the
ones available in R. For spatial analyses (separate from spatial 
statistics)
I've used GRASS for > 20 years and it heavily uses Python. I also use 
Python
(along with emacs, awk, sed, and grep) for cleaning and organizing 
data. For

writing, I use LaTeX (a markup language) and the LyX GUI front end.

  Python has a lot of support for scientific and financial analyses, 
as does

R. Considering there are a gazillion programming languages available (and
used for essential applications, such as GnuCash (written in guile, a 
scheme

variant) which I use for business and personal bookkeeping, picking the
"best" one is strictly a personal matter. I prefer emacs, my system and
network admin friends prefer vi. In linux, at least, there are so many
options for doing a task that sometimes it's difficult to decide which to
use in a given situation.

  If the languages you know do all you need then learn a new one only if
it's to scratch an itch. :-)



  My software development productivity increased by a factor of 
maybe 30 by using first S-Plus then R, including writing R packages, 
then RStudio and writing Rmarkdown vignettes.



        1.  I started writing Fortran in 1963.  I've written 
assembly language for multiple machines, Cobol, Lisp, and other 
language.  I started using S-Plus in the early 1990s and abandoned it 
for R when I needed "debug" for some S-Plus code.  Developing R packages 
improved my software development productivity by a factor of 10, because 
the discipline of creating unit tests in "\examples" made it so much 
easier to debug and maintain -- AND share with others.



        2.  I've also written some Python, though not much.  I used 
Emacs until I found RStudio.  Vi and Emacs are not tools you can give to 
someone, who is only marginally computer literate and expect them to be 
productive in a reasonable period of time.  By contrast, if someone 
knows enough to be able to install R and RStudio, I can give them some R 
code and be confident that they will get something useful from the 
experience in a relatively short period of time.  You can't do that with 
vi and Emacs unless they already know those applications.



        3.  Recently, I've started writing RMarkdown vignettes, and 
that further increased my productivity.



          3.1.  Two years ago, I told I client I was going to 
prepare and Rmarkdown vignette to document what I did with their data.  
My sales guy said absolutely, we were NOT going to give the client an 
Rmarkdown vignette.  I spent a week analyzing the data and 6 months 
answering questions from the team mostly by pointing them to certain 
lines in the vignette, occasionally by extending it.  In the middle of 
that, we learned that the client required our analysis to be 
verifiable.  After that, the vignette became a primary deliverable.



          3.2.  More recently, another client asked me to 
explain principal components.  This client was moderately facile with 
software but not with R nor vector spaces.  I gave him an Rmarkdown 
vignette that included a principal components on some data he gave me 
done both with a single command and step by step supplemented with a 
simple discussion of a one-dimensional subspace of two-dimensional 
space.  He was happy.



        4.  I invite all to review and improve the discussion in 
the Wikipedia article on "Software repository".  This a table with a 
discussion of "Selected repositories", much of which I wrote 8 years 
ago.  It's heavily biased toward CRAN, because that's what I know the 
best, and I've so far been unable to find anyone with the expertise and 
interest in improving it.  This article averaged 290 views per day over 
the past 90 days, over 26,000 in the past 3 months.  If you can improve 
that article, an audience that size might be worth talking to.



   Spencer Graves



Best regards,

Rich

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing li

Re: [R] deparseDots to get names of all arguments?

[Spencer Graves]

On 2018-02-20 20:52, William Dunlap wrote:
> Does substitute(...()) do what you want?


