date:20120705



Hello,

Your eval(tests$rule[1]) needs a slight modification to get the results.



Try this:
tests-read.table(text=
 rule
 info$country=='Greenland'
 info$age50
 ,sep=,header=TRUE,stringsAsFactors=FALSE)


info-data.frame(first=rep(NA,5),country=c(GReenland,Iceland,Ireland,Greenland,Greenland)
 ,age=c(30,55,66,79,80),name=c(Mary,Paul,Robert,John,Ivan))
#1st condition

eval(parse(text=tests$rule[1]))
[1] FALSE FALSE FALSE  TRUE  TRUE

#2nd condition

eval(parse(text=tests$rule[2]))
[1] FALSE  TRUE  TRUE  TRUE  TRUE

# tests[1,1] condition: subset info
info[eval(parse(text=tests$rule[1])),]
  first   country age name
4    NA Greenland  79 John
5    NA Greenland  80 Ivan

#tests[2,1] condition: subset info
info[eval(parse(text=tests$rule[2])),]
  first   country age   name
2    NA   Iceland  55   Paul
3    NA   Ireland  66 Robert
4    NA Greenland  79   John
5    NA Greenland  80   Ivan

A.K.





- Original Message -
From: New RUser newruser2...@gmail.com
To: r-help@r-project.org
Cc: 
Sent: Tuesday, July 3, 2012 12:24 PM
Subject: [R] evaluating expressions contained in a dataframe

#I have a dataframe called tests that contain character expressions.  These
characters are rules that use data from within another dataframe.  Is there
any way within R I can access the rules in the dataframe called tests, and
then evaluate these rules?



#An example may better explain what I am trying to accomplish:



tests - data.frame(matrix(data=c(info$country == 'Greenland', info$age
 50), nrow=2, ncol=1))

names(tests) - rule



info - data.frame(matrix(data=NA, nrow=5, ncol=3))

names(info) - c(first, country, age)

info$name - c(Mary, Paul, Robert, John, Ivan)

info$country - c(GReenland, Iceland, Ireland, Greenland,
Greenland)

info$age - c(30, 55, 66, 79, 80)



#e.g. for

info$country == 'Greenland'



#I want:

info$country == 'Greenland'

[1] FALSE FALSE FALSE  TRUE  TRUE

#e.g.
info$country == 'Greenland'

info$age  50



#I tried this, but it does not work:

eval(tests$rule[1])

    [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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
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] Adding Text to a persp plot using specific coordinates

2012-07-05 Thread Benjamin Dubreuil


Hi folks,

I'm experiencing some hassle to add some text on a persp plot...

Here is the code to generate the persp plot:
x - seq(-1.95, 1.95, length = 30)
y - seq(-1.95, 1.95, length = 30)
z - outer(x, y, function(a,b) a*b^2)
persp(x, y, z,xlim=c(-2,2),ylim=c(-2,2),zlim=c(-8,8), phi=30, 
theta=-30,nticks=8,ticktype=detailed)

I've tried the text() function  :
text(x=0,y=0,z=0,texts=O)

It returns the following error message:
Error: evaluation nested too deeply: infinite recursion / 
options(expressions=)?

I've seen that text3d from the rgl library could add text on a plot3d object or 
a persp object.
But when I try this:
text3d(x=0,y=0,z=1,texts=O)
The result is that R opens a new window with the string O printed in the new 
window. And no text is added to my previous persp plot.

I've seen that maybe using trans3d would help but after many tries, I gave up. 
This function did not allow me to plot text with the specified coordinates.

Any ideas on how adding some text or labels to an existing persp plot using the 
coordinates I've entered?

Thanking you in anticipation.

Dubreuil Benjamin
Research Assistant in Bioinformatics
Michnick Lab - Dept of Biochemistry - Université de Montréal

  
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Return



Hi,
I guess this is what you are looking for:

 dat1 - read.table(text=
 Date  Stock1  Stock2  Stock3    Market
 01/01/2000    1  2  3    4
 01/02/2000    5  6  7    8
 01/03/2000    1  2  3    4
 01/04/2000    5  6  7    8
 , header=TRUE, stringsAsFactors=FALSE)

dat2-data.frame(Date=as.Date(dat1[,1],format=%m/%d/%Y),dat1[,2:4])
library(zoo)
Stocks-as.matrix(dat1[,2:4])
Stockreturn-zoo(Stocks)
Stockreturn-diff(log(Stockreturn))
Stockreturn-data.frame(Stockreturn)

Stockreturn1-Stockreturn
 Stockreturn1[1,]-NA
colnames(Stockreturn1[1,])-colnames(Stockreturn)



dat3-data.frame(Date=dat2[,1], rbind(Stockreturn1[1,],Stockreturn))
row.names(dat3)-1:nrow(dat3)
 dat3
    Date    Stock1    Stock2 Stock3
1 2000-01-01    NA    NA NA
2 2000-01-02  1.609438  1.098612  0.8472979
3 2000-01-03 -1.609438 -1.098612 -0.8472979
4 2000-01-04  1.609438  1.098612  0.8472979



A.K.




- Original Message -
From: Akhil dua akhil.dua...@gmail.com
To: r-help@r-project.org
Cc: 
Sent: Thursday, July 5, 2012 12:58 AM
Subject: [R] Return

Hello Every one
I have data on Stock prices and I want to calculate the return on all the
stocks
and then replace all the stock prices with the returns

can any one tell me how to do

My data is in the format given below

Date              Stock1  Stock2  Stock3
01/01/2000        1          2          3
01/02/2000        5          6          7
01/03/2000        1          2          3
01/04/2000        5          6          7


Thanks

    [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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
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] Maximum Likelihood Estimation Poisson distribution mle {stats4}

2012-07-05 Thread chamilka

Hi everyone!
I am using the mle {stats4} to estimate the parameters of distributions by
MLE method. I have a problem with the examples they provided with the
mle{stats4} html files. Please check the example and my question below!
*Here is the mle html help file * 
http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html
http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html 

*In the example provided with the help *
 od - options(digits = 5)
 x - 0:10*#generating Poisson counts*
 y - c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)  *#generating the
 frequesncies*
 
 ## Easy one-dimensional MLE:
 nLL - function(lambda) -sum(stats::dpois(y, lambda, log=TRUE))  *#they
 define the Poisson negative loglikelihood*
 fit0 - mle(nLL, start = list(lambda = 5), nobs = NROW(y)) * #they
 estimate the Poisson parameter using mle*
 fit0  *#they call the output*

Call:
mle(minuslogl = nLL, start = list(lambda = 5), nobs = NROW(y))

Coefficients:
lambda 
11.545   * #this is their estimated Lambda Vallue.*

*Now my question is in a Poisson distribution the Maximum Likelihood
estimator of the mean parameter lambda is  the sample mean, so if we
calculate the sample mean of that generated Poisson distribution manually
using R we get  the below!*

 sample.mean- sum(x*y)/sum(y)
 sample.mean
[1] 3.5433

*This is the contradiction!! *
Here I am getting the estimate as 3.5433(which is reasonable as most of the
values are clustered around 3), but mle code gives the estimate 11.545(which
may not be correct as this is out side the range 0:10)

Why this contradiction? 

--
View this message in context: 
http://r.789695.n4.nabble.com/Maximum-Likelihood-Estimation-Poisson-distribution-mle-stats4-tp4635464.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Adding Text to a persp plot using specific coordinates

2012-07-05 Thread Uwe Ligges




On 05.07.2012 06:45, Benjamin Dubreuil wrote:


Hi folks,

I'm experiencing some hassle to add some text on a persp plot...

Here is the code to generate the persp plot:
x - seq(-1.95, 1.95, length = 30)
y - seq(-1.95, 1.95, length = 30)
z - outer(x, y, function(a,b) a*b^2)
persp(x, y, z,xlim=c(-2,2),ylim=c(-2,2),zlim=c(-8,8), phi=30, 
theta=-30,nticks=8,ticktype=detailed)

I've tried the text() function  :
text(x=0,y=0,z=0,texts=O)

It returns the following error message:

Error: evaluation nested too deeply: infinite recursion / options(expressions=)?


I've seen that text3d from the rgl library could add text on a plot3d object or 
a persp object.
But when I try this:
text3d(x=0,y=0,z=1,texts=O)
The result is that R opens a new window with the string O printed in the new 
window. And no text is added to my previous persp plot.

I've seen that maybe using trans3d would help but after many tries, I gave up. 
This function did not allow me to plot text with the specified coordinates.


Yes, trans3d:
 x - seq(-1.95, 1.95, length = 30)
 y - seq(-1.95, 1.95, length = 30)
 z - outer(x, y, function(a,b) a*b^2)
 pmat - persp(x, y, z,xlim=c(-2,2),ylim=c(-2,2),zlim=c(-8,8), phi=30, 
theta=-30,nticks=8,ticktype=detailed)

 text(trans3d(0,0,0,pmat), Hello World!)

Best,
Uwe Ligges





Any ideas on how adding some text or labels to an existing persp plot using the 
coordinates I've entered?

Thanking you in anticipation.

Dubreuil Benjamin
Research Assistant in Bioinformatics
Michnick Lab - Dept of Biochemistry - Université de Montréal


[[alternative HTML version deleted]]



__
R-help@r-project.org mailing list
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
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] how to analyse non parametric test

2012-07-05 Thread Anil Kumar

Please i am Anilkumar G.V studieng MBA final sem for this data i want to
find out non parametric tests please help me

-- 
Anilkumar G.V
Jr,MBA
__
R-help@r-project.org mailing list
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] stlf algorithm failure

2012-07-05 Thread Christian Scherer


   Dear R-helpers,
   currently I am writing a thesis using R in forecasting scenarios.
   No the time is shortening and I wanted to set up all test cases, including
   the STLF algorithm of the forecast package.
   I am using 15 minutes (96 a day) data of two weeks to forecast one week...
   The frequency used is 672 (so two weeks)
   This should be fine because it has to be at least 2 priods..
   Unfortunately the stlf algorithm claims that my time series is not periodic
   or has less than two periods . But both is definitely true... If I add one
   more value it works but this would falsen the forecast and lead to more
   problems since I use different granularities and had to add 8 more values in
   the worst case
   I have this problem only with the stlf algorithm. Holt Winters and other
   ones work perfectly...
   Do you know any solution for this problem?
   A fast answer would be really great because I am very close to the release
   of my work for my university
   Kind regards and thanks in advance
   Christian


   Ihr WEB.DE Postfach immer dabei: die kostenlose WEB.DE Mail App für iPhone
   und Android.
   [1]https://produkte.web.de/freemail_mobile_startseite/

References

   1. https://produkte.web.de/freemail_mobile_startseite/
__
R-help@r-project.org mailing list
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] MS-DOS script R

2012-07-05 Thread FJ M


I have the following in a batch file TLT.BAT:
 
C:\Program Files\R\R-2.13.2\bin\x64\R.exe CMD BATCH
C:\Users\Frank\Documents\R\Scripts\TLT_2012.txt 
C:\Users\Frank\Documents\R\Scripts\TLT_2012.out
PAUSE 
 
The TLT_2012.txt has my R code in it. The TLT_2012.out has the output from R. 
Look to TLT_2012.out for problems with your batch file.
 
Frank
Chicago, IL
 

 Date: Wed, 4 Jul 2012 05:44:01 -0700
 From: cindy.dolom...@insa-lyon.fr
 To: r-help@r-project.org
 Subject: [R] MS-DOS  script R
 
 Hi,
 I would like to run R with a script from MS-DOS.
 R is in My Documents and my script too.
 How to do?
 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/MS-DOS-script-R-tp4635398.html
 Sent from the R help mailing list archive at Nabble.com.
 
 __
 R-help@r-project.org mailing list
 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
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] Maximum Likelihood Estimation Poisson distribution mle {stats4}

2012-07-05 Thread S Ellison

 -Original Message-
  sample.mean- sum(x*y)/sum(y)
  sample.mean
 [1] 3.5433
 
 *This is the contradiction!! *
 Here I am getting the estimate as 3.5433(which is reasonable 
 as most of the values are clustered around 3), but mle code 
 gives the estimate 11.545(which may not be correct as this is 
 out side the range 0:10)
 
 Why this contradiction? 
 
 

Ermm.. the sample mean is mean(y) which is 11.545

I deduce that you and the help page have different views on what the sample y 
represents.

i also note that x does not figure at all in the help page's log-likelihood, 
suggesting that y is a simple set of counts, whereas you have interpreted x as 
the number of instances of each y. That appears not to be the case.

S


 

***
This email and any attachments are confidential. Any use...{{dropped:8}}

__
R-help@r-project.org mailing list
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] Maximum Likelihood Estimation Poisson distribution mle {stats4}

2012-07-05 Thread peter dalgaard


On Jul 5, 2012, at 10:48 , chamilka wrote:

 Hi everyone!
 I am using the mle {stats4} to estimate the parameters of distributions by
 MLE method. I have a problem with the examples they provided with the
 mle{stats4} html files. Please check the example and my question below!
 *Here is the mle html help file * 
 http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html
 http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html 
 
 *In the example provided with the help *
 od - options(digits = 5)
 x - 0:10*#generating Poisson counts*
 y - c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)  *#generating the
 frequesncies*
 
 ## Easy one-dimensional MLE:
 nLL - function(lambda) -sum(stats::dpois(y, lambda, log=TRUE))  *#they
 define the Poisson negative loglikelihood*
 fit0 - mle(nLL, start = list(lambda = 5), nobs = NROW(y)) * #they
 estimate the Poisson parameter using mle*
 fit0  *#they call the output*
 
 Call:
 mle(minuslogl = nLL, start = list(lambda = 5), nobs = NROW(y))
 
 Coefficients:
 lambda 
 11.545   * #this is their estimated Lambda Vallue.*
 
 *Now my question is in a Poisson distribution the Maximum Likelihood
 estimator of the mean parameter lambda is  the sample mean, so if we
 calculate the sample mean of that generated Poisson distribution manually
 using R we get  the below!*
 
 sample.mean- sum(x*y)/sum(y)
 sample.mean
 [1] 3.5433
 
 *This is the contradiction!! *
 Here I am getting the estimate as 3.5433(which is reasonable as most of the
 values are clustered around 3), but mle code gives the estimate 11.545(which
 may not be correct as this is out side the range 0:10)
 
 Why this contradiction? 

You misunderstand the setup. y are 11 Poisson counts, x is a dose variable used 
further down in the example. So

 mean(y)
[1] 11.54545

Your sample.mean would be relevant if there were 127 count measurements, 26 of 
which were 0, 17 were 1, etc. But then the likelihood would be different:

 x - 0:10
 nLL - function(lambda) -sum(y*stats::dpois(x, lambda, log=TRUE))
 mle(nLL, start = list(lambda = 5), nobs = NROW(y))

Call:
mle(minuslogl = nLL, start = list(lambda = 5), nobs = NROW(y))

Coefficients:
 lambda 
3.54328 




 
 --
 View this message in context: 
 http://r.789695.n4.nabble.com/Maximum-Likelihood-Estimation-Poisson-distribution-mle-stats4-tp4635464.html
 Sent from the R help mailing list archive at Nabble.com.
 
 __
 R-help@r-project.org mailing list
 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.

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

__
R-help@r-project.org mailing list
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] Comparing crossing survival curves

2012-07-05 Thread Vito Muggeo (UniPa)


hi isabel,
You have to decide if focus is on the survival curves or hazards.. 
Crossing hazards do not imply crossing survival curves


If you are dealing with crossing hazards, and you are interested in 
testing for an effect of a covariate (presumably with a crossing hazard 
effect), then a standard Cox model framework based on the martingale 
representation (start, stop, event) (rather than (time, event)) will 
suffice


Finally, if you are interested in estimating the crossing point you 
could have a look to the package flexCrossHaz (currently in the 
Archive.. Let me know if you are interested in becoming maintainer..:-) 
)


http://cran.r-project.org/src/contrib/Archive/flexCrossHaz/

best,
vito


Il 05/07/2012 12.37, Isabel Borges ha scritto:


 Hi
I want to compare the survival curves in two groups. Because the hazards are
not proportional (the curves cross) the log rank test or Cox proportional
hazard test are not suitable. How should such curves be compared? Comands
are welcome
Thanks in advance
__
R-help@r-project.org mailing list
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.



--

Vito M.R. Muggeo
Dip.to Sc Statist e Matem `Vianelli'
Università di Palermo
viale delle Scienze, edificio 13
90128 Palermo - ITALY
tel: 091 23895240
fax: 091 485726
http://dssm.unipa.it/vmuggeo

__
R-help@r-project.org mailing list
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] 2D image correlation/Packages for 2D CCA?

2012-07-05 Thread Grace, Miriam

Hello,

I was just wondering if anyone could recommend a package for R that calculates 
2D image correlation, e.g. by 2D canonical correspondence analysis?

Thanks a lot!

MG

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Import single variables from SPSS

2012-07-05 Thread Marion Wenty

Dear all,
I have got a very big SPSS dataframe and I would like to just import one or
a few variables (the dataframe has got a lot of colums).
I used the package foreign but I couldn't find anything in there for my
problem.
Thank you very much for your help in advance.
Marion

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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 analyse non parametric test

2012-07-05 Thread John Kane

Please read the posting guidelines.  So far we have no idea of what you are 
doing or how you are doing it.

John Kane
Kingston ON Canada


 -Original Message-
 From: anilgv...@gmail.com
 Sent: Thu, 5 Jul 2012 15:11:20 +0530
 To: r-help@r-project.org
 Subject: [R] how to analyse non parametric test
 
 Please i am Anilkumar G.V studieng MBA final sem for this data i want to
 find out non parametric tests please help me
 
 --
 Anilkumar G.V
 Jr,MBA


Share photos  screenshots in seconds...
TRY FREE IM TOOLPACK at http://www.imtoolpack.com/default.aspx?rc=if1
Works in all emails, instant messengers, blogs, forums and social networks.

__
R-help@r-project.org mailing list
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] EM algorithm to find MLE of coeff in mixed effects model

2012-07-05 Thread John Kane

I don't believe that R-help permits pdf files.  A useful workaround is to post 
it to a file hosting site like MediaFire and post the link here.
John Kane
Kingston ON Canada

 -Original Message-
 From: jimmycl...@gmail.com
 Sent: Wed, 4 Jul 2012 22:56:02 -0400
 To: pauljoh...@gmail.com
 Subject: Re: [R] EM algorithm to find MLE of coeff in mixed effects model

 Dear Paul,

 Thank you for your suggestion. I was moved by the fact that people are so
 nice to help learners and ask for nothing.
 With your help, I made some changes to my code and add more comments, try
 to make things more clear.
 If this R email list allow me to upload a pdf file to illustrate the
 formula, it will be great.
 The reason I do not use lme4 is that later I plan to use this for a more
 complicated model (Y,T), Y is the same response of mixed model and T is a
 drop out process.
 (Frankly I did it for the more complicated model first and got NaN
 hessian
 after one iteration, so I turned to the simple model.)
 In the code, the m loop is the EM iterations. About efficiency, thank you
 again for pointing it out. I compared sapply and for loop, they are tie
 and
 for loop is even better sometimes.
 In a paper by Bates, he mentioned that the asymptotic properties of beta
 is
 kind of independent of the other two parameters. But it seems that paper
 was submitted but I did not find it on google scholar.
 Not sure if it is the reason for my results. That is why I hope some
 expert
 who have done some simulation similar may be willing to give some
 suggestion.
 I may turn to other methods to calculate the conditional expection of the
 latent variable as the same time.

 Modified code is as below:

 # library(PerformanceAnalytics)
 # install.packages(gregmisc)
 # install.packages(statmod)
 library(gregmisc)
 library(MASS)
 library(statmod)

 ## function to calculate loglikelihood
 loglike - function(datai = data.list[[i]], vvar = var.old,
 beta = beta.old, psi = psi.old) {
 temp1 - -0.5 * log(det(vvar * diag(nrow(datai$Zi)) + datai$Zi %*%
 psi %*% t(datai$Zi)))
 temp2 - -0.5 * t(datai$yi - datai$Xi %*% beta) %*% solve(vvar *
 diag(nrow(datai$Zi)) + datai$Zi %*% psi %*% t(datai$Zi)) %*%
 (datai$yi - datai$Xi %*% beta)
 temp1 + temp2
 }

 ## functions to evaluate the conditional expection, saved as Efun v2.R
 ## Eh1new=E(bibi')
 ## Eh2new=E(X'(y-Zbi))
 ## Eh3new=E(bi'Z'Zbi)
 ## Eh4new=E(Y-Xibeta-Zibi)'(Y-Xibeta-Zibi)
 ## Eh5new=E(Xibeta-yi)'Zibi
 ## Eh6new=E(bi)

 Eh1new - function(datai = data.list[[i]], weights.m = weights.mat) {
 bi - datai$b
 tempb - bi * rep(sqrt(weights.m[, 1] * weights.m[, 2]),
 2)  #quadratic b, so needsqrt
 t(tempb) %*% tempb/pi
 }  # end of Eh1

 # Eh2new=E(X'(y-Zbi))
 Eh2new - function(datai = data.list[[i]], weights.m = weights.mat) {
 bi - datai$b
 tempb - bi * rep(weights.m[, 1] * weights.m[, 2], 2)
 tt - t(datai$Xi) %*% datai$yi - t(datai$Xi) %*% datai$Zi %*%
 colSums(tempb)/pi
 c(tt)
 }  # end of Eh2

 # Eh3new=E(b'Z'Zbi)
 Eh3new - function(datai = data.list[[i]], weights.m = weights.mat) {
 bi - datai$b
 tempb - bi * rep(sqrt(weights.m[, 1] * weights.m[, 2]),
 2)  #quadratic b, so need sqrt
 sum(sapply(as.list(data.frame(datai$Zi %*% t(tempb))),
 function(s) {
 sum(s^2)
 }))/pi
 }  # end of Eh3

 # Eh4new=E(Y-Xibeta-Zibi)'(Y-Xibeta-Zibi)
 Eh4new - function(datai = data.list[[i]], weights.m = weights.mat,
 beta = beta.old) {
 bi - datai$b
 tt - sapply(as.list(ata.frame(c(datai$yi - datai$Xi %*%
 beta) - datai$Zi %*% t(bi))), function(s) {
 sum(s^2)
 }) * (weights.m[, 1] * weights.m[, 2])
 sum(tt)/pi
 }  # end of Eh4

 Eh4newv2 - function(datai = data.list[[i]], weights.m = weights.mat,
 beta = beta.old) {
 bi - datai$b
 v - weights.m[, 1] * weights.m[, 2]
 temp - c()
 for (i in 1:length(v)) {
 temp[i] - sum(((datai$yi - datai$Xi %*% beta - datai$Zi %*%
 bi[i, ]) * sqrt(v[i]))^2)
 }
 sum(temp)/pi
 }  # end of Eh4

 # Eh5new=E(Xibeta-yi)'Zib
 Eh5new - function(datai = data.list[[i]], weights.m = weights.mat,
 beta = beta.old) {
 bi - datai$b
 tempb - bi * rep(weights.m[, 1] * weights.m[, 2], 2)
 t(datai$Xi %*% beta - datai$yi) %*% (datai$Zi %*% t(tempb))
 sum(t(datai$Xi %*% beta - datai$yi) %*% (datai$Zi %*%
 t(tempb)))/pi
 }

 Eh6new - function(datai = data.list[[i]], weights.m = weights.mat) {
 bi - datai$b
 tempw - weights.m[, 1] * weights.m[, 2]
 for (i in 1:nrow(bi)) {
 bi[i, ] - bi[i, ] * tempw[i]
 }
 colMeans(bi)/pi
 }  # end of Eh6

 ## the main R script
 ### initial the values and generate the data
 ##
 n - 100   #number of
 observations
 beta - c(-0.5, 1)   #true coefficient of
 fixed
 effects
 vvar - 2

Re: [R] Return on Stock Market

if(!require(TTR)){install.packages(TTR); library(TTR)}
? ROC

Michael

On Wed, Jul 4, 2012 at 11:20 PM, Akhil dua akhil.dua...@gmail.com wrote:
 Hello Every one
 I have data on Stock prices and I want to calculate the return on all the
 stocks
 and then replace all the stock prices with the returns

 can any one tell me how to do

 My data is in the format given below

 Date  Stock1  Stock2  Stock3
 01/01/20001  2  3
 01/02/20005  6  7
 01/03/20001  2  3
 01/04/20005  6  7


 Thanks

 [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 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
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] Create a function automatically from lm formula and coefficients?

2012-07-05 Thread taheri

Hi,
I need to create a function from lm formula and coefficients to use it in my
c++ code later.
but when I do it as you said 
require(rms) 
f - ols( ) 
g - Function(f) 
g(x1=2,x2=3,...) 
I realize that it didn't give me the same result as predict.lm?
how can I reach a function to give me the same results in predict?
I really need it, please answer me.

Regards,
Taheri 

--
View this message in context: 
http://r.789695.n4.nabble.com/Create-a-function-automatically-from-lm-formula-and-coefficients-tp4433854p4635470.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Hosmer-Lemeshow test for Cox model

2012-07-05 Thread jane.wong

Dear list,

Usually we use Hosmer-Lemeshow test to test the goodness of fit for logistic
model, but if I use it to test for Cox model, how can I get the observed
probability for each group?
Suppose I calculated the 5-year predicted probability using Cox model, then
I split the dataset into 10 group according to this predicted probability.
We should compare the observed probability with predicted probability within
each group,but how to calculate this observed probability, should I use
Kaplan-Meier to estimate it?  how should I modify the following
program,thanks.

hosmerlem = function(y, yhat, g=10) {
  cutyhat = cut(yhat,
 breaks = quantile(yhat, probs=seq(0,
   1, 1/g)), include.lowest=TRUE)
  obs = xtabs(cbind(1 - y, y) ~ cutyhat)
  expect = xtabs(cbind(1 - yhat, yhat) ~ cutyhat)
  chisq = sum((obs - expect)^2/expect)
  P = 1 - pchisq(chisq, g - 2)
  return(list(chisq=chisq,p.value=P))
}

--
View this message in context: 
http://r.789695.n4.nabble.com/Hosmer-Lemeshow-test-for-Cox-model-tp4635482.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] function curve() swap axes

2012-07-05 Thread Boudewijn Verkooijen

Dear all,

I'm using the curve() function to plot discharge Q against water depth a.
However, I would like to have a graph of water depth a plotted against
discharge Q. How can this be done?
Minimal working example:
S0 = 0.004
n = 0.04
tanalpha = 1.4/1.5
par(mar = c(5,5,1,1)) # b, l, t, r
curve((sqrt(S0)/n)*(0.035+(0.7+(x-0.1)/tanalpha)*(x-0.1))*((0.035+(0.7+(x-0.1)/tanalpha)*(x-0.1))/(2*sqrt((0.7/2)^2+0.1^2)+2*sqrt((x-0.1)^2+((x-0.1)/tanalpha)^2)))^(2/3),0.1,1.55,
lwd = 3, col = royalblue4, ann = F, axes = T)
title(xlab = parse(text='a~bgroup([, m, ])'))
title(ylab = parse(text='Q~bgroup([, m^3/s, ])'))
box()
I tried to find the inverse function, but that doesn't seem to exist.
Thank you for support,
Boudewijn

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Maximum Likelihood Estimation Poisson distribution mle {stats4}

2012-07-05 Thread chamilka

Thank you S Ellison-2 for your reply. I will understand it with Prof.Peter
Dalgaard's answer.. 

--
View this message in context: 
http://r.789695.n4.nabble.com/Maximum-Likelihood-Estimation-Poisson-distribution-mle-stats4-tp4635464p4635484.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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 check convergence of arima model

2012-07-05 Thread Sajeeka Nanayakkara

Thanks for your advice. 

Sajeeka

 From: Bert Gunter gunter.ber...@gene.com

Cc: Rui Barradas ruipbarra...@sapo.pt; r-help@r-project.org 
r-help@r-project.org 
Sent: Thursday, July 5, 2012 12:43 AM
Subject: Re: [R] how to check convergence of arima model

1. This is a statistical question. Please do not post further to this list. It 
is about R, and you have summarily dismissed all attempts to answer your R 
questions as unhelpful. So you need to look elsewhere.

2. Consult a statistician -- you use the statistical words, but do not 
understand what they mean. There often is NO single model that both maximizes 
likelihood and minimizes AIC (depending on the models one fits).

-- Bert

ote:

Hi,

Thanks for your explanation. But still I didn't get the answer which I need.

You have mentioned the code which can obtain AIC values for all models at 
once. My question is; the procedure of selecting the suitable model to predict 
using R package.

If I select the model which produces the smallest AIC and maximized log 
likelihood values, as the suitable model is it correct?

Sajeeka Nanayakkara

 From: Rui Barradas ruipbarra...@sapo.pt

Cc: r-help@r-project.org
Sent: Wednesday, July 4, 2012 3:38 PM
Subject: Re: [R] how to check convergence of arima model

Hello,

Put the fitted models in a list and then use lapply with AIC(). Like this

set.seed(1)
x - 1:100 + sqrt(1:100 + runif(100)) + rnorm(100)
models - list()
models[[1]] - arima(diff(x), order = c(1, 0, 0))  # Just to show
models[[2]] - arima(diff(x), order = c(1, 0, 1))  # several
models[[3]] - arima(diff(x), order = c(2, 0, 2))  # models
models[[4]] - arima(diff(x), order = c(2, 0, 3))
lapply(models, AIC)

Or run each model at a time through AIC(), whichever suits better.

Hope this helps

Rui Barradas

Em 04-07-2012 10:22, Sajeeka Nanayakkara escreveu:
 Hi,

 I need to predict exchange rates using time series. So according to ACF
 and PACF knowledge, mixed model (ARIMA) be the appropriate and now, I
 need to find order of the model (p,d,q). So, several models were fitted
 to select the suitable model using arima().

 Could you please tell me the procedure of selecting the correct order as
 I don't have enough time to search?

 Thank you.

 Sajeeka Nanayakkara

 *From:* Rui Barradas ruipbarra...@sapo.pt

 *Cc:* r-help@r-project.org
 *Sent:* Wednesday, July 4, 2012 2:58 PM
 *Subject:* Re: [R] how to check convergence of arima model

 Hello,

 Inline.

 Em 04-07-2012 09:35, Sajeeka Nanayakkara escreveu:
   Hi,

   Sorry, since I didn't see the earlier message I resend it.

   I read the help page that you mentioned. But the problem is for all
   models, code is zero. According to that, all models were converged.
   Considering AIC value the best model is selected.

 No, arima() does not select models by AIC. That is the default behavior
 of ar(); arima() does NOT select models, it selects, using optim, values
 for the parameters of a specified model. You must choose the orders
 yourself.

 Hope this helps,

 Rui Barradas

   Is that correct procedure?

   The R code which was used is;
   model1-arima(rates,c(1,1,1))
   model1
   model1$code
   [1] 0

   Sajeeka Nanayakkara

   *From:* Rui Barradas ruipbarra...@sapo.pt mailto:ruipbarra...@sapo.pt

   *Cc:* r-help@r-project.org mailto:r-help@r-project.org
   *Sent:* Wednesday, July 4, 2012 2:01 PM
   *Subject:* Re: [R] how to check convergence of arima model

   Hello,

   Sorry, but do you read the answers to your posts?
   Inline.

   Em 04-07-2012 08:02, Sajeeka Nanayakkara escreveu:
     I have already fitted several models
     using R code; arima(rates,c(p,d,q))

   And I have already answered to a question starting like this yesterday.
   In the mean time, the subject line changed.

     As I heard, best model produce the
     smallest AIC value, but maximum likelihood estimation procedure
 optimizer
     should converge.

     How to check whether maximum likelihood estimation procedure
   optimizer has converged or not?

   Yes, it was this question, the subject line was 'question'...

   ... And the answer was: read the manual, that I quoted, by the way.

   It now changed to: read the manual, period.

   Rui Barradas

        [[alternative HTML version deleted]]

     __
     R-help@r-project.org mailto:R-help@r-project.org
 mailto:R-help@r-project.org mailto:R-help@r-project.org mailing list
     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] i need help in documentation

2012-07-05 Thread purushothaman

Hi,

i am new in R development ,

so i need help in documentation from comments in R file

for example

sample-function(filepath)
{

##title read csv file
##author Purushoth
##description this function is used to read a csv file
output-read.csv(filepath)
   return(output)
}

i need to get html document file using this comments


Thanks 
B.Purushothaman

--
View this message in context: 
http://r.789695.n4.nabble.com/i-need-help-in-documentation-tp4635471.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] vector entry in matix

2012-07-05 Thread Thomas C.

hi,

i'm trying to figure out if there's any possibility to write a whole vector
into a matrix or data.frame or something like that. i don't mean
transormation. Here an example:

   [,1]  [,2]
[1,] a d
[2,] b e
[3,] c f


where e.g.  a is a-c(0,1) vector of length 2, b a vector of length 4,... (i
know that the matrix enties are strings :)). i'm trying to put some
variables into a matrix or data.frame, but i couldn't handle it. is
something like that possible in R?

thanks for your help!

--
View this message in context: 
http://r.789695.n4.nabble.com/vector-entry-in-matix-tp4635478.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] skipped correlation

2012-07-05 Thread qinjiaolong

hello,Everyone!
I am a freshman to use R. Can anybody tell me where has scor function which 
achieves the skipped correlation?
Thank you very much!

Bset wishes!
Jiaolong Qin
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Invalid input in 'utf8towcs' when saving script file

2012-07-05 Thread Marine Andersson

Hello,

When I try to save my script file before closing the R console session I get 
this error.

Error: invalid input 'C:\Documents and Settings\\\datafile' in 
'utf8towcs'  

Does anyone know what can cause this error?