   That's the key.  Thanks very much.
       Spencer Graves

>
> > myFunc <- function(x, ...) substitute(...())
> > myFunc(y=1/(1:10), x=sin(3:1), z=stop("Oops"), "untagged arg")
> $y
> 1/(1:10)
>
> $z
> stop("Oops")
>
> [[3]]
> [1] "untagged arg"
>
> > names(.Last.value)
> [1] "y" "z" ""
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com <http://tibco.com>
>
> On Tue, Feb 20, 2018 at 2:36 PM, Spencer Graves 
> <spencer.gra...@effectivedefense.org 
> <mailto:spencer.gra...@effectivedefense.org>> wrote:
>
> Hi, All:
>
>
>   How can I get the names of all the arguments in dots(...)?
>
>
>   I'm able to get the name of the first argument but not the
> second:
>
>
>
> deparseDots <- function(...){
>   deparse(substitute(...))
> }
> a <- 1
> b <- 2
> deparseDots(a, b)
> [1] "a"
>
>
>   I'd like to get c('a', 'b').
>
>
>   Thanks,
>   Spencer Graves
>
>
> > sessionInfo()
> R version 3.4.3 (2017-11-30)
> Platform: x86_64-apple-darwin15.6.0 (64-bit)
> Running under: macOS High Sierra 10.13.3
>
> Matrix products: default
> BLAS:
> 
> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> LAPACK:
> 
> /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics  grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.3 tools_3.4.3    yaml_2.1.16
>
> __
> R-help@r-project.org <mailto:R-help@r-project.org> mailing list --
> To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> <https://stat.ethz.ch/mailman/listinfo/r-help>
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> <http://www.R-project.org/posting-guide.html>
> and provide commented, minimal, self-contained, reproducible code.
>
>


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] deparseDots to get names of all arguments?

[Spencer Graves]

Hi, All:


  How can I get the names of all the arguments in dots(...)?


  I'm able to get the name of the first argument but not the second:



deparseDots <- function(...){
  deparse(substitute(...))
}
a <- 1
b <- 2
deparseDots(a, b)
[1] "a"


  I'd like to get c('a', 'b').


  Thanks,
  Spencer Graves


> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.3

Matrix products: default
BLAS: 
/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: 
/Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib


locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

loaded via a namespace (and not attached):
[1] compiler_3.4.3 tools_3.4.3    yaml_2.1.16

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Draft proposal for Searching R Packages

[Spencer Graves]

Hello, All:


  I just posted a "Draft Proposal for improving the ability of R 
users to search R packages" to Wikiversity 
(https://en.wikiversity.org/wiki/Draft_Proposal_for_improving_the_ability_of_R_users_to_search_R_packages). 




  You are all invited to rewrite it in any way you think is more 
likely to produce the most useful result.  Wikimedia invites 
contributors to "be bold but not reckless", writing from a neutral point 
of view citing credible sources.  I do NOT want to do this project:  I 
think the world will be better if it is done, and I think others are 
better equipped to actually do it -- or manage others doing it -- than I 
am.



  If you read this, you will see that it contains critical gaps.  I 
hope one or more of you will fill these critical gaps or help find 
others who will.



  As indicated there, the next major deadline is April 1.  This 
sounds like lots of time, except that the key thing that is missing in 
this draft proposal is principal investigator(s).  Without PI(s), it 
won't fly.



  Thanks,
  Spencer Graves, PhD
  Founder
  EffectivedDefense.org
  7300 W. 107th St. # 506
  Overland Park, KS 66212
ph:  408-655-4567

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Scraping info from a web site?

[Spencer Graves]

Hi, All:


  What would you suggest one use to read the data on members of the 
US Congress and their positions on net neutrality from 
"https://www.battleforthenet.com/scoreboard; into R?



  I found recommendations for the "rvest" package to "Easily 
Harvest (Scrape) Web Pages".  I tried the following:



URL <- 'https://www.battleforthenet.com/scoreboard/'
library(rvest)
Bftn <- read_html(URL)
str(Bftn)


List of 2
 $ node:
 $ doc :
 - attr(*, "class")= chr [1:2] "xml_document" "xml_node"


   However, I don't know what to do with .


  The "Selectorgadget" vignette with rvest suggested selecting what 
I wanted on the web page and pasting that as an argument into 
"html_node".  This led me to try the following:



Bftn_nodes <- html_nodes(Bftn,
    '.psb-unknown , #house, #senate, #senate p')


str(Bftn_nodes)
List of 4
 $ :List of 2
  ..$ node:
  ..$ doc :
  ..- attr(*, "class")= chr "xml_node"
 $ :List of 2
  ..$ node:
  ..$ doc :
  ..- attr(*, "class")= chr "xml_node"
 $ :List of 2
  ..$ node:
  ..$ doc :
  ..- attr(*, "class")= chr "xml_node"
 $ :List of 2
  ..$ node:
  ..$ doc :
  ..- attr(*, "class")= chr "xml_node"
 - attr(*, "class")= chr "xml_nodeset"


  This seems like it may be progress, but I'm still confused on 
what to do next.  Or maybe I should be using a different package? Or 
posting this question to someplace else like StackOverflow.com?



  Thanks,
  Spencer Graves

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Searching R Packages

[Spencer Graves]

Hello, All:


	  Might you have time to review the article I recently posted to 
Wikiversity on "Searching R Packages" 
(https://en.wikiversity.org/wiki/Searching_R_Packages)?



	  Please edit this yourself or propose changes in the associated 
"Discuss" page or in an email to this list or to me.



	  My goal in this is to invite readers to turn that article into a 
proposal for improving the search capabilities in R that would 
ultimately be funded by, e.g., The R Foundation.



  What do you think?


  Please forward this to anyone you think might be interested.


  Best Wishes,
  Spencer Graves, PhD
  Founder
  EffectiveDefense.org
  7300 W. 107th St. # 506
  Overland Park, KS 66212

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Getting all possible combinations

[Spencer Graves]

On 2017-08-23 11:35 AM, Bert Gunter wrote:

ummm, Ista, it's 2^n.



  or (2^n-1) if the empty set is not considered as a "combination" 
;-)  spencer


Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Aug 23, 2017 at 8:52 AM, Ista Zahn  wrote:

On Wed, Aug 23, 2017 at 11:33 AM, Christofer Bogaso
 wrote:

Hi again,

I am exploring if R can help me to get all possible combinations of
members in a group.

Let say I have a group with 5 members : A, B, C, D, E

Now I want to generate all possible unique combinations with all
possible lengths from that group e.g.

1st combination : A
2nd combination : B
.
5th combination : E
6th combination : A, B
7th combination : B, C

last combination: A, B, C, D, E

Ideally, I have a fairly large group so am looking for some
programmatic way to generate all possible combinations.

Be careful, the number of combinations grows pretty quickly. You can
calculate the number ahead of time with

sum(choose(n, 1:n))

where n is the number of values in your group.

--Ista


Any help will be highly appreciated.

Thanks for your time.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Convert Factor to Date

[Spencer Graves]

On 2017-08-22 2:04 PM, Patrick Casimir wrote:
>
> This is large data set Spencer. What about when the dates change as below:
>