I use the RGui  (R verison 2.14.0) in Windows and the problem appears when I 
try to re-save the script file. Using Save as and rename it works. 



Kind regards,

Marine Andersson
__
R-help@r-project.org mailing list
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] function curve() swap axes

2012-07-05 Thread Duncan Murdoch


On 05/07/2012 8:34 AM, Boudewijn Verkooijen wrote:

Dear all,

I'm using the curve() function to plot discharge Q against water depth a.
However, I would like to have a graph of water depth a plotted against
discharge Q. How can this be done?
curve() is designed for plotting y vs x where y is a function of x, so I 
think you need to do it yourself.  Simply compute a vector of a values 
using seq(), compute the corresponding Q values using your formula, and 
then use


plot(Q, a, type=l)

You can add the lwd and other arguments too if you like.

Duncan Murdoch

Minimal working example:
S0 = 0.004
n = 0.04
tanalpha = 1.4/1.5
par(mar = c(5,5,1,1)) # b, l, t, r
curve((sqrt(S0)/n)*(0.035+(0.7+(x-0.1)/tanalpha)*(x-0.1))*((0.035+(0.7+(x-0.1)/tanalpha)*(x-0.1))/(2*sqrt((0.7/2)^2+0.1^2)+2*sqrt((x-0.1)^2+((x-0.1)/tanalpha)^2)))^(2/3),0.1,1.55,
lwd = 3, col = royalblue4, ann = F, axes = T)
title(xlab = parse(text='a~bgroup([, m, ])'))
title(ylab = parse(text='Q~bgroup([, m^3/s, ])'))
box()
I tried to find the inverse function, but that doesn't seem to exist.
Thank you for support,
Boudewijn

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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
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] empty cell when running GEE for binary data

2012-07-05 Thread Yue

Hi all,

My data are binary and within-subject correlated; there are three factors of
interest and two of them are within-subject. So, I have considered modelling
the data using a binomial regression with a GEE approach (which can be
achieved using the function geeglm). One problem is that I got some empty
cells, so I can't simply use logit as a link function. I was wondering if
you know any existing R solution for this? 

also, I tired to use cauchit as the link function, but it turned out that
within the function geeglm cauchit is not available. Any idea on this? 

Many thanks!
Yue

--
View this message in context: 
http://r.789695.n4.nabble.com/empty-cell-when-running-GEE-for-binary-data-tp4635483.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Maximum Likelihood Estimation Poisson distribution mle {stats4}

2012-07-05 Thread chamilka

Thank you very much Professor .Peter Dalgaard for your kind explanations..
This made my work easy.. I am struggling with this for more than 2 days and
now I got the correct reply. 
Thank again. 

--
View this message in context: 
http://r.789695.n4.nabble.com/Maximum-Likelihood-Estimation-Poisson-distribution-mle-stats4-tp4635464p4635485.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] 7 days confusion over lists

2012-07-05 Thread Wageningen-eR

Hello,

I am a Masters student and I am working on my thesis modelling smallholder
farms using a program in R.  I have modified the original code and I am
having some issues with lists that I cannot figure out.

Originally, I had list file defining lists such as: Param, Crop1, Crop1,
Soil, etc.  (ex. Param - list() ).  Their subsets were listed as
Crop1$CContent for example and there was quite a few of them.  There is a
run file that gets the list file going in the following code:

#--Initialising the lists to store variable values
tmp - init_lists()
Param   - tmp[[1]]
Crop1   - tmp[[2]]
Fert- tmp[[3]]
Meteo   - tmp[[4]]
Soil- tmp[[5]]
RainPattern - tmp[[6]]
Crop2   - tmp[[7]]
Cropres - tmp[[8]]
rm(tmp)

The problem here is that the lists get confused with each other; that is
elements of Soil appear in Crop2.  In the run file, I changed the order of
the lists (for example Fert - tmp[[5]] and Crop2 -tmp[[3]]) and it changes
which ones are confused with what; with some lists not being confused at
all.  I cannot find why this is a problem as the tmps are removed at the end
of the command list shown below and each element is clearly defined as a
part of its given list with (list name)$(Sublist maybe)$(specific element
name)

Either way, I changed the original lists to be more specific, for example:

Crop$ - list(
CContent - NA,
NContent - NA,
PContent - NA,
KContent - NA,
K - list(
uptakegivenN,
uptakegivenP),
dryMatterContent
...etc.

The issue then became that it stops at a certain point accepting the
assigned values and keeps them as null.  That is, the list contains an
element that states Crop2$minYieldN - NA but the value becomes NULL when it
is run.   Also, the list, say Param, contains both:

[[1]]
[1] NA

[[2]]
[1] NA

[[3]]
[[3]][[1]]
[1] NA

[[3]][[2]]
[1] NA
 
and some of the value names (up to a point)

$inertCRTR
[1] 0.001

$humificationFactor
[1] 0.25

$fractionStabilisedSOMC
[1] 0.2

$growthEffectMicroorganisms
[1] 0.6

Is it perhaps that the list is too long?  Please let me know if anything
comes to mind, it would be great help.

Thank you!


Regards,

-Igor Milosavljevic
Wageningen University and Research Center

--
View this message in context: 
http://r.789695.n4.nabble.com/7-days-confusion-over-lists-tp4635489.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Hosmer-Lemeshow test for Cox model

2012-07-05 Thread Frank Harrell

Any method that requires binning is problematic.  Instead, take a look at the
calibrate function in the rms package.  There is a new option for continuous
calibration curves for survival models. 
Frank

jane.wong wrote
 
 Dear list,
 
 Usually we use Hosmer-Lemeshow test to test the goodness of fit for
 logistic model, but if I use it to test for Cox model, how can I get the
 observed probability for each group?
 Suppose I calculated the 5-year predicted probability using Cox model,
 then I split the dataset into 10 group according to this predicted
 probability. We should compare the observed probability with predicted
 probability within each group,but how to calculate this observed
 probability, should I use Kaplan-Meier to estimate it?  how should I
 modify the following program,thanks.
 
 hosmerlem = function(y, yhat, g=10) {
   cutyhat = cut(yhat,
  breaks = quantile(yhat, probs=seq(0,
1, 1/g)), include.lowest=TRUE)
   obs = xtabs(cbind(1 - y, y) ~ cutyhat)
   expect = xtabs(cbind(1 - yhat, yhat) ~ cutyhat)
   chisq = sum((obs - expect)^2/expect)
   P = 1 - pchisq(chisq, g - 2)
   return(list(chisq=chisq,p.value=P))
 }
 


-
Frank Harrell
Department of Biostatistics, Vanderbilt University
--
View this message in context: 
http://r.789695.n4.nabble.com/Hosmer-Lemeshow-test-for-Cox-model-tp4635482p4635492.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Invalid input in 'utf8towcs' when saving script file

2012-07-05 Thread Duncan Murdoch


On 05/07/2012 10:21 AM, Marine Andersson wrote:

Hello,

When I try to save my script file before closing the R console session I get 
this error.

Error: invalid input 'C:\Documents and Settings\\\datafile' in 
'utf8towcs'

Does anyone know what can cause this error?


I imagine it is converting some non-ascii character.  But 2.14.0 isn't 
current, so it might be a bug that has since been fixed.


Duncan Murdoch



I use the RGui  (R verison 2.14.0) in Windows and the problem appears when I 
try to re-save the script file. Using Save as and rename it works.



Kind regards,

Marine Andersson
__
R-help@r-project.org mailing list
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
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] function curve() swap axes



On Jul 5, 2012, at 8:34 AM, Boudewijn Verkooijen wrote:


Dear all,

I'm using the curve() function to plot discharge Q against water  
depth a.

However, I would like to have a graph of water depth a plotted against
discharge Q. How can this be done?
Minimal working example:
S0 = 0.004
n = 0.04
tanalpha = 1.4/1.5
par(mar = c(5,5,1,1)) # b, l, t, r
curve((sqrt(S0)/n)*(0.035+(0.7+(x-0.1)/ 
tanalpha)*(x-0.1))*((0.035+(0.7+(x-0.1)/tanalpha)*(x-0.1))/ 
(2*sqrt((0.7/2)^2+0.1^2)+2*sqrt((x-0.1)^2+((x-0.1)/ 
tanalpha)^2)))^(2/3),0.1,1.55,

lwd = 3, col = royalblue4, ann = F, axes = T)
title(xlab = parse(text='a~bgroup([, m, ])'))
title(ylab = parse(text='Q~bgroup([, m^3/s, ])'))
box()
I tried to find the inverse function, but that doesn't seem to exist.


R does not perform computer algebra. If you wanted a numerical  
approach, you can construct a close fit to that function with  
approxfun() and then reverse the x and y roles to create an inverse.  
Actually, since curve returns a list with x and y components you could  
also do this:


xycurv - curve((sqrt(S0)/n)*(0.035+(0.7+(x-0.1)/ 
tanalpha)*(x-0.1))*((0.035+(0.7+(x-0.1)/tanalpha)*(x-0.1))/ 
(2*sqrt((0.7/2)^2+0.1^2)+2*sqrt((x-0.1)^2+((x-0.1)/ 
tanalpha)^2)))^(2/3),0.1,1.55,

+ lwd = 3, col = royalblue4, ann = F, axes = T)

plot(xycurv$y, xycurv$x)


--

David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
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] Different level set when predicting with e1071's Naive Bayes classifier

2012-07-05 Thread Joao Azevedo

Hi!

I'm using the Naive Bayes classifier provided by the e1071 package (
http://cran.r-project.org/web/packages/e1071) and I've noticed that the
predict function has a different behavior when the level set of the columns
used for prediction is different from the ones used for fitting. From
inspecting the predict.naiveBayes I came to the conclusion that this is due
to the conversion of factors to their internal codes using the data.matrix
function. For example, consider the following piece of R code:

 library(mlbench)
 library(e1071)
 data(HouseVotes84)
 model - naiveBayes(Class ~ ., data = HouseVotes84)
 head(HouseVotes84)
   Class   V1 V2 V3   V4   V5 V6 V7 V8 V9 V10  V11  V12 V13 V14 V15  V16
1 republicann  y  nyy  y  n  n  n   y NAy   y   y   ny
2 republicann  y  nyy  y  n  n  n   nny   y   y   n NA
3   democrat NA  y  y NAy  y  n  n  n   nyn   y   y   nn
4   democratn  y  yn NA  y  n  n  n   nyn   y   n   ny
5   democraty  y  yny  y  n  n  n   ny NA   y   y   yy
6   democratn  y  yny  y  n  n  n   nnn   y   y   yy
 predict(model, HouseVotes84[1,-1])
[1] republican
Levels: democrat republican
 new.data - data.frame(V1=n, V2=y, V3=n, V4=y, V5=y, V6=y,
V7=n, V8=n, V9=n, V10=y, V11=NA_character_, V12=y, V13=y,
V14=y, V15=n, V16=y, stringsAsFactors=TRUE)
 predict(model, new.data)
[1] democrat
Levels: democrat republican

I haven't used other classification methods in R, so I'm unsure if this is
what is expected from the application of the predict function. Is this a
bug or the expected behavior?

Thanks!

--
Joao.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Adjusting MaxNwts in MICE Package

2012-07-05 Thread jtizzle36

Hi Rachel,

I am having the same problem! My data set is positing around 4400 weights
required.

Have you found a solution to this? Does anyone else know how to adjust this
default to run MICE successfully?

Thanks,
Justin

--
View this message in context: 
http://r.789695.n4.nabble.com/Adjusting-MaxNwts-in-MICE-Package-tp3178628p4635495.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] i need help in documentation

R does not, to my knowledge, have anything quite like Python's
docstrings (which seems to be what you are talking about) but you
might look at Roxygen2 on CRAN which should get you started in this
direction.

Best,
Michael

On Thu, Jul 5, 2012 at 7:37 AM, purushothaman purushothama...@ge.com wrote:
 Hi,

 i am new in R development ,

 so i need help in documentation from comments in R file

 for example

 sample-function(filepath)
 {

 ##title read csv file
 ##author Purushoth
 ##description this function is used to read a csv file
 output-read.csv(filepath)
return(output)
 }

 i need to get html document file using this comments


 Thanks
 B.Purushothaman

 --
 View this message in context: 
 http://r.789695.n4.nabble.com/i-need-help-in-documentation-tp4635471.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 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
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] vector entry in matix

It is possible to put dimensionality on a list (i.e., a generic
vector), which might be what you're looking for.

x - list(1:4, letters[1:4], function(x,y) x + y, rnorm(50))
dim(x) - c(2,2)

x[[1,2]]

x[[2,2]]

x[[3,2]] # Error

Best,
Michael

On Thu, Jul 5, 2012 at 8:19 AM, Thomas C. thomas.csa...@gmail.com wrote:
 hi,

 i'm trying to figure out if there's any possibility to write a whole vector
 into a matrix or data.frame or something like that. i don't mean
 transormation. Here an example:

[,1]  [,2]
 [1,] a d
 [2,] b e
 [3,] c f


 where e.g.  a is a-c(0,1) vector of length 2, b a vector of length 4,... (i
 know that the matrix enties are strings :)). i'm trying to put some
 variables into a matrix or data.frame, but i couldn't handle it. is
 something like that possible in R?

 thanks for your help!

 --
 View this message in context: 
 http://r.789695.n4.nabble.com/vector-entry-in-matix-tp4635478.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 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
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] 7 days confusion over lists

Could you make a reproducible example?
[http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example]
I can't run any of your code as is. A few comments inline.

On Thu, Jul 5, 2012 at 9:44 AM, Wageningen-eR igor.milosavlje...@wur.nl wrote:
 Hello,

 I am a Masters student and I am working on my thesis modelling smallholder
 farms using a program in R.  I have modified the original code and I am
 having some issues with lists that I cannot figure out.

 Originally, I had list file defining lists such as: Param, Crop1, Crop1,
 Soil, etc.  (ex. Param - list() ).  Their subsets were listed as
 Crop1$CContent for example and there was quite a few of them.  There is a
 run file that gets the list file going in the following code:

 #--Initialising the lists to store variable values
 tmp - init_lists()
 Param   - tmp[[1]]
 Crop1   - tmp[[2]]
 Fert- tmp[[3]]
 Meteo   - tmp[[4]]
 Soil- tmp[[5]]
 RainPattern - tmp[[6]]
 Crop2   - tmp[[7]]
 Cropres - tmp[[8]]
 rm(tmp)

 The problem here is that the lists get confused with each other; that is
 elements of Soil appear in Crop2.  In the run file, I changed the order of
 the lists (for example Fert - tmp[[5]] and Crop2 -tmp[[3]]) and it changes
 which ones are confused with what; with some lists not being confused at
 all.  I cannot find why this is a problem as the tmps are removed at the end
 of the command list shown below and each element is clearly defined as a
 part of its given list with (list name)$(Sublist maybe)$(specific element
 name)

 Either way, I changed the original lists to be more specific, for example:

 Crop$ - list(
 CContent - NA,
 NContent - NA,
 PContent - NA,
 KContent - NA,
 K - list(
 uptakegivenN,
 uptakegivenP),
 dryMatterContent
 ...etc.


This almost certainly doesn't work. Crop$ - ...  should be a syntax error.

 The issue then became that it stops at a certain point accepting the
 assigned values and keeps them as null.  That is, the list contains an
 element that states Crop2$minYieldN - NA but the value becomes NULL when it
 is run.   Also, the list, say Param, contains both:

 [[1]]
 [1] NA

 [[2]]
 [1] NA

 [[3]]
 [[3]][[1]]
 [1] NA

 [[3]][[2]]
 [1] NA

 and some of the value names (up to a point)

 $inertCRTR
 [1] 0.001

 $humificationFactor
 [1] 0.25

 $fractionStabilisedSOMC
 [1] 0.2

 $growthEffectMicroorganisms
 [1] 0.6

 Is it perhaps that the list is too long?  Please let me know if anything
 comes to mind, it would be great help.


No, it's not a length thing. It might be a partial matching thing though.

x - list()

x$a - 5

x$ab - 10

x$ba - 15

print(x$b) # where's x$b?

It's recommended to use the double `[[` in programming applications to
avoid this trouble.

Best,
Michael

 Thank you!


 Regards,

 -Igor Milosavljevic
 Wageningen University and Research Center

 --
 View this message in context: 
 http://r.789695.n4.nabble.com/7-days-confusion-over-lists-tp4635489.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 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
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] skipped correlation

library(sos)
findFun(scor)

will get you going in the right direction but I'm not sure I see a
scor function (I presume you're looking for the robust correlation
metric). Do you have a citation for such a function? For a work
around, robust::covRob gives robust covariance which possibly could be
scaled down to correlation.

Best,
Michael

On Thu, Jul 5, 2012 at 8:49 AM, qinjiaolong qinjiaol...@126.com wrote:
 hello,Everyone!
 I am a freshman to use R. Can anybody tell me where has scor function which 
 achieves the skipped correlation?
 Thank you very much!

 Bset wishes!
 Jiaolong Qin
 [[alternative HTML version deleted]]

 __
 R-help@r-project.org mailing list
 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
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] 7 days confusion over lists

2012-07-05 Thread Jeff Newmiller

I think you need to (re)read the posting guide and An Introduction to R and 
try posting again. Some food for thought:

a) You refer to list files, but this is not a standard term. As the PG says, 
you need to supply a self-contained example, which would either include 
internal objects in dput form, or text data in strings read as though from 
files (e.g. use the text argument).

b) You may benefit from using indexing by character strings rather than numeric 
index to avoid mixups in sequencing.

c) I think Crop$ is a typo?

d) The claim that it stops accepting the assigned values is more likely to be 
an error on your part than R being arbitrary. I may be going out on a limb 
here, but be sure you understand that modifications to data within functions 
are local, and you have to explicitly return changes if you want them to 
persist after the function returns.
---
Jeff NewmillerThe .   .  Go Live...
DCN:jdnew...@dcn.davis.ca.usBasics: ##.#.   ##.#.  Live Go...
  Live:   OO#.. Dead: OO#..  Playing
Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
/Software/Embedded Controllers)   .OO#.   .OO#.  rocks...1k
--- 
Sent from my phone. Please excuse my brevity.

Wageningen-eR igor.milosavlje...@wur.nl wrote:

Hello,

I am a Masters student and I am working on my thesis modelling
smallholder
farms using a program in R.  I have modified the original code and I am
having some issues with lists that I cannot figure out.

Originally, I had list file defining lists such as: Param, Crop1,
Crop1,
Soil, etc.  (ex. Param - list() ).  Their subsets were listed as
Crop1$CContent for example and there was quite a few of them.  There is
a
run file that gets the list file going in the following code:

#--Initialising the lists to store variable values
tmp - init_lists()
Param   - tmp[[1]]
Crop1   - tmp[[2]]
Fert- tmp[[3]]
Meteo   - tmp[[4]]
Soil- tmp[[5]]
RainPattern - tmp[[6]]
Crop2   - tmp[[7]]
Cropres - tmp[[8]]
rm(tmp)

The problem here is that the lists get confused with each other; that
is
elements of Soil appear in Crop2.  In the run file, I changed the order
of
the lists (for example Fert - tmp[[5]] and Crop2 -tmp[[3]]) and it
changes
which ones are confused with what; with some lists not being confused
at
all.  I cannot find why this is a problem as the tmps are removed at
the end
of the command list shown below and each element is clearly defined as
a
part of its given list with (list name)$(Sublist maybe)$(specific
element
name)

Either way, I changed the original lists to be more specific, for
example:

Crop$ - list(
CContent - NA,
NContent - NA,
PContent - NA,
KContent - NA,
K - list(
uptakegivenN,
uptakegivenP),
dryMatterContent
...etc.

The issue then became that it stops at a certain point accepting the
assigned values and keeps them as null.  That is, the list contains an
element that states Crop2$minYieldN - NA but the value becomes NULL
when it
is run.   Also, the list, say Param, contains both:

[[1]]
[1] NA

[[2]]
[1] NA

[[3]]
[[3]][[1]]
[1] NA

[[3]][[2]]
[1] NA
 
and some of the value names (up to a point)

$inertCRTR
[1] 0.001

$humificationFactor
[1] 0.25

$fractionStabilisedSOMC
[1] 0.2

$growthEffectMicroorganisms
[1] 0.6

Is it perhaps that the list is too long?  Please let me know if
anything
comes to mind, it would be great help.

Thank you!


Regards,

-Igor Milosavljevic
Wageningen University and Research Center

--
View this message in context:
http://r.789695.n4.nabble.com/7-days-confusion-over-lists-tp4635489.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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
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] reshape2 errors on data frame


  I've successfully reformatted data frames from long to wide with reshape2,
but this time I'm getting errors that I want to understand and resolve.
Here's the data frame structure and the results of the melt() and dcast()
functions:

str(waterchem)
'data.frame':   128412 obs. of  8 variables:
 $ site: Factor w/ 64 levels D-1,D-2,D-3,..: 1 1 1 1 1 1 1 ...
 $ sampdate: Date, format: 2007-12-12 2007-12-12 ...
 $ preeq0  : logi  TRUE TRUE TRUE TRUE TRUE TRUE ...
 $ param   : Factor w/ 37 levels Ag,Al,Alk_tot,..: 1 2 8 17 3 4 ...
 $ quant   : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...
 $ ceneq1  : logi  TRUE FALSE TRUE FALSE FALSE FALSE ...
 $ floor   : num  0 0.106 0 231 231 0.011 0 0 0 100 ...
 $ ceiling : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...

chem.melt - melt(waterchem, idvars = c('site', 'sampdate', 'preeq0', 'param', 
'ceneq1', 'floor', 'ceiling'))

Using site, preeq0, param, ceneq1 as id variables

chem.cast - dcast(chem.melt, site + sampdate + preeq0 + ceneq1 + floor + 
ceiling ~ param)

Error in eval(expr, envir, enclos) : object 'sampdate' not found

  Because these data have some censored data there is the logical indicator
(ceneq1) to identify censored and uncensored values the the interval ends
(floor and ceiling) for multiply censored values. One factor of analytical
interest whether the sampdate is pre- or post-event; that uses the logical
indicator preeq0.

  Please point out where my melt() and dcast() syntax was incorrect. I will
provide more information if needed.

TIA,

Rich

__
R-help@r-project.org mailing list
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] empty cell when running GEE for binary data

2012-07-05 Thread Özgür Asar

Dear Yu,

What do you mean exactly by exmpty cell ?

But you can try, the following packages which might help you: gee and yags.
But I am not sure.

Best
Ozgur

--
View this message in context: 
http://r.789695.n4.nabble.com/empty-cell-when-running-GEE-for-binary-data-tp4635483p4635504.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Fast trace of inverse

2012-07-05 Thread Doran, Harold

Suppose I have a square matrix A like the toy below

set.seed(1234)
(A - matrix(rnorm(9), nrow = 3))

I want to trace of the inverse of A. I could do

 sum(diag(solve(A)))
[1] 1.259641

Or I could also do

 sum(1/eigen(A)$values)
[1] 1.259641+0i

Now, my actual problem involves a very large, square dense matrix. Is step 2 
still the best R-ish way of doing this or is there a smarter and fast 
implementation for such cases?

Harold


[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Import single variables from SPSS

2012-07-05 Thread Eik Vettorazzi

Hi Marion,
package memisc does what you want, just have a look at ?importers.

Hth
Eik

Am 05.07.2012 15:05, schrieb Marion Wenty:
 Dear all,
 I have got a very big SPSS dataframe and I would like to just import one or
 a few variables (the dataframe has got a lot of colums).
 I used the package foreign but I couldn't find anything in there for my
 problem.
 Thank you very much for your help in advance.
 Marion
 
   [[alternative HTML version deleted]]
 
 __
 R-help@r-project.org mailing list
 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.
 


-- 
Eik Vettorazzi

Department of Medical Biometry and Epidemiology
University Medical Center Hamburg-Eppendorf

Martinistr. 52
20246 Hamburg

T ++49/40/7410-58243
F ++49/40/7410-57790

--
Pflichtangaben gemäß Gesetz über elektronische Handelsregister und 
Genossenschaftsregister sowie das Unternehmensregister (EHUG):

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg

Vorstandsmitglieder: Prof. Dr. Guido Sauter (Vertreter des Vorsitzenden), Dr. 
Alexander Kirstein, Joachim Prölß, Prof. Dr. Dr. Uwe Koch-Gromus 

__
R-help@r-project.org mailing list
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] RODBC tables

2012-07-05 Thread Marc Schwartz


On Jul 4, 2012, at 10:10 AM, Lorcan Treanor wrote:

 Dear Sir/Madam,
 
 I am desperately in need of some help. I am trying to access tables from
 the oracle database and inserting them into R via a data frame and I keep
 getting an error saying that Error in .Call(C_RODBCFetchRows,
 attr(channel, handle_ptr), max, buffsize,  :
  negative length vectors are not allowed.
 
 My connection is fine and my code for this is:
 check-odbcConnect(dsn=,uid=*,pwd=**)
 
 There are terms instead of the *'s but I am not sure if I should disclose
 them because this is work-related. I have looked all over the internet and
 tried hundreds of solutions but have had no luck.
 
 These are the code I tried to use to get the table i called ANYTHING into
 R for which the negative length vectors errors came up.
 
 sqlTables(check,schema=**)
 nowfetchmewillwheaton-sqlFetch(check,ANYTHING)
 
 Do the errors imply that my connection is wrong, my code is wrong or that
 the table is not in the correct place in oracle.
 
 Please let me know if you can help or if you can give me the email address
 of someone who can.
 
 Kind Regards,
 
 Lorcan Treanor


You don't need to post the content of the *s. That is not needed, so you do 
not need to compromise your security.

This issue has come up before and I don't know, other than in one case years 
ago, that a definitive solution was ever posted. It seemed to be otherwise 
associated with 64 bit installations and there were some hints of integer 
overflow or an ODBC driver stability issue, but I don't recall that being 
confirmed. 

In the one case where Prof. Ripley had posted a work-around, it was back in 
2002 and involved querying tables with an underscore ('_') in the table name. I 
don't know that this issue is still relevant as I use RODBC on OSX (Fedora 
Linux for years previously) to access Oracle tables and views and they do have 
underscores in the names.

Some comments:

1. You are better off subscribing to and posting this query to the r-sig-db 
list which is focused on R and databases. More info here:

  https://stat.ethz.ch/mailman/listinfo/r-sig-db

Be sure to include information about your OS, R version including 32 or 64 bit. 
See the R Posting Guide for additional information on what default info to 
include in a post.

2. Any chance that you do not have appropriate permission to access the 
ANYTHING table? You may want to verify that with your DBAdmin. Is that 
actually the name of the table?

3. Try using:

   nowfetchmewilwheaton - sqlQuery(check, select * from ANYTHING)
  
and see if that works. 

Regards,

Marc Schwartz

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame

2012-07-05 Thread John Kane

It would be very helpful to have some sample data to play with.  str() shows 
the structure of the data set but it is not the data.

Something like dput(head(100))  would probably be enough.



John Kane
Kingston ON Canada


 -Original Message-
 From: rshep...@appl-ecosys.com
 Sent: Thu, 5 Jul 2012 08:46:31 -0700 (PDT)
 To: r-help@r-project.org
 Subject: [R] reshape2 errors on data frame
 
I've successfully reformatted data frames from long to wide with
 reshape2,
 but this time I'm getting errors that I want to understand and resolve.
 Here's the data frame structure and the results of the melt() and dcast()
 functions:
 
 str(waterchem)
 'data.frame': 128412 obs. of  8 variables:
   $ site: Factor w/ 64 levels D-1,D-2,D-3,..: 1 1 1 1 1 1 1 ...
   $ sampdate: Date, format: 2007-12-12 2007-12-12 ...
   $ preeq0  : logi  TRUE TRUE TRUE TRUE TRUE TRUE ...
   $ param   : Factor w/ 37 levels Ag,Al,Alk_tot,..: 1 2 8 17 3 4
 ...
   $ quant   : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...
   $ ceneq1  : logi  TRUE FALSE TRUE FALSE FALSE FALSE ...
   $ floor   : num  0 0.106 0 231 231 0.011 0 0 0 100 ...
   $ ceiling : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...
 chem.melt - melt(waterchem, idvars = c('site', 'sampdate', 'preeq0',
 'param', 'ceneq1', 'floor', 'ceiling'))
 Using site, preeq0, param, ceneq1 as id variables
 chem.cast - dcast(chem.melt, site + sampdate + preeq0 + ceneq1 + floor
 + ceiling ~ param)
 Error in eval(expr, envir, enclos) : object 'sampdate' not found
 
Because these data have some censored data there is the logical
 indicator
 (ceneq1) to identify censored and uncensored values the the interval ends
 (floor and ceiling) for multiply censored values. One factor of
 analytical
 interest whether the sampdate is pre- or post-event; that uses the
 logical
 indicator preeq0.
 
Please point out where my melt() and dcast() syntax was incorrect. I
 will
 provide more information if needed.
 
 TIA,
 
 Rich
 
 __
 R-help@r-project.org mailing list
 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.


FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks  orcas on your 
desktop!

__
R-help@r-project.org mailing list
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] vector entry in matix



On Jul 5, 2012, at 11:22 AM, R. Michael Weylandt wrote:


It is possible to put dimensionality on a list (i.e., a generic
vector), which might be what you're looking for.

x - list(1:4, letters[1:4], function(x,y) x + y, rnorm(50))
dim(x) - c(2,2)

x[[1,2]]

x[[2,2]]

x[[3,2]] # Error


That constructs a 2 x 2 matrix whose elements are lists:

 x
 [,1][,2]
[1,] Integer,4   ?
[2,] Character,4 Numeric,50
 is.matrix(x)
[1] TRUE

I suppose one could take that approach to constructing an Excel-mimic,  
since the functional element survives that passage:


 x[1,2][[1]](3,4)
[1] 7




Best,
Michael

On Thu, Jul 5, 2012 at 8:19 AM, Thomas C. thomas.csa...@gmail.com  
wrote:

hi,

i'm trying to figure out if there's any possibility to write a  
whole vector

into a matrix or data.frame or something like that. i don't mean
transormation. Here an example:

  [,1]  [,2]
[1,] a d
[2,] b e
[3,] c f


where e.g.  a is a-c(0,1) vector of length 2, b a vector of length  
4,... (i

know that the matrix enties are strings :)). i'm trying to put some
variables into a matrix or data.frame, but i couldn't handle it. is
something like that possible in R?


The matrix classes objects loose their names, however. You will not  
have a,b, ... as handles in that matrix. You could create row and  
column names.




thanks for your help!




David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
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] vector entry in matix

2012-07-05 Thread Thomas C.

well thank you, i think we get closer to my problem. but i meant it in a
different way. maybe i describe what i intended to do:

i have number of triangles which i'd like to store in a list, matrix,...etc.
i thought it could look sth. like that:

trianglenode1node2node3   .
 1   c(x1,y1) c(x2,y3)  c(x3,y3)
 1   c(x4,y4) c(x5,y5)  c(x6,y6)
.
.
.

i know that i could just make more rows for the x/y values but the problem
is, that i need to store more than these properties (say the neighbours of
these nodes and their coordinates) and i thought it would be more convenient
to save these as vectors. it was just a thought... is this possible?



--
View this message in context: 
http://r.789695.n4.nabble.com/vector-entry-in-matix-tp4635478p4635509.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] vector entry in matix

Hi,
I think it is better to store vectors in to list when the vectors are of 
different lengths.

#Consider these cases,
#vectors of equal length

set.seed(1)
 list1-list(a=rnorm(5,15),b=rnorm(5,25),c=1:5,d=runif(5,0.4),e=16:20,f=rep(1,5))

mat1-cbind(rbind(list1[[1]],list1[[2]],list1[[3]]),(rbind(list1[[4]],list1[[5]],list1[[6]])))
mat1
 [,1] [,2] [,3] [,4] [,5]   [,6]   [,7]
[1,] 16.43302 16.98040 14.63278 13.95587 15.56972  0.5371949  0.7574272
[2,] 24.86495 27.40162 24.96076 25.68974 25.02800 16.000 17.000
[3,]  1.0  2.0  3.0  4.0  5.0  1.000  1.000
   [,8]   [,9]  [,10]
[1,]  0.7449233  0.4462386  0.4213243
[2,] 18.000 19.000 20.000
[3,]  1.000  1.000  1.000

dat1-data.frame(list1)

dat1
 a    b c d  e f
1 16.43302 24.86495 1 0.5371949 16 1
2 16.98040 27.40162 2 0.7574272 17 1
3 14.63278 24.96076 3 0.7449233 18 1
4 13.95587 25.68974 4 0.4462386 19 1
5 15.56972 25.02800 5 0.4213243 20 1
#vectors of uneual length
#works with list

list2-list(a=rnorm(5,15),b=rnorm(10,25),c=5:15,d=runif(3,0.4),e=1:5,f=rep(1:3,3))
 list2
$a
[1] 15.36594 15.24841 15.06529 15.01916 15.25734

$b
 [1] 24.35099 24.88083 25.66414 26.10097 25.14377 24.88225 24.08793 23.56241
 [9] 24.20291 26.25408

$c
 [1]  5  6  7  8  9 10 11 12 13 14 15

$d
[1] 0.8679909 0.9283714 0.6478745

$e
[1] 1 2 3 4 5

$f
[1] 1 2 3 1 2 3 1 2 3


#Warning or Errors in matrix and dataframe
mat2-cbind(rbind(list2[[1]],list2[[2]],list2[[3]]),(rbind(list2[[4]],list2[[5]],list2[[6]])))
Warning messages:
1: In rbind(list2[[1]], list2[[2]], list2[[3]]) :
  number of columns of result is not a multiple of vector length (arg 1)
2: In rbind(list2[[4]], list2[[5]], list2[[6]]) :
  number of columns of result is not a multiple of vector length (arg 2)


  dat2-data.frame(list2)
Error in data.frame(a = c(15.3659411230492, 15.2484126488726, 
15.0652881816716,  : 
  arguments imply differing number of rows: 5, 10, 11, 3, 9

#So, it would be better to store it as a list.