 � Have you tried what I suggested?� What were the results? Spencer

>
> COL1  COL2
> Jan-141-Aug-16
> Feb-141-Aug-16
> Mar-141-Aug-16
> Apr-141-Aug-16
> May-141-Aug-16
> Jun-141-Aug-16
> Jul-141-Aug-16
> Aug-141-Aug-16
> Sep-141-Aug-16
> Oct-141-Aug-16
> Nov-141-Aug-16
> Dec-141-Aug-16
> Jan-151-Aug-16
> Feb-151-Aug-16
> Mar-151-Aug-16
> Apr-151-Aug-16
> May-151-Aug-16
> Jun-151-Aug-16
> Jul-151-Aug-16
> Aug-151-Aug-16
> Sep-151-Aug-16
> Oct-151-Aug-16
> Nov-151-Aug-16
> Dec-151-Aug-16
> Jan-161-Aug-16
> Feb-161-Aug-16
> Mar-161-Aug-16
> Apr-161-Aug-16
> May-161-Aug-16
> Jun-161-Aug-16
> Jul-161-Aug-16
> Aug-161-Aug-16
> Sep-161-Aug-16
> Oct-161-Aug-16
>
>
>
>
>
>
>
> ----
> *From:* R-help <r-help-boun...@r-project.org> on behalf of Spencer 
> Graves <spencer.gra...@effectivedefense.org>
> *Sent:* Tuesday, August 22, 2017 2:49 PM
> *To:* r-help@r-project.org
> *Subject:* Re: [R] Convert Factor to Date
>
>
> On 2017-08-22 1:30 PM, Patrick Casimir wrote:
> > Dear R Fellows,
> >
> >
> > I Have a dataset( data1) with 2 columns of date showing a class of 
> factor. How to convert them to date? Then compare them, keep the 
> greater date only in a new column. Using as.Date to change the class 
> to Date but the data becomes NA.
>
>
> �� When I specified a format with the second date, I got the desired
> behavior:
>
>
> �> as.Date(factor('1-Nov-16'), '%d-%b-%y')
> [1] "2016-11-01"
> �> as.Date('Nov-16', '%b-%y')
> [1] NA
> �> as.Date(factor('Nov-16'), '%b-%y')
> [1] NA
> �> as.Date('Nov-16', '%b-%y')
> [1] NA
>
>
> �� To convert the first column, I pasted "1-" in front:
>
>
> as.Date(paste0('1-', factor('Nov-16')), '%d-%b-%y')
>
>
> �� Hope this helps.� Spencer
>
> > Much Thanks
> >
> >
> > COL1��� COL2
> > Apr-16� 1-Nov-16
> > May-16� 1-Nov-16
> > Jun-16� 1-Nov-16
> > Jul-16� 1-Nov-16
> > Aug-16� 1-Nov-16
> > Sep-16� 1-Nov-16
> > Oct-16� 1-Nov-16
> > Nov-16� 1-Nov-16
> > Dec-16� 1-Nov-16
> > Jan-17� 1-Nov-16
> > Feb-17� 1-Nov-16
> > Mar-17� 1-Nov-16
> > Apr-17� 1-Nov-16
> > May-17� 1-Nov-16
> > Jun-17� 1-Nov-16
> > Jul-17� 1-Nov-16
> > Aug-17� 1-Nov-16
> > Sep-17� 1-Nov-16
> >
> >
> >��� [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help=02%7C01%7Cpatrcasi%40nova.edu%7C6abf3517ab5f407427d308d4e98e9efd%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C0%7C0%7C636390246143633480=jwTeb%2BvH0bbkXdckgzE6PJZ3gDl9d1%2F3t9K%2BxDtjyls%3D=0
> > PLEASE do read the posting guide 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.R-project.org%2Fposting-guide.html=02%7C01%7Cpatrcasi%40nova.edu%7C6abf3517ab5f407427d308d4e98e9efd%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C0%7C0%7C636390246143633480=GUAR582xxtA88KLkQC1oPnvyNecfUyXjV9MrIziJicU%3D=0
> > and provide commented, minimal, self-contained, reproducible code.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help=02%7C01%7Cpatrcasi%40nova.edu%7C6abf3517ab5f407427d308d4e98e9efd%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C0%7C0%7C636390246143633480=jwTeb%2BvH0bbkXdckgzE6PJZ3gDl9d1%2F3t9K%2BxDtjyls%3D=0
> PLEASE do read the posting guide 
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.R-project.org%2Fposting-guide.html=02%7C01%7Cpatrcasi%40nova.edu%7C6abf3517ab5f407427d308d4e98e9efd%7C2c2b2d312e3e4df1b571fb37c042ff1b%7C0%7C0%7C636390246143633480=GUAR582xxtA88KLkQC1oPnvyNecfUyXjV9MrIziJicU%3D=0
> and provide commented, minimal, self-contained, reproducible code.


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Convert Factor to Date

[Spencer Graves]

On 2017-08-22 1:30 PM, Patrick Casimir wrote:

Dear R Fellows,


I Have a dataset( data1) with 2 columns of date showing a class of factor. How 
to convert them to date? Then compare them, keep the greater date only in a new 
column. Using as.Date to change the class to Date but the data becomes NA.