#But, you can still convert vectors of unequal lengths to data frame or matrix 
with NAs.
library(zoo)
a-zoo(1:8,1:14)
b-zoo(5:8,3:5)
c-zoo(1:5,2:5)
 list3-list(a,b,c)
 z-zoo()
 for(i in 1:length(list3)) z-merge(z,get(list3[[i]]))
 names(z)-unlist(list3)
 z
   a  b  c
1  1 NA NA
2  2 NA  1
3  3  5  2
4  4  6  3
5  5  7  4
6  6 NA NA
7  7 NA NA
8  8 NA NA
9  1 NA NA
10 2 NA NA
11 3 NA NA
12 4 NA NA
13 5 NA NA
14 6 NA NA
 z1-data.frame(z)
is.data.frame(z1)
[1] TRUE
 str(z1)
'data.frame':    14 obs. of  3 variables:
 $ a: int  1 2 3 4 5 6 7 8 1 2 ...
 $ b: int  NA NA 5 6 7 NA NA NA NA NA ...
 $ c: int  NA 1 2 3 4 NA NA NA NA NA ...
z2-as.matrix(z)

A.K.




- Original Message -
From: Thomas C. thomas.csa...@gmail.com
To: r-help@r-project.org
Cc: 
Sent: Thursday, July 5, 2012 9:19 AM
Subject: [R] vector entry in matix

hi,

i'm trying to figure out if there's any possibility to write a whole vector
into a matrix or data.frame or something like that. i don't mean
transormation. Here an example:

       [,1]  [,2]
[1,] a d
[2,] b e
[3,] c f


where e.g.  a is a-c(0,1) vector of length 2, b a vector of length 4,... (i
know that the matrix enties are strings :)). i'm trying to put some
variables into a matrix or data.frame, but i couldn't handle it. is
something like that possible in R?

thanks for your help!

--
View this message in context: 
http://r.789695.n4.nabble.com/vector-entry-in-matix-tp4635478.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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
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] i need help in documentation

2012-07-05 Thread Bert Gunter

See also the inlinedocs package, which might be closer to what you're
looking for.

-- Bert

On Thu, Jul 5, 2012 at 8:17 AM, R. Michael Weylandt 
michael.weyla...@gmail.com wrote:

 R does not, to my knowledge, have anything quite like Python's
 docstrings (which seems to be what you are talking about) but you
 might look at Roxygen2 on CRAN which should get you started in this
 direction.

 Best,
 Michael

 On Thu, Jul 5, 2012 at 7:37 AM, purushothaman purushothama...@ge.com
 wrote:
  Hi,
 
  i am new in R development ,
 
  so i need help in documentation from comments in R file
 
  for example
 
  sample-function(filepath)
  {
 
  ##title read csv file
  ##author Purushoth
  ##description this function is used to read a csv file
  output-read.csv(filepath)
 return(output)
  }
 
  i need to get html document file using this comments
 
 
  Thanks
  B.Purushothaman
 
  --
  View this message in context:
 http://r.789695.n4.nabble.com/i-need-help-in-documentation-tp4635471.html
  Sent from the R help mailing list archive at Nabble.com.
 
  __
  R-help@r-project.org mailing list
  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
 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.




-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Exclude missing values on only 1 variable

2012-07-05 Thread Eiko Fried

Hello,

I have many hundred variables in my longitudinal dataset and lots of
missings. In order to plot data I need to remove missings.

If I do
 data - na.omit(data)
that will reduce my dataset to 2% of its original size ;)

So I only need to listwise delete missings on 3 variables (the ones I am
plotting).

data$variable1 -na.omit(data$variable1)
does not work.

Thank you

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] NADA Data Frame Format: Wide or Long?

2012-07-05 Thread Jean V Adams

Rich,

I am not familiar with the NADA package, but the reference manual (
http://cran.r-project.org/web/packages/NADA/NADA.pdf) has many examples 
using several data sets included in the package.  Look up one of the 
functions that you plan to use, run the example in R, and look at the data 
that is used in the example to see how it is organized.

Jean

Rich Shepard rshep...@appl-ecosys.com wrote on 07/03/2012 11:57:30 AM:

I have water chemistry data with censored values (i.e., those less 
than
 reporting levels) in a data frame with a narrow (i.e., database table)
 format. The structure is:
 
   $ site: Factor w/ 64 levels D-1,D-2,D-3,..: 1 1 1 1 1 1 1 1 
...
   $ sampdate: Date, format: 2007-12-12 2007-12-12 ...
   $ preeq0  : logi  TRUE TRUE TRUE TRUE TRUE TRUE ...
   $ param   : Factor w/ 37 levels Ag,Al,Alk_tot,..: 1 2 8 17 3 4 9 
...
   $ quant   : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...
   $ ceneq1  : logi  TRUE FALSE TRUE FALSE FALSE FALSE ...
   $ floor   : num  0 0.106 0 231 231 0.011 0 0 0 100 ...
   $ ceiling : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...
 
The logical 'preeq0' separates sampdate into two groups; 'ceneq1'
 indicates censored/uncensored values; 'floor' and 'ceiling' are the 
minima
 and maxima for censored values.
 
The NADA package methods will be used, but I have not found 
information on
 whether this format or the wide (i.e., spreadsheet) format should be 
used.
 The NADA.pdf document doesn't tell me; at least, I haven't found the 
answer
 there. I can apply reshape2 to melt and re-cast the data in wide format 
if
 that's what is appropriate. Please provide a pointer to documents I can 
read
 for an answer to this and related questions.
 
 Rich

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] empty cell when running GEE for binary data

2012-07-05 Thread Yue

hi Ozgur,

Thanks for your reply! by empty cell I mean there was a condition in which
all participants showed the same response (let's say response A). In other
words, the probability of A, according to the present data, was 100%; this
led to the empty cell for non-A. The odds or p(A) would be 1/0, so it's not
appropriate to use logit as the link function. 

I don't think, but not sure, gee would work, but i will try the other
package you suggested! 

Thanks!
Yue

--
View this message in context: 
http://r.789695.n4.nabble.com/empty-cell-when-running-GEE-for-binary-data-tp4635483p4635513.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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.

You have failed to provide a complete, coherent description of what you
wish to do. In the absence of such a description, all suggestions are just
guesses. You need to think carefully about what information you want to
associate with each triangle and the appropriate data structure to use to
do this. You might do well to talk with a computer scientist about this. An
object-oriented framework seems like the natural approach. This also sounds
like the sort of thing Bioconductor might already have, so search around
there, perhaps posting on their Help list.

-- Bert

On Thu, Jul 5, 2012 at 9:37 AM, Thomas C. thomas.csa...@gmail.com wrote:

well thank you, i think we get closer to my problem. but i meant it in a
different way. maybe i describe what i intended to do:

i have number of triangles which i'd like to store in a list,
matrix,...etc.
i thought it could look sth. like that:

trianglenode1node2node3 .
1 c(x1,y1) c(x2,y3) c(x3,y3)
1 c(x4,y4) c(x5,y5) c(x6,y6)
.
.
.

i know that i could just make more rows for the x/y values but the problem
is, that i need to store more than these properties (say the neighbours of
these nodes and their coordinates) and i thought it would be more
convenient
to save these as vectors. it was just a thought... is this possible?

--
View this message in context:
http://r.789695.n4.nabble.com/vector-entry-in-matix-tp4635478p4635509.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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.

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Exclude missing values on only 1 variable



On Jul 5, 2012, at 1:25 PM, Eiko Fried wrote:


Hello,

I have many hundred variables in my longitudinal dataset and lots of
missings. In order to plot data I need to remove missings.

If I do

data - na.omit(data)

that will reduce my dataset to 2% of its original size ;)

So I only need to listwise delete missings on 3 variables (the ones  
I am

plotting).

data$variable1 -na.omit(data$variable1)


?complete.cases  # returns a logical vector

data[ complete.cases( data[ , c(var1, var2, var3]) , ]


David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame


On Thu, 5 Jul 2012, John Kane wrote:


It would be very helpful to have some sample data to play with.


John,

  dput() doesn't want to cooperate so here are 100 rows from the raw data
file that can be input with read.table(sample.dat, header = T, sep = |):

'site'|'sampdate'|'preeq0'|'param'|'quant'|'ceneq1'|'floor'|'ceiling'
'A'|'2007-12-12'|1|'Ag'|0.005|1|0|0.005
'A'|'2007-12-12'|1|'Al'|0.106|0|0.106|0.106
'A'|'2007-12-12'|1|'CO3'|1|1|0|1
'A'|'2007-12-12'|1|'HCO3'|231.000|0|231.000|231.000
'A'|'2007-12-12'|1|'Alk_tot'|231.000|0|231.000|231.000
'A'|'2007-12-12'|1|'As'|0.011|0|0.011|0.011
'A'|'2007-12-12'|1|'Ba'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Be'|0.002|1|0|0.002
'A'|'2007-12-12'|1|'Bi'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Ca'|100.000|0|100.000|100.000
'A'|'2007-12-12'|1|'Cd'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Cl'|1.430|0|1.430|1.430
'A'|'2007-12-12'|1|'Co'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Cr'|0.006|1|0|0.006
'A'|'2007-12-12'|1|'Cu'|0.024|0|0.024|0.024
'A'|'2007-12-12'|1|'DO'|4.960|0|4.960|4.960
'A'|'2007-12-12'|1|'Fe'|4.110|0|4.110|4.110
'A'|'2007-12-12'|1|'K'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Mg'|9.560|0|9.560|9.560
'A'|'2007-12-12'|1|'Mn'|0.035|0|0.035|0.035
'A'|'2007-12-12'|1|'Mo'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Na'|0.970|0|0.970|0.970
'A'|'2007-12-12'|1|'NH4'|0.01|1|0|0.01
'A'|'2007-12-12'|1|'NO3-NO2'|0.293|0|0.293|0.293
'A'|'2007-12-12'|1|'Pb'|0.025|0|0.025|0.025
'A'|'2007-12-12'|1|'pH'|7.800|0|7.800|7.800
'A'|'2007-12-12'|1|'Sb'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'SC'|630.000|0|630.000|630.000
'A'|'2007-12-12'|1|'Se'|0.001|0|0.001|0.001
'A'|'2007-12-12'|1|'SO4'|65.800|0|65.800|65.800
'A'|'2007-12-12'|1|'Sr'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'TDS'|320.000|0|320.000|320.000
'A'|'2007-12-12'|1|'Tl'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'V'|0.001|1|0|0.001
'A'|'2007-12-12'|1|'Zn'|11.400|0|11.400|11.400
'A'|'2008-03-15'|1|'Ag'|0.005|1|0|0.005
'A'|'2008-03-15'|1|'Al'|0.08|1|0|0.08
'A'|'2008-03-15'|1|'CO3'|1|1|0|1
'A'|'2008-03-15'|1|'HCO3'|228.000|0|228.000|228.000
'A'|'2008-03-15'|1|'Alk_tot'|228.000|0|228.000|228.000
'A'|'2008-03-15'|1|'As'|0.001|0|0.001|0.001
'A'|'2008-03-15'|1|'Ba'|0.001|1|0|0.001
'A'|'2008-03-15'|1|'Be'|0.002|1|0|0.002
'A'|'2008-03-15'|1|'Bi'|0.001|1|0|0.001
'A'|'2008-03-15'|1|'Ca'|88.400|0|88.400|88.400
'A'|'2008-03-15'|1|'Cd'|0.001|1|0|0.001
'A'|'2008-03-15'|1|'Cl'|1.340|0|1.340|1.340
'A'|'2008-03-15'|1|'Co'|0.001|1|0|0.001
'A'|'2008-03-15'|1|'Cr'|0.006|1|0|0.006
'A'|'2008-03-15'|1|'Cu'|0.014|0|0.014|0.014
'A'|'2008-03-15'|1|'DO'|9.910|0|9.910|9.910
'A'|'2008-03-15'|1|'Fe'|0.309|0|0.309|0.309
'A'|'2008-03-15'|1|'Hg'|0.001|1|0|0.001
'A'|'2008-03-15'|1|'K'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Ag'|0.005|1|0|0.005
'B-2'|'1992-02-29'|0|'Al'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'As'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Ba'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Be'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Bi'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Ca'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Cd'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Cl'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Co'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Cr'|0.03|1|0|0.03
'B-2'|'1992-02-29'|0|'Cu'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Fe'|1.2|1|0|1.2
'B-2'|'1992-02-29'|0|'Hg'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'K'|19.800|0|19.800|19.800
'B-2'|'1992-02-29'|0|'Mg'|1|1|0|1
'B-2'|'1992-02-29'|0|'Mn'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Mo'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Na'|0.03|1|0|0.03
'B-2'|'1992-02-29'|0|'NH4'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Pb'|0.025|0|0.025|0.025
'B-2'|'1992-02-29'|0|'pH'|8.480|0|8.480|8.480
'B-2'|'1992-02-29'|0|'Sb'|0.01|1|0|0.01
'B-2'|'1992-02-29'|0|'Se'|0.003|1|0|0.003
'B-2'|'1992-02-29'|0|'Sr'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'TDS'|15|1|0|15
'B-2'|'1992-02-29'|0|'Tl'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'V'|0.001|1|0|0.001
'B-2'|'1992-02-29'|0|'Zn'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Ag'|0.005|1|0|0.005
'B-2'|'1992-04-02'|0|'Al'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'As'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Ba'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Be'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Bi'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Ca'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Cd'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Cl'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Co'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Cr'|0.03|1|0|0.03
'B-2'|'1992-04-02'|0|'Cu'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Fe'|1.2|1|0|1.2
'B-2'|'1992-04-02'|0|'Hg'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'K'|0.001|1|0|0.001
'B-2'|'1992-04-02'|0|'Mg'|1|1|0|1
'B-2'|'1992-04-02'|0|'Mn'|0.001|1|0|0.001

Rich

__
R-help@r-project.org mailing list
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 problem about WLS

2012-07-05 Thread jacquesliu

thanks a lot, it works

On Thu, Jul 5, 2012 at 11:40 AM, Thomas Lumley-2 [via R] 
ml-node+s789695n4635453...@n4.nabble.com wrote:

 On Thu, Jul 5, 2012 at 11:40 AM, jacquesliu [hidden 
 email]http://user/SendEmail.jtp?type=nodenode=4635453i=0
 wrote:

  I was asked to do a WLS estimation, so I thought of lm() with weights
 like
  wls=lm(Y~X-1,weight=INC)
 
  however, it gives different result as below code, which use the formula
 of
  WLS
  y-Y*INC^-0.5
  x-X*INC^-0.5
  wls=lm(y~x-1)
 
  Can anybody explain to me why the first code can not give the right
 answer?

 The two examples are using the opposite weights.  To replicate the
 answer from the second approach with lm, use weight=INC^-1

 In lm(), observations with high weights have more, um, weight. They
 influence the results more than observations with low weight.  Your
 code does the opposite.

-thomas
 --
 Thomas Lumley
 Professor of Biostatistics
 University of Auckland

 __
 [hidden email] http://user/SendEmail.jtp?type=nodenode=4635453i=1mailing 
 list
 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.


 --
  If you reply to this email, your message will be added to the discussion
 below:
 http://r.789695.n4.nabble.com/a-problem-about-WLS-tp4635446p4635453.html
  To unsubscribe from a problem about WLS, click 
 herehttp://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=4635446code=amFjcXVlc2xpdUBnbWFpbC5jb218NDYzNTQ0NnwxNTkzNzg0MjQx
 .
 NAMLhttp://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml




-- 
Liu,Jacques


--
View this message in context: 
http://r.789695.n4.nabble.com/a-problem-about-WLS-tp4635446p4635523.html
Sent from the R help mailing list archive at Nabble.com.
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame

2012-07-05 Thread Nordlund, Dan (DSHS/RDA)

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Rich Shepard
 Sent: Thursday, July 05, 2012 10:36 AM
 To: r-help@r-project.org
 Subject: Re: [R] reshape2 errors on data frame

 On Thu, 5 Jul 2012, John Kane wrote:

  It would be very helpful to have some sample data to play with.

 John,

dput() doesn't want to cooperate so here are 100 rows from the raw
 data
 file that can be input with read.table(sample.dat, header = T, sep =
 |):

 'site'|'sampdate'|'preeq0'|'param'|'quant'|'ceneq1'|'floor'|'ceiling'
 'A'|'2007-12-12'|1|'Ag'|0.005|1|0|0.005

snip

 'B-2'|'1992-04-02'|0|'Mn'|0.001|1|0|0.001

 Rich

Rich, 

The melt syntax you provided in a previous email runs without error on the data 
that you just supplied.  So, your comment that dput() doesn't want to 
cooperate suggests that maybe there is a problem with your waterchem data 
frame.  Maybe someone else will have more insight into the problem.