  When I specified a format with the second date, I got the desired 
behavior:



> as.Date(factor('1-Nov-16'), '%d-%b-%y')
[1] "2016-11-01"
> as.Date('Nov-16', '%b-%y')
[1] NA
> as.Date(factor('Nov-16'), '%b-%y')
[1] NA
> as.Date('Nov-16', '%b-%y')
[1] NA


  To convert the first column, I pasted "1-" in front:


as.Date(paste0('1-', factor('Nov-16')), '%d-%b-%y')


  Hope this helps.  Spencer


Much Thanks


COL1COL2
Apr-16  1-Nov-16
May-16  1-Nov-16
Jun-16  1-Nov-16
Jul-16  1-Nov-16
Aug-16  1-Nov-16
Sep-16  1-Nov-16
Oct-16  1-Nov-16
Nov-16  1-Nov-16
Dec-16  1-Nov-16
Jan-17  1-Nov-16
Feb-17  1-Nov-16
Mar-17  1-Nov-16
Apr-17  1-Nov-16
May-17  1-Nov-16
Jun-17  1-Nov-16
Jul-17  1-Nov-16
Aug-17  1-Nov-16
Sep-17  1-Nov-16


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Rounding of problem with sum command in R

[Spencer Graves]

On 2017-08-22 9:26 AM, niharika singhal wrote:

Hello I have a vector
v=c(0.0886,0.1744455,0.1379778,0.1209769,0.1573065,0.1134463,0.2074027)
when i do
sum(v)
or
0.0886+0.1744455+0.1379778+0.1209769+0.1573065+0.1134463+0.2074027
i am getting output as 1



No:  That's only the display:


> sum(v)-1
[1] 1.6e-07


  hope this helps.  Spencer


But if i add them manually i get
1.0026
I do not want to round of my value since it effect my code further
Can anyone suggest how can i avoid this.

Thanks & Regards
Niharika Singhal

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] weight in lm

[Spencer Graves]

On 2017-08-14 5:53 AM, peter dalgaard wrote:

On 14 Aug 2017, at 10:13 , Troels Ring <tr...@gvdnet.dk> wrote:

Dear friends - I hope you will accept a naive question on lm: R version 3.4.1, 
Windows 10

I have 204 "baskets" of three types corresponding to factor F, each of size from 2 to 33 
containing measurements, and need to know if the standard deviation on the measurements  in each 
basket,sdd, is different across types, F. Plotting the observed sdd  versus the sizes from 2 to 33, 
called "k" , does show a decreasing spread as k increases towards 33.

I tried lm(sdd ~ F,weight=k) and got different results if omitting the weight 
argument but would it be the correct way to use sqrt(k) as weight instead?


I doubt that there is a "correct" way, but theory says that if the baskets have the same 
SD and data are normally distributed, then the variance of the sample VARIANCE is proportional to 
1/f = 1/(k-1). Weights in lm are inverse-variance, so the "natural" thing to do would 
seem to be to regress the square of sdd with weights (k-1).

(If the distribution is not normal, the variance of the sample variance is 
complicated by a term that involves both n and the excess kurtosis, whereas the 
variance of the sample SD is complicated in any case. All according to the 
gospel of St.Google.)



  The Wikipedia article on "standard deviation" gives the more 
general formula.  (That article does NOT give a citation for that 
formula.  I you know one, please add it -- or post it here, to make it 
easier for someone else to add it.)



  Thanks, Peter.
  Spencer Graves


-pd



Best wishes

Troels Ring
Aalborg, Denmark

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Kalman filter for a time series

[Spencer Graves]

On 2017-07-29 11:26 PM, Staff wrote:

I found an example at
http://www.bearcave.com/finance/random_r_hacks/kalman_smooth.html



  That example is signed by "Ian Kaplan".  There's a box at the 
bottom of the page for you to email him.




shown
below.  But it seems the structSSM function has been removed from KFAS
library



  or it never was part of KFAS.  I don't know.



so it won't run.  Does anyone know how to fix the code so that it
runs?



  Have you tried the vignette with KFAS?