Sorry I can't be of more help,

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204

__
R-help@r-project.org mailing list
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] Removing rows if certain elements are found in character string

2012-07-05 Thread MacQueen, Don

Perhaps I've missed something, but if it's really true that the goal is to
remove rows if the first non-zero element is D or d, then how about
this:

tmp - gsub('0','',df$ch)
first - substr(tmp,1,1)
subset(df, tolower(first) != 'd')

and of course it could be rolled up into a single expression, but I wrote
it in several steps to make it easy to follow. No need to wrap one's brain
around regular expressions (which is hard for me!)

-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 7/2/12 3:48 PM, Claudia Penaloza claudiapenal...@gmail.com wrote:

I would like to remove rows from the following data frame (df) if there
are
only two specific elements found in the df$ch character string (I want to
remove rows with only 0  D or 0  d). Alternatively, I would like
to remove rows if the first non-zero element is D or d.


 ch count
1  00D0 0.007368;
2  00d0 0.002456;
3  0T00 0.007368;
4  0TD0 0.007368;
5  0T00 0.002456;
6  0Td0 0.002456;
7  T000 0.007368;
8  T0D0 0.007368;
9  T000 0.002456;
10 T0d0 0.002456;


I tried the following but it doesn't work if there is more than one
character per string:

df - df[!df$ch %in% c(0,D),]
df - df[!df$ch %in% c(0,d),]

Any help greatly appreciated,
Claudia

   [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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
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] Exclude missing values on only 1 variable

2012-07-05 Thread Bert Gunter

Be careful!! The plots could be potentially misleading. The problem is the
nature of the missingness. The approach you are taking is based on assuming
MCAR missingness (look it up, if necessary). If that is not the case --
e.g. if there is censoring, MAR, or informative missingness -- the plots
may be completely misleading.

Missingness in longitudinal data is a very difficult issue. If this is
something you don't know about already, I strongly suggest that you consult
a statistician who does -- not all of us do (I know almost nothing, for
example).

-- Bert


On Thu, Jul 5, 2012 at 10:34 AM, David Winsemius dwinsem...@comcast.netwrote:


 On Jul 5, 2012, at 1:25 PM, Eiko Fried wrote:

  Hello,

 I have many hundred variables in my longitudinal dataset and lots of
 missings. In order to plot data I need to remove missings.

 If I do

 data - na.omit(data)

 that will reduce my dataset to 2% of its original size ;)

 So I only need to listwise delete missings on 3 variables (the ones I am
 plotting).

 data$variable1 -na.omit(data$variable1)


 ?complete.cases  # returns a logical vector

 data[ complete.cases( data[ , c(var1, var2, var3]) , ]


 David Winsemius, MD
 West Hartford, CT

 __**
 R-help@r-project.org mailing list
 https://stat.ethz.ch/mailman/**listinfo/r-helphttps://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.




-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame


On Thu, 5 Jul 2012, Nordlund, Dan (DSHS/RDA) wrote:


The melt syntax you provided in a previous email runs without error on the
data that you just supplied.  So, your comment that dput() doesn't want
to cooperate suggests that maybe there is a problem with your waterchem
data frame.  Maybe someone else will have more insight into the problem.


Dan,

  Huh! Isn't that interesting? I'll re-read the data into a data frame and
see if that makes a difference.

  I wonder if the issue is with the logical columns; I've not used them
before, only dates, factors, and numerals. I'll try without the logicals and
see if there's a difference.

Thanks for the insight,

Rich

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame

2012-07-05 Thread R. Michael Weylandt michael.weyla...@gmail.com


On Thu, 5 Jul 2012, Rich Shepard wrote:


 I wonder if the issue is with the logical columns; I've not used them
before, only dates, factors, and numerals. I'll try without the logicals
and see if there's a difference.


  Nope. Same problem as before.

  Someone, please provide a process I can apply to figure out the error in
the data frame.

Rich

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame



On Jul 5, 2012, at 1:28 PM, Rich Shepard rshep...@appl-ecosys.com wrote:

 On Thu, 5 Jul 2012, Rich Shepard wrote:
 
 I wonder if the issue is with the logical columns; I've not used them
 before, only dates, factors, and numerals. I'll try without the logicals
 and see if there's a difference.
 
  Nope. Same problem as before.
 
  Someone, please provide a process I can apply to figure out the error in
 the data frame.
 

What do you mean it won't cooperate? Error message?

Michael

 Rich
 
 __
 R-help@r-project.org mailing list
 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
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] reshape2 errors on data frame


Hello,

Just to give it a try, you've written 'idvars' when it's 'id.vars'. 
After correction I no longer have the error. But, as expected, the 
result 'chem.cast' has lots and lots of NAs.



chem.cast - dcast(chem.melt,
site + sampdate + preeq0 + ceneq1 + floor + ceiling ~ param)

# First 6 rows
head(chem.cast)
  site   sampdate preeq0 ceneq1 floor ceiling AgAl Alk_totAs Ba 
Be Bi Ca Cd
1A 2007-12-12   TRUE  FALSE 0.001   0.001 NANA  NANA NA 
NA NA NA NA
2A 2007-12-12   TRUE  FALSE 0.011   0.011 NANA  NA 0.011 NA 
NA NA NA NA
3A 2007-12-12   TRUE  FALSE 0.024   0.024 NANA  NANA NA 
NA NA NA NA
4A 2007-12-12   TRUE  FALSE 0.025   0.025 NANA  NANA NA 
NA NA NA NA
5A 2007-12-12   TRUE  FALSE 0.035   0.035 NANA  NANA NA 
NA NA NA NA
6A 2007-12-12   TRUE  FALSE 0.106   0.106 NA 0.106  NANA NA 
NA NA NA NA
  Cl Co CO3 CrCu DO Fe HCO3 Hg  K MgMn Mo Na NH4 NO3-NO2Pb 
pH Sb SCSe
1 NA NA  NA NANA NA NA   NA NA NA NANA NA NA  NA  NANA 
NA NA NA 0.001
2 NA NA  NA NANA NA NA   NA NA NA NANA NA NA  NA  NANA 
NA NA NANA
3 NA NA  NA NA 0.024 NA NA   NA NA NA NANA NA NA  NA  NANA 
NA NA NANA
4 NA NA  NA NANA NA NA   NA NA NA NANA NA NA  NA  NA 0.025 
NA NA NANA
5 NA NA  NA NANA NA NA   NA NA NA NA 0.035 NA NA  NA  NANA 
NA NA NANA
6 NA NA  NA NANA NA NA   NA NA NA NANA NA NA  NA  NANA 
NA NA NANA

  SO4 Sr TDS Tl  V Zn
1  NA NA  NA NA NA NA
2  NA NA  NA NA NA NA
3  NA NA  NA NA NA NA
4  NA NA  NA NA NA NA
5  NA NA  NA NA NA NA
6  NA NA  NA NA NA NA

# Now the last 6 rows
tail(chem.cast)
   site   sampdate preeq0 ceneq1 floor ceilingAgAl Alk_tot 
AsBaBe
49  B-2 1992-02-29  FALSE   TRUE 0  15.000NANA  NANA 
   NANA
50  B-2 1992-04-02  FALSE   TRUE 0   0.001NA 0.001  NA 0.001 
0.001 0.001
51  B-2 1992-04-02  FALSE   TRUE 0   0.005 0.005NA  NANA 
   NANA
52  B-2 1992-04-02  FALSE   TRUE 0   0.030NANA  NANA 
   NANA
53  B-2 1992-04-02  FALSE   TRUE 0   1.000NANA  NANA 
   NANA
54  B-2 1992-04-02  FALSE   TRUE 0   1.200NANA  NANA 
   NANA
  BiCaCdClCo CO3   CrCu DO  Fe HCO3Hg K 
MgMn Mo
49NANANANANA  NA   NANA NA  NA   NANANA 
NANA NA
50 0.001 0.001 0.001 0.001 0.001  NA   NA 0.001 NA  NA   NA 0.001 0.001 
NA 0.001 NA
51NANANANANA  NA   NANA NA  NA   NANANA 
NANA NA
52NANANANANA  NA 0.03NA NA  NA   NANANA 
NANA NA
53NANANANANA  NA   NANA NA  NA   NANANA 
 1NA NA
54NANANANANA  NA   NANA NA 1.2   NANANA 
NANA NA

   Na NH4 NO3-NO2 Pb pH Sb SC Se SO4 Sr TDS Tl  V Zn
49 NA  NA  NA NA NA NA NA NA  NA NA  15 NA NA NA
50 NA  NA  NA NA NA NA NA NA  NA NA  NA NA NA NA
51 NA  NA  NA NA NA NA NA NA  NA NA  NA NA NA NA
52 NA  NA  NA NA NA NA NA NA  NA NA  NA NA NA NA
53 NA  NA  NA NA NA NA NA NA  NA NA  NA NA NA NA
54 NA  NA  NA NA NA NA NA NA  NA NA  NA NA NA NA


Hope this helps,

Rui Barradas

Em 05-07-2012 19:28, Rich Shepard escreveu:

On Thu, 5 Jul 2012, Rich Shepard wrote:


 I wonder if the issue is with the logical columns; I've not used them
before, only dates, factors, and numerals. I'll try without the logicals
and see if there's a difference.


   Nope. Same problem as before.

   Someone, please provide a process I can apply to figure out the error in
the data frame.

Rich

__
R-help@r-project.org mailing list
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
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] reshape2 errors on data frame


On Thu, 5 Jul 2012, R. Michael Weylandt michael.weyla...@gmail.com wrote:


What do you mean it won't cooperate? Error message?


Michael,

  I get the command echoed rather than results.

Rich

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame

2012-07-05 Thread Nordlund, Dan (DSHS/RDA)

 -Original Message-
 From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
 project.org] On Behalf Of Rich Shepard
 Sent: Thursday, July 05, 2012 11:29 AM
 To: r-help@r-project.org
 Subject: Re: [R] reshape2 errors on data frame

 On Thu, 5 Jul 2012, Rich Shepard wrote:

   I wonder if the issue is with the logical columns; I've not used
 them
  before, only dates, factors, and numerals. I'll try without the
 logicals
  and see if there's a difference.

Nope. Same problem as before.

Someone, please provide a process I can apply to figure out the
 error in
 the data frame.

 Rich

Rich,

I apologize that I did not read your original post carefully enough.  I missed 
that your problem was with the dcast() function.  I am not very familiar with 
the reshape package, but maybe I can give you some ideas of how to proceed.  
When I ran your melt syntax there was no error message, however there was a 
messages saying Using site, sampdate, param as id variables.  That is, not 
all of the ID variables specified were used. So the chem.melt data frame did 
not have all the ID variables in it.  Therefore, when I tried to run the 
dcast() syntax that you gave, it could not find some of variables specified.  
In your case, the error message stated that it could not find sampdate.  If you 
run

str(chem.melt)

do you see the variable sampdate?  I am not sure how you are wanting to 
re-shape your data, but when you specify a variable in dcast(), it needs to be 
in the dataframe you are working with.

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204

__
R-help@r-project.org mailing list
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] Silencing the output of install.packages()

2012-07-05 Thread craigcitro

Is there a way to suppress the output of 'install.packages()'? I have
seen that the 'download.file' function has a 'quiet' option but I do
not know how to use it.

I do not see any good reason to allow that. A user should see if
software is being installed.

Hi Uwe,

I have a proposed use-case. We run a series of unit tests in R, and want to
plug them into various continuous build/test frameworks. Part of our system
involves being able to install packages, so we need to actually run a unit
test that uses `install.packages`. For better or worse, many of these depend
on parsing the output of a test run; it's a lot of silly work to make them
parse the additional `install.packages` output (as opposed to the much
simpler `[\w]+: \.+` output from something like testthat in the case of
success).

Two questions:
* Is there another workaround? I'm planning on some ugly hackery on our
side to deal with this, but would love something cleaner.
* If I were willing to write the patch, would turning these statements into
something we could suppress be acceptable for R?

Thanks!
-cc

--
View this message in context:
http://r.789695.n4.nabble.com/Silencing-the-output-of-install-packages-tp4631947p4635525.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Confused about multiple imputation with rms or Hmisc packages

2012-07-05 Thread Mohiuddin, Jahan

Hello,
I'm working on a Cox Proportional Hazards model for a cancer data set  that has 
missing values for the categorical variable Grade in less than 10% of the 
observations.  I'm not a statistician, but based on my readings of Frank 
Harrell's book it seems to be a candidate for using multiple imputation 
technique(s).  I understand the concepts behind imputation, but using the 
functions in rms and Hmisc is confounding me.  For instance, whether to use 
transcan or aregImpute.

Here is a sample of my data: https://dl.dropbox.com/u/1852742/sample.csv

Drawing from Chapter 8 of Harrell's book, this is what I've been toying with:

#recurfree_survival_fromsx  is survival time, rf_obs_sx codes for events as a 
binary variable.

#The CPH model I would like to fit, using Ograde_dx as the variable for overall 
grade at
#diagnosis, ord_nodes as an ordinal variable for the # lymph nodes involved.
obj=with(mydata, Surv(recurfree_survival_fromsx,rf_obs_sx))
mod=cph(obj~ord_nodes+Ograde_dx+ERorPR+HER2_Sum,data=mydata,x=T,y=T)
#Impute missing data
mydata.transcan=transcan(~Ograde_dx+tumorsize+ord_nodes+simp_stage_path+afam+
Menopause+Age,imputed=T,n.impute=10)
summary(mydata.transcan)

The issues I have are:

a)  In your opinion(s), should I even be imputing this data?  Is it 
appropriate here?

b)  Even after reading the help pages and Harrell's book, I'm not sure I 
used the correct imputation method, and whether I should be using transcan or 
aregImpute.

c)   In the output of summary(transcan), is R-squared the best value to 
describe how reliably the function could predict Ograde_dx?  What is an 
acceptable level?

d)  Do I use the function fit.mult.impute to fit my final cph model?

I appreciate your help with this as it is a somewhat confusing topic.  I hope I 
gave you all the information you need to answer my questions.

Sincerely,
Jahan








[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Conditional Logistic regression with random effects / 2 random effects logit models

2012-07-05 Thread YAddo

Dear All:

I am stuck on this problem and I could use some help from folks out there.  
I want to  build a conditional logistic model with random  effects or
logistic regression with 2 random effects.  I have data on mothers and their
kids.  I want to condition 1 mom predictor(0/1)  and also for sibling
clustering (multiple  kids per mom).

I would appreciate any info on a package to use, and a help on writing the
codes. 

Variables : 
MomID as random 1 ,  momcondpredictor(0/1) as random 2 , mommainpredictor +
covariate

kidoutcome(0/1)  regressed mompredictor1  + covariates  +  the 2 random
effects.

Many thanks for your help.

YA



--
View this message in context: 
http://r.789695.n4.nabble.com/Conditional-Logistic-regression-with-random-effects-2-random-effects-logit-models-tp4635528.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] Histogram

2012-07-05 Thread Jim Silverton

I have a column of 1000 datapoints from the normal distribution with mean 2
and variance 4. How can I get a histogram of these observations with 20
bins with each bin having 50 observations?

-- 
Thanks,
Jim.

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Exclude missing values on only 1 variable

HI,
Try this:
set.seed(1)
dat1-data.frame(var1=c(rep(NA,3),1:3),var2=c(1:4,NA,5),var3=c(1:5,NA),var4=rnorm(6,15),var5=runif(6,0.2),var6=rep(NA,6))
 
 dat1[rowSums(is.na(dat1[,c(var1,var2,var3)]))==0,]
 var1 var2 var3 var4  var5 var6
4    1    4    4 16.59528 0.5981594   NA

A.K.





- Original Message -
From: Eiko Fried tor...@gmail.com
To: r-help@r-project.org
Cc: 
Sent: Thursday, July 5, 2012 1:25 PM
Subject: [R] Exclude missing values on only 1 variable

Hello,

I have many hundred variables in my longitudinal dataset and lots of
missings. In order to plot data I need to remove missings.

If I do
 data - na.omit(data)
that will reduce my dataset to 2% of its original size ;)

So I only need to listwise delete missings on 3 variables (the ones I am
plotting).

data$variable1 -na.omit(data$variable1)
does not work.

Thank you

    [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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.

Hi,Try this:


__
R-help@r-project.org mailing list
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] Fw: Exclude missing values on only 1 variable

HI,
Try this:
set.seed(1)
dat1-data.frame(var1=c(rep(NA,3),1:3),var2=c(1:4,NA,5),var3=c(1:5,NA),var4=rnorm(6,15),var5=runif(6,0.2),var6=rep(NA,6))
 
 dat1[rowSums(is.na(dat1[,c(var1,var2,var3)]))==0,]
 var1 var2 var3 var4  var5 var6
4    1    4    4 16.59528 0.5981594   NA

A.K.





- Original Message -
From: Eiko Fried tor...@gmail.com
To: r-help@r-project.org
Cc: 
Sent: Thursday, July 5, 2012 1:25 PM
Subject: [R] Exclude missing values on only 1 variable

Hello,

I have many hundred variables in my longitudinal dataset and lots of
missings. In order to plot data I need to remove missings.

If I do
 data - na.omit(data)
that will reduce my dataset to 2% of its original size ;)

So I only need to listwise delete missings on 3 variables (the ones I am
plotting).

data$variable1 -na.omit(data$variable1)
does not work.

Thank you

    [[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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.

Hi,Try this:

__
R-help@r-project.org mailing list
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] GEE with Inverse Probability Weights

2012-07-05 Thread RFrank

Thanks -- extremely helpful.  But what is the mechanism by which this
analysis corrects for the fact that my subjects are clustered (twins)?

--
View this message in context: 
http://r.789695.n4.nabble.com/GEE-with-Inverse-Probability-Weights-tp4633172p4635533.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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] colored nodes in dendrogram

2012-07-05 Thread Ondřej Mikula

Dear list,
is there a way how to add information to internal nodes (branching
points) in dendrogram created via plot.agnes function (package
cluster)?
I wish to place colored circles on the nodes, but I don't know how to proceed...
I'll be grateful for any suggestion
Ondřej

-- 
Ondřej Mikula

Institute of Animal Physiology and Genetics
Academy of Sciences of the Czech Republic
Veveri 97, 60200 Brno, Czech Republic

Institute of Vertebrate Biology
Academy of Sciences of the Czech Republic
Studenec 122, 67502 Konesin, Czech Republic

__
R-help@r-project.org mailing list
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] Histogram

2012-07-05 Thread Sarah Goslee

Hi Jim,

You can't specify both number of bins and bin size. You can specify
breaks: either the number of bins or the location of breakpoints. A
histogram with 20 bins of 50 observations each must by definition come
from a uniform distribution.

What are you trying to accomplish?

Sarah

On Thu, Jul 5, 2012 at 3:29 PM, Jim Silverton jim.silver...@gmail.com wrote:
 I have a column of 1000 datapoints from the normal distribution with mean 2
 and variance 4. How can I get a histogram of these observations with 20
 bins with each bin having 50 observations?

 --
 Thanks,
 Jim.


-- 
Sarah Goslee
http://www.functionaldiversity.org

__
R-help@r-project.org mailing list
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] reshape2 errors on data frame


Hello,

Inline

Em 05-07-2012 20:21, Nordlund, Dan (DSHS/RDA) escreveu:

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of Rich Shepard
Sent: Thursday, July 05, 2012 11:29 AM
To: r-help@r-project.org
Subject: Re: [R] reshape2 errors on data frame

On Thu, 5 Jul 2012, Rich Shepard wrote:


  I wonder if the issue is with the logical columns; I've not used

them

before, only dates, factors, and numerals. I'll try without the

logicals

and see if there's a difference.


Nope. Same problem as before.

Someone, please provide a process I can apply to figure out the
error in
the data frame.

Rich



Rich,

I apologize that I did not read your original post carefully enough.  I missed that your 
problem was with the dcast() function.  I am not very familiar with the reshape package, 
but maybe I can give you some ideas of how to proceed.  When I ran your melt syntax there 
was no error message, however there was a messages saying Using site, sampdate, 
param as id variables.  That is, not all of the ID variables specified were used. 
So the chem.melt data frame did not have all the ID variables in it.  Therefore, when I 
tried to run the dcast() syntax that you gave, it could not find some of variables 
specified.  In your case, the error message stated that it could not find sampdate.  If 
you run



I should have said that in my earlier post. It's implicit in the 
misspeling of the argument 'id.vars', an argument of melt() not of 
dcast(). Therefore, melt() issues a warning, the warning in the OP.


I'll reproduce it here:


 chem.melt - melt(waterchem,
+ idvars = c('site', 'sampdate', 'preeq0', 'param', 'ceneq1', 'floor', 
'ceiling'))

Using site, preeq0, param, ceneq1 as id variables


Hope this helps,

Rui Barradas


str(chem.melt)

do you see the variable sampdate?  I am not sure how you are wanting to 
re-shape your data, but when you specify a variable in dcast(), it needs to be 
in the dataframe you are working with.


Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA 98504-5204


__
R-help@r-project.org mailing list
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
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] Exclude missing values on only 1 variable



On Jul 5, 2012, at 1:34 PM, David Winsemius wrote:



On Jul 5, 2012, at 1:25 PM, Eiko Fried wrote:


Hello,

I have many hundred variables in my longitudinal dataset and lots of
missings. In order to plot data I need to remove missings.

If I do

data - na.omit(data)

that will reduce my dataset to 2% of its original size ;)

So I only need to listwise delete missings on 3 variables (the ones  
I am

plotting).

data$variable1 -na.omit(data$variable1)


?complete.cases  # returns a logical vector

data[ complete.cases( data[ , c(var1, var2, var3]) , ]

data[ complete.cases( data[ , c(var1, var2, var3) ] ) , ]

Er, need to add a right - paren  -here  ---^



--

David Winsemius, MD
West Hartford, CT

__
R-help@r-project.org mailing list
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] Histogram


Hello,

Try the following.

x - rnorm(1000, mean=2, sd=2)
p - seq(0, 1, by=1/20)
quant - quantile(x, probs=p)
hist(x, breaks=quant)


The method is absolutely general, that's why I've separated the several 
steps, to make it clear.


Hope this helps,

Rui Barradas

Em 05-07-2012 20:29, Jim Silverton escreveu:

I have a column of 1000 datapoints from the normal distribution with mean 2
and variance 4. How can I get a histogram of these observations with 20
bins with each bin having 50 observations?



__
R-help@r-project.org mailing list
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] GEE with Inverse Probability Weights

2012-07-05 Thread Joshua Wiley

Hi Frank,

It clusters by twin, that is why in Dr. Lumley's example, the id was
twin pair, not individual, and the SE is adjusted accordingly.

Cheers,

Josh

On Thu, Jul 5, 2012 at 12:10 PM, RFrank spark...@gmail.com wrote:
 Thanks -- extremely helpful.  But what is the mechanism by which this
 analysis corrects for the fact that my subjects are clustered (twins)?

 --
 View this message in context: 
 http://r.789695.n4.nabble.com/GEE-with-Inverse-Probability-Weights-tp4633172p4635533.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 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.



-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

__
R-help@r-project.org mailing list
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] Histogram

2012-07-05 Thread Sarah Goslee

There's no reason you can't do that with normally-distributed data,
though I'm not sure why you'd want to. My point was rather that you
can't specify the bin width and size both. If you let the bin size
vary, this will work:

set.seed(1234)
mydata - rnorm(1000, mean = 2, sd = 4)
mydata.hist - hist(mydata, breaks=quantile(mydata, probs=seq(0, 1,
length.out = length(mydata)/50 + 1)))
mydata.hist$counts


Sarah

On Thu, Jul 5, 2012 at 3:37 PM, Jim Silverton jim.silver...@gmail.com wrote:
 Thanks Sarah!!
 Ok so if I have say x = runif(1000,0,1) say instead if the normal and I want
 a histogram with bins that have an equal number of observations. For example
 if I want each bin to have 50 observations, how do I do this?



 On Thu, Jul 5, 2012 at 3:34 PM, Sarah Goslee sarah.gos...@gmail.com wrote:

 Hi Jim,

 You can't specify both number of bins and bin size. You can specify
 breaks: either the number of bins or the location of breakpoints. A
 histogram with 20 bins of 50 observations each must by definition come
 from a uniform distribution.

 What are you trying to accomplish?

 Sarah

 On Thu, Jul 5, 2012 at 3:29 PM, Jim Silverton jim.silver...@gmail.com
 wrote:
  I have a column of 1000 datapoints from the normal distribution with
  mean 2
  and variance 4. How can I get a histogram of these observations with 20
  bins with each bin having 50 observations?
 
  --
  Thanks,
  Jim.


-- 
Sarah Goslee
http://www.functionaldiversity.org

__
R-help@r-project.org mailing list
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] Histogram

2012-07-05 Thread Duncan Murdoch


On 05/07/2012 3:34 PM, Sarah Goslee wrote:

Hi Jim,

You can't specify both number of bins and bin size. You can specify
breaks: either the number of bins or the location of breakpoints. A
histogram with 20 bins of 50 observations each must by definition come
from a uniform distribution.


Only if the bins are equal in size.  You could set the bins to 
quantiles, for the following ugly plot:


hist(x, breaks=quantile(x, seq(0, 1, by=0.05)))

Duncan Murdoch



What are you trying to accomplish?

Sarah

On Thu, Jul 5, 2012 at 3:29 PM, Jim Silverton jim.silver...@gmail.com wrote:
 I have a column of 1000 datapoints from the normal distribution with mean 2
 and variance 4. How can I get a histogram of these observations with 20
 bins with each bin having 50 observations?

 --
 Thanks,
 Jim.




__
R-help@r-project.org mailing list
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] Histogram


Hello,

With the confusion between bin size and width the OP started, I'll 
repost my answer with a final line. Sorry for the repetition.



h - hist(x, breaks=quantile(x, probs=seq(0, 1, by=1/20)))
h$counts
[1] 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50


Hope this helps,

Rui Barradas

Em 05-07-2012 20:47, Sarah Goslee escreveu:

There's no reason you can't do that with normally-distributed data,
though I'm not sure why you'd want to. My point was rather that you
can't specify the bin width and size both. If you let the bin size
vary, this will work:

set.seed(1234)
mydata - rnorm(1000, mean = 2, sd = 4)
mydata.hist - hist(mydata, breaks=quantile(mydata, probs=seq(0, 1,
length.out = length(mydata)/50 + 1)))
mydata.hist$counts


Sarah

On Thu, Jul 5, 2012 at 3:37 PM, Jim Silverton jim.silver...@gmail.com wrote:

Thanks Sarah!!
Ok so if I have say x = runif(1000,0,1) say instead if the normal and I want
a histogram with bins that have an equal number of observations. For example
if I want each bin to have 50 observations, how do I do this?



On Thu, Jul 5, 2012 at 3:34 PM, Sarah Goslee sarah.gos...@gmail.com wrote:


Hi Jim,

You can't specify both number of bins and bin size. You can specify
breaks: either the number of bins or the location of breakpoints. A
histogram with 20 bins of 50 observations each must by definition come
from a uniform distribution.

What are you trying to accomplish?

Sarah

On Thu, Jul 5, 2012 at 3:29 PM, Jim Silverton jim.silver...@gmail.com
wrote:

I have a column of 1000 datapoints from the normal distribution with
mean 2
and variance 4. How can I get a histogram of these observations with 20
bins with each bin having 50 observations?

--
Thanks,
Jim.






__
R-help@r-project.org mailing list
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] How to do non-parametric Anova for comparing two lm models?

2012-07-05 Thread Michael

I am trying to compare two lm models, one including a categorical variable
and the other excluding the variable...

The residuals of both lm fits are highly non-Gaussian.

Could you please give me some pointers?

Thank you!

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] NADA Data Frame Format: Wide or Long?

2012-07-05 Thread MacQueen, Don

I haven't used NADA functions in quite a while, but from what I recall,
you will likely be using the narrow format, and sub-setting as needed
for the different analytes.

As Jean suggested, the examples in the help pages for the NADA function(s)
of interest should make it clear.

This example follows exactly the example in ?cenros.

  with( subset(yourdataframe, param=='Ag'),  cenros(quant,ceneq1) )

This should do a simple censored summary statistica calculation for silver
(assuming quant contains your reporting level for censored results, which
appears to be the case).

I'd also suggest you try to load your data so that site and param are not
factors, though this could depend on your ultimate analysis.

-Don

-- 
Don MacQueen

Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062





On 7/3/12 9:57 AM, Rich Shepard rshep...@appl-ecosys.com wrote:

   I have water chemistry data with censored values (i.e., those less than
reporting levels) in a data frame with a narrow (i.e., database table)
format. The structure is:

  $ site: Factor w/ 64 levels D-1,D-2,D-3,..: 1 1 1 1 1 1 1 1
...
  $ sampdate: Date, format: 2007-12-12 2007-12-12 ...
  $ preeq0  : logi  TRUE TRUE TRUE TRUE TRUE TRUE ...
  $ param   : Factor w/ 37 levels Ag,Al,Alk_tot,..: 1 2 8 17 3 4 9
...
  $ quant   : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...
  $ ceneq1  : logi  TRUE FALSE TRUE FALSE FALSE FALSE ...
  $ floor   : num  0 0.106 0 231 231 0.011 0 0 0 100 ...
  $ ceiling : num  0.005 0.106 1 231 231 0.011 0.001 0.002 0.001 100 ...

   The logical 'preeq0' separates sampdate into two groups; 'ceneq1'
indicates censored/uncensored values; 'floor' and 'ceiling' are the minima
and maxima for censored values.

   The NADA package methods will be used, but I have not found
information on
whether this format or the wide (i.e., spreadsheet) format should be used.
The NADA.pdf document doesn't tell me; at least, I haven't found the
answer
there. I can apply reshape2 to melt and re-cast the data in wide format if
that's what is appropriate. Please provide a pointer to documents I can
read
for an answer to this and related questions.

Rich

__
R-help@r-project.org mailing list
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
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] reshape2 errors on data frame [RESOLVED]


On Thu, 5 Jul 2012, Rui Barradas wrote:


Just to give it a try, you've written 'idvars' when it's 'id.vars'.


Rui,

  Oops! That was the problem. No matter how often I looked at the syntax I
kept missing that.


Hope this helps,


  Most definitely!

Thanks for spotting it,

Rich

__
R-help@r-project.org mailing list
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] Histogram

2012-07-05 Thread Sarah Goslee

Which gives Jim two ways to arrive at exactly the same result, just
different means of specifying the probs for quantile().

Sarah

On Thu, Jul 5, 2012 at 4:01 PM, Rui Barradas ruipbarra...@sapo.pt wrote:
 Hello,

 With the confusion between bin size and width the OP started, I'll repost my
 answer with a final line. Sorry for the repetition.


 h - hist(x, breaks=quantile(x, probs=seq(0, 1, by=1/20)))
 h$counts
 [1] 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50 50


 Hope this helps,

 Rui Barradas

 Em 05-07-2012 20:47, Sarah Goslee escreveu:

 There's no reason you can't do that with normally-distributed data,
 though I'm not sure why you'd want to. My point was rather that you
 can't specify the bin width and size both. If you let the bin size
 vary, this will work:

 set.seed(1234)
 mydata - rnorm(1000, mean = 2, sd = 4)
 mydata.hist - hist(mydata, breaks=quantile(mydata, probs=seq(0, 1,
 length.out = length(mydata)/50 + 1)))
 mydata.hist$counts


 Sarah

 On Thu, Jul 5, 2012 at 3:37 PM, Jim Silverton jim.silver...@gmail.com
 wrote:

 Thanks Sarah!!
 Ok so if I have say x = runif(1000,0,1) say instead if the normal and I
 want
 a histogram with bins that have an equal number of observations. For
 example
 if I want each bin to have 50 observations, how do I do this?



 On Thu, Jul 5, 2012 at 3:34 PM, Sarah Goslee sarah.gos...@gmail.com
 wrote:


 Hi Jim,

 You can't specify both number of bins and bin size. You can specify
 breaks: either the number of bins or the location of breakpoints. A
 histogram with 20 bins of 50 observations each must by definition come
 from a uniform distribution.

 What are you trying to accomplish?

 Sarah

 On Thu, Jul 5, 2012 at 3:29 PM, Jim Silverton jim.silver...@gmail.com
 wrote:

 I have a column of 1000 datapoints from the normal distribution with
 mean 2
 and variance 4. How can I get a histogram of these observations with 20
 bins with each bin having 50 observations?

 --
 Thanks,
 Jim.





__
R-help@r-project.org mailing list
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] vector entry in matix

2012-07-05 Thread Christian Brechbühler

To second Bert Gunter: you may get better answers if you give us a complete
description.

On Thu, Jul 5, 2012 at 12:37 PM, Thomas C. thomas.csa...@gmail.com wrote:

 i have number of triangles which i'd like to store in a list,
 matrix,...etc.
 i thought it could look sth. like that:

 trianglenode1node2node3   .
  1   c(x1,y1) c(x2,y3)  c(x3,y3)
  1   c(x4,y4) c(x5,y5)  c(x6,y6)


You already indicate that that's not the whole truth, but if it was you
could consider one of two approaches:
* Rather than a 2D array (also called matrix) use a 3D array, with
dimensions n.triangle x 3 x 2.
* You could use a n.triangle x 3 matrix of complex numbers.  That may look
like a sneaky trick to put a vector into a matrix element, but some
operations of planar geometry can written elegantly.  E.g., distance
between a and b is abs(a-b).