  Hope this helps.
      Spencer Graves


library(KFAS)
library(tseries)
library(timeSeries)
library(zoo)
library(quantmod)

getDailyPrices = function( tickerSym, startDate, endDate )
{
   prices = get.hist.quote( instrument = tickerSym, start = startDate,
end = endDate,
quote="AdjClose", provider="yahoo",
compression="d",  quiet=T)

   prices.ts = ts(prices)
   return( prices.ts )
}

kalmanFilter = function( x )
{
   t = x
   if (class(t) != "ts") {
 t = ts(t)
   }
   ssModel = structSSM( y = t, distribution="Gaussian")
   ssFit = fitSSM(inits=c(0.5*log(var(t)), 0.5*log(var(t))), model = ssModel )
   kfs = KFS( ssFit$model, smoothing="state", nsim=length(t))
   vals = kfs$a
   lastVal = vals[ length(vals)]
   return(lastVal)
}

Start = "2011-01-01"
End   = "2012-12-31"
SandP = "^GSPC"

windowWidth = 20
tsLength = 100

SAndP.ts = getDailyPrices( SandP, Start, End )
SAndP.ts = SAndP.ts[1:tsLength]
SAndP.smoothed = rollapply( data=SAndP.ts, width=windowWidth, FUN=kalmanFilter)

par(mfrow=c(1,1))
prices = coredata( SAndP.ts[windowWidth:length(SAndP.ts)])
plot(prices, col="blue", type="l")
lines(coredata(SAndP.smoothed), col="magenta")
par(mfrow=c(1,1))

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Nash equilibrium and other game theory tools implemented in networks using igraph or similar

[Spencer Graves]

On 2017-06-28 11:36 AM, Suzen, Mehmet wrote:

Hello Chris,

I was implying you are capable enough to implement it, while you have
already identify a research paper. If there is no package out there,
uploading to CRAN would help future user too. I am more than happy to
help if you want to implement from scratch.



  sos::findFn("nash equilibrium") identified 4 packages: antitrust, 
GNE, GPGame, and nopp.  I found GNE mentioned earlier in this thread but 
not the other three.  Similar searches for "nash equilibrium networ" and 
"nash equilibrium networks" returned no matches.



  By the way, one of the sessions at useR!2017 in Brussels next 
week will discuss "Navigating the R package universe".  This will 
provide a brief overview of tools currently available, followed by a 
general discussion of what people would want in tools to make it easier 
to find and use what you want in contributed packages, now well over 
10,000.  The planned discussion will briefly cover the "sos" package, 
"RDocumentation.org", METACRAN (www.r-pkg.org), "Task views", and other 
tools.



  We're hoping that this session will facilitate the development of 
one or more teams to collaborate on the following:



* Creating common interfaces for different approaches to 
essentially the same problem, like "optimx".



* Improving "Task views".


* Improving search capabilities.


  If you can make it to useR!2017, we hope to see you in this 
session, Wed. July 5, from 17:00 - 18:30 in the main meeting room. If 
you might like to help with this but can't make Brussels, please stay 
tuned for further announcements or contact me after the conference for 
further information.



  Spencer Graves


p.s.  Please excuse if I highjacked this thread to promote this session, 
but I didn't see any mention of the sos package or RDocumentation.org, 
so it seemed appropriate.



Best,
Mehmet

On 27 June 2017 at 17:45, Chris Buddenhagen <cbuddenha...@gmail.com> wrote:

Does anyone know of some code, and examples that implement game theory/Nash
equilibrium hypothesis testing using existing packages like igraph/statnet
or similar?

Perhaps along the lines of this article:

Zhang, Y., Aziz-Alaoui, M. A., Bertelle, C., & Guan, J. (2014). Local Nash
Equilibrium in Social Networks, *4*, 6224.

Best,
Chris Buddenhagen
cbuddenha...@gmail.com

 [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Nash equilibrium and other game theory tools implemented in networks using igraph or similar

[Spencer Graves]

On 2017-06-28 5:40 AM, Jeff Newmiller wrote:

Showing your work so that someone else can either see something you missed or 
share in the joy when a rare answer comes through is what elevates such a 
posting from spam to shared research.


A "fortune"?


  sg

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.