It all depends on what you want to do.  BTW, what do you consider a
neighbor of a triangle?
*
*
If you are working with a triangle mesh, it might be better to hold the
vertices in a double matrix (n.vertex x 2) and represent the triangles as
indices into it, i.e., as an integer matrix (n.triangle x 3).  You may use
more columns in either matrix to represent more attributes.  If you find
out you need columns of different types, consider a data frame.

/Christian

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] NADA Data Frame Format: Wide or Long?


On Thu, 5 Jul 2012, MacQueen, Don wrote:


This example follows exactly the example in ?cenros.



   with( subset(yourdataframe, param=='Ag'),  cenros(quant,ceneq1) )



This should do a simple censored summary statistica calculation for silver
(assuming quant contains your reporting level for censored results, which
appears to be the case).


Don,

  That makes sense to me. I was hoping to avoid subsetting the data frame
for each of the 37 chemical parameters, but ... I will review the use of
with().


I'd also suggest you try to load your data so that site and param are not
factors, though this could depend on your ultimate analysis.


  I do need to differentiate results by site and chemical paramater.

Many thanks,

Rich

__
R-help@r-project.org mailing list
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] vector entry in matix

2012-07-05 Thread Joshua Wiley

Hi Thomas,

This is non trivial to do, but if you will be working with this sort
of data and are inclined to do some programming, you might consider
creating a new class.  S4 classes and methods are quite flexible, and
you can allow them to lean on or inherit from existing classes such as
matrices.  For example, your class might consist of three lists and a
data frame.  The length of each list would be forced to be equal to
the number of rows in the data frame.  Each element of each list would
support a length 2 numeric vector (or integer vector or whatever it is
you need).  THe lists then would hold nodes 1 - 3, and the data frame
would hold other information.  You can similarly write methods so that
for your special class,

d[1, 1] would return c(x1, y1), essentially you create a mix of lists
and a matrix with all the necessary constraints, and you develop
methods that allow you to operate on this in a way that is sensible
for your data.

This is stab in the dark, but if you happen to be dealing with social
network style data, (triangles and neighbors make me think of that),
you should investigate existing packages for that as they may already
have their own classes/have a way they expect data to be structured.
Off the top of my head, the package sna comes to mind as a starting
place to look (though I am not personally very familiar with it).

Cheers,

Josh

On Thu, Jul 5, 2012 at 9:37 AM, Thomas C. thomas.csa...@gmail.com wrote:
 well thank you, i think we get closer to my problem. but i meant it in a
 different way. maybe i describe what i intended to do:

 i have number of triangles which i'd like to store in a list, matrix,...etc.
 i thought it could look sth. like that:

 trianglenode1node2node3   .
  1   c(x1,y1) c(x2,y3)  c(x3,y3)
  1   c(x4,y4) c(x5,y5)  c(x6,y6)
 .
 .
 .

 i know that i could just make more rows for the x/y values but the problem
 is, that i need to store more than these properties (say the neighbours of
 these nodes and their coordinates) and i thought it would be more convenient
 to save these as vectors. it was just a thought... is this possible?



 --
 View this message in context: 
 http://r.789695.n4.nabble.com/vector-entry-in-matix-tp4635478p4635509.html
 Sent from the R help mailing list archive at Nabble.com.

 __
 R-help@r-project.org mailing list
 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.



-- 
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

__
R-help@r-project.org mailing list
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] trouble installing Rmpi on a debian machine

2012-07-05 Thread Erin Hodgess

Dear R People:

I'm having trouble installing Rmpi on a debian machine.

Here is my output:
bccd@node000:~$ /bccd/home/bccd
bccd@node000:~$
bccd@node000:~$ export RMPI_TYPE=OPENMPI
bccd@node000:~$ R CMD INSTALL Rmpi_0.5-9.tar.gz
* installing to library '/bccd/home/bccd/R/x86_64-pc-linux-gnu-library/2.15'
* installing *source* package 'Rmpi' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
Trying to find libmpi.so or libmpich.a ...
checking for main in -lmpi... yes
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
** Creating default NAMESPACE file
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\
-DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\
-DPACKAGE_BUGREPORT=\\ -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I  -DMPI2 -DOPENMPI -fpic
-O3 -pipe  -g  -c RegQuery.c -o RegQuery.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -DPACKAGE_NAME=\\
-DPACKAGE_TARNAME=\\ -DPACKAGE_VERSION=\\ -DPACKAGE_STRING=\\
-DPACKAGE_BUGREPORT=\\ -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -I  -DMPI2 -DOPENMPI -fpic
-O3 -pipe  -g  -c Rmpi.c -o Rmpi.o
In file included from Rmpi.c:18:
Rmpi.h:2:17: error: mpi.h: No such file or directory
In file included from Rmpi.c:18:
Rmpi.h:15: error: expected '=', ',', ';', 'asm' or '__attribute__'
before 'mpitype'
Rmpi.c:24: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
Rmpi.c:25: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
Rmpi.c:26: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
Rmpi.c:27: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
Rmpi.c:28: error: expected '=', ',', ';', 'asm' or '__attribute__'
before '*' token
Rmpi.c: In function 'mpi_initialize':
Rmpi.c:57: warning: implicit declaration of function 'MPI_Initialized'
Rmpi.c:76: warning: implicit declaration of function 'MPI_Init'
Rmpi.c:81: warning: implicit declaration of function 'MPI_Errhandler_set'
Rmpi.c:81: error: 'MPI_COMM_WORLD' undeclared (first use in this function)
Rmpi.c:81: error: (Each undeclared identifier is reported only once
Rmpi.c:81: error: for each function it appears in.)
Rmpi.c:81: error: 'MPI_ERRORS_RETURN' undeclared (first use in this function)
Rmpi.c:82: error: 'MPI_COMM_SELF' undeclared (first use in this function)
Rmpi.c:83: error: 'comm' undeclared (first use in this function)
Rmpi.c:83: error: 'MPI_Comm' undeclared (first use in this function)
Rmpi.c:83: error: expected expression before ')' token
Rmpi.c:83: error: expected ';' before 'R_chk_calloc'
Rmpi.c:84: error: 'status' undeclared (first use in this function)
Rmpi.c:84: error: 'MPI_Status' undeclared (first use in this function)
Rmpi.c:84: error: expected expression before ')' token
Rmpi.c:84: error: expected ';' before 'R_chk_calloc'
Rmpi.c:85: error: 'datatype' undeclared (first use in this function)
Rmpi.c:85: error: 'MPI_Datatype' undeclared (first use in this function)
Rmpi.c:85: error: expected expression before ')' token
Rmpi.c:85: error: expected ';' before 'R_chk_calloc'
Rmpi.c:86: error: 'info' undeclared (first use in this function)
Rmpi.c:86: error: 'MPI_Info' undeclared (first use in this function)
Rmpi.c:86: error: expected expression before ')' token
Rmpi.c:86: error: expected ';' before 'R_chk_calloc'
Rmpi.c:87: error: 'MPI_INFO_NULL' undeclared (first use in this function)
Rmpi.c:88: error: 'request' undeclared (first use in this function)
Rmpi.c:88: error: 'MPI_Request' undeclared (first use in this function)
Rmpi.c:88: error: expected expression before ')' token
Rmpi.c:88: error: expected ';' before 'R_chk_calloc'
Rmpi.c:89: error: 'MPI_REQUEST_NULL' undeclared (first

[R] trouble installing Rmpi on a debian machine: please ignore

2012-07-05 Thread Erin Hodgess

It was looking for the mpi.h file.

Sorry for the trouble.


-- 
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodg...@gmail.com

__
R-help@r-project.org mailing list
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] EM algorithm to find MLE of coeff in mixed effects model

2012-07-05 Thread Jie

Seems that I found the problem.
The degree of freedom was missing as a denominator...
Thank you for your help.
Best wishes,
Jie
On Thu, Jul 5, 2012 at 9:28 AM, John Kane jrkrid...@inbox.com wrote:

 I don't believe that R-help permits pdf files.  A useful workaround is to
 post it to a file hosting site like MediaFire and post the link here.
 John Kane
 Kingston ON Canada


  -Original Message-
  From: jimmycl...@gmail.com
  Sent: Wed, 4 Jul 2012 22:56:02 -0400
  To: pauljoh...@gmail.com
  Subject: Re: [R] EM algorithm to find MLE of coeff in mixed effects model
 
  Dear Paul,
 
  Thank you for your suggestion. I was moved by the fact that people are so
  nice to help learners and ask for nothing.
  With your help, I made some changes to my code and add more comments, try
  to make things more clear.
  If this R email list allow me to upload a pdf file to illustrate the
  formula, it will be great.
  The reason I do not use lme4 is that later I plan to use this for a more
  complicated model (Y,T), Y is the same response of mixed model and T is a
  drop out process.
  (Frankly I did it for the more complicated model first and got NaN
  hessian
  after one iteration, so I turned to the simple model.)
  In the code, the m loop is the EM iterations. About efficiency, thank you
  again for pointing it out. I compared sapply and for loop, they are tie
  and
  for loop is even better sometimes.
  In a paper by Bates, he mentioned that the asymptotic properties of beta
  is
  kind of independent of the other two parameters. But it seems that paper
  was submitted but I did not find it on google scholar.
  Not sure if it is the reason for my results. That is why I hope some
  expert
  who have done some simulation similar may be willing to give some
  suggestion.
  I may turn to other methods to calculate the conditional expection of the
  latent variable as the same time.
 
  Modified code is as below:
 
  # library(PerformanceAnalytics)
  # install.packages(gregmisc)
  # install.packages(statmod)
  library(gregmisc)
  library(MASS)
  library(statmod)
 
  ## function to calculate loglikelihood
  loglike - function(datai = data.list[[i]], vvar = var.old,
  beta = beta.old, psi = psi.old) {
  temp1 - -0.5 * log(det(vvar * diag(nrow(datai$Zi)) + datai$Zi %*%
  psi %*% t(datai$Zi)))
  temp2 - -0.5 * t(datai$yi - datai$Xi %*% beta) %*% solve(vvar *
  diag(nrow(datai$Zi)) + datai$Zi %*% psi %*% t(datai$Zi)) %*%
  (datai$yi - datai$Xi %*% beta)
  temp1 + temp2
  }
 
  ## functions to evaluate the conditional expection, saved as Efun v2.R
  ## Eh1new=E(bibi')
  ## Eh2new=E(X'(y-Zbi))
  ## Eh3new=E(bi'Z'Zbi)
  ## Eh4new=E(Y-Xibeta-Zibi)'(Y-Xibeta-Zibi)
  ## Eh5new=E(Xibeta-yi)'Zibi
  ## Eh6new=E(bi)
 
  Eh1new - function(datai = data.list[[i]], weights.m = weights.mat) {
  bi - datai$b
  tempb - bi * rep(sqrt(weights.m[, 1] * weights.m[, 2]),
  2)  #quadratic b, so needsqrt
  t(tempb) %*% tempb/pi
  }  # end of Eh1
 
 
  # Eh2new=E(X'(y-Zbi))
  Eh2new - function(datai = data.list[[i]], weights.m = weights.mat) {
  bi - datai$b
  tempb - bi * rep(weights.m[, 1] * weights.m[, 2], 2)
  tt - t(datai$Xi) %*% datai$yi - t(datai$Xi) %*% datai$Zi %*%
  colSums(tempb)/pi
  c(tt)
  }  # end of Eh2
 
 
  # Eh3new=E(b'Z'Zbi)
  Eh3new - function(datai = data.list[[i]], weights.m = weights.mat) {
  bi - datai$b
  tempb - bi * rep(sqrt(weights.m[, 1] * weights.m[, 2]),
  2)  #quadratic b, so need sqrt
  sum(sapply(as.list(data.frame(datai$Zi %*% t(tempb))),
  function(s) {
  sum(s^2)
  }))/pi
  }  # end of Eh3
 
  # Eh4new=E(Y-Xibeta-Zibi)'(Y-Xibeta-Zibi)
  Eh4new - function(datai = data.list[[i]], weights.m = weights.mat,
  beta = beta.old) {
  bi - datai$b
  tt - sapply(as.list(ata.frame(c(datai$yi - datai$Xi %*%
  beta) - datai$Zi %*% t(bi))), function(s) {
  sum(s^2)
  }) * (weights.m[, 1] * weights.m[, 2])
  sum(tt)/pi
  }  # end of Eh4
 
  Eh4newv2 - function(datai = data.list[[i]], weights.m = weights.mat,
  beta = beta.old) {
  bi - datai$b
  v - weights.m[, 1] * weights.m[, 2]
  temp - c()
  for (i in 1:length(v)) {
  temp[i] - sum(((datai$yi - datai$Xi %*% beta - datai$Zi %*%
  bi[i, ]) * sqrt(v[i]))^2)
  }
  sum(temp)/pi
  }  # end of Eh4
 
  # Eh5new=E(Xibeta-yi)'Zib
  Eh5new - function(datai = data.list[[i]], weights.m = weights.mat,
  beta = beta.old) {
  bi - datai$b
  tempb - bi * rep(weights.m[, 1] * weights.m[, 2], 2)
  t(datai$Xi %*% beta - datai$yi) %*% (datai$Zi %*% t(tempb))
  sum(t(datai$Xi %*% beta - datai$yi) %*% (datai$Zi %*%
  t(tempb)))/pi
  }
 
  Eh6new - function(datai = data.list[[i]], weights.m = weights.mat) {
  bi - datai$b
  tempw - weights.m[, 1] * weights.m[, 2]
  for (i in 1:nrow(bi)) {
  bi[i, ] - bi[i, ] * tempw[i]
  }

Re: [R] GEE with Inverse Probability Weights

2012-07-05 Thread Thomas Lumley

If you're going to reply to something from two weeks ago, it's helpful
to include more of the conversation.

However, the mechanism is straightforward. The standard error
estimator assumes only that observations in different clusters are
independent: it approximates the variance of the estimating functions
by the empirical variance of the cluster totals of the estimating
functions, and uses the delta method to convert this to a variance for
the coefficients. It's the same as GEE.

In this simple setting it's the same as the GEE variance estimator.

- thomas

On Fri, Jul 6, 2012 at 7:40 AM, Joshua Wiley jwiley.ps...@gmail.com wrote:
Hi Frank,

It clusters by twin, that is why in Dr. Lumley's example, the id was
twin pair, not individual, and the SE is adjusted accordingly.

Cheers,

Josh

On Thu, Jul 5, 2012 at 12:10 PM, RFrank spark...@gmail.com wrote:
Thanks -- extremely helpful. But what is the mechanism by which this
analysis corrects for the fact that my subjects are clustered (twins)?

--
View this message in context:
http://r.789695.n4.nabble.com/GEE-with-Inverse-Probability-Weights-tp4633172p4635533.html
Sent from the R help mailing list archive at Nabble.com.

__
R-help@r-project.org mailing list
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.

--
Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles
https://joshuawiley.com/

__
R-help@r-project.org mailing list
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.

--
Thomas Lumley
Professor of Biostatistics
University of Auckland

__
R-help@r-project.org mailing list
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] Fwd: An application for a master's student in statistics

2012-07-05 Thread Arlington Llerena Martinez

Profesor Simon N. Wood

As a student from the Masters on statistics at Nacional University I am
writing to you to ask for some information due to knowledge on the field I
am working on
I wonder if you are so kind as to help out with the mathematical and
stadistical details as well as information about the funtion  predict.gam
{mgcv} which is part of the packet   mgcv from the software R.

I really appreciate both the interest and time you can give to my request.
Your faithfully

Arlington Zahìr Llerena

Bogota, Colombia





-- 
*
*
*


El alma se nutre a través del silencio,

el estudio, el consumo justo, el contacto con la naturaleza

y el conocimiento de uno mismo

Alberto D. Fraila Oliver

Arlington Zahìr Llerena...!!!*



-- 
*
*
*


El alma se nutre a través del silencio,

el estudio, el consumo justo, el contacto con la naturaleza

y el conocimiento de uno mismo

Alberto D. Fraila Oliver

Arlington Zahìr Llerena...!!!*

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Plotting the probability curve from a logit model with 10 predictors

2012-07-05 Thread Abraham Mathew

I have a logit model with about 10 predictors and I am trying to plot the
probability curve for the model.

Y=1 = 1 / 1+e^-z  where  z=B0 + B1X1 + ... + BnXi

If the model had only one predictor, I know to do something like below.

mod1 = glm(factor(won) ~ as.numeric(bid), data=mydat,
family=binomial(link=logit))

all.x - expand.grid(won=unique(won), bid=unique(bid))
y.hat.new - predict(mod1, newdata=all.x, type=response)
plot(bid-000:250,predict(mod1,newdata=data.frame(bid-c(000:250)),type=response),
lwd=5, col=blue, type=l)


I'm not sure how to proceed when I have 10 or so predictors in the logit
model. Do I simply expand the
expand.grid() function to include all the variables?

So my question is how do I form a plot of a logit probability curve when I
have 10 predictors?

would be nice to do this in ggplot2.

Thanks!


-- 
*Abraham Mathew
Statistical Analyst
www.amathew.com
720-648-0108
@abmathewks*

[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list
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] Silencing the output of install.packages()