Re: [R] I need help in seeing the code

2014-07-21 Thread PIKAL Petr
Hi Anyway. AFAIK your code looks OK to me, provided you want find the number of rows without NA in each file. Petr > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > project.org] On Behalf Of Sarah Goslee > Sent: Tuesday, July 22, 2014 8:22 AM > To: D

Re: [R] I need help in seeing the code

2014-07-21 Thread Sarah Goslee
Hi Darius, This is the main R-help list. We don't know anything about your Coursera class, including what your code is supposed to do. Not only that, this list has a no homework policy. You need to use the discussion group associated with your course, or whatever materials it provides, to get ass

[R] I need help in seeing the code

2014-07-21 Thread Darius Mulia
Hi there, I am Darius and I am taking the R Programming course in Coursera. I have a problem that I had spent so much looking for the problem. I wrote my code and I believe that the code works perfectly fine because it produces the result as what the course demanded. However, when I tried to submi

Re: [R] 1st el of a list of vectors

2014-07-21 Thread Hervé Pagès
Hi Carol, On 07/21/2014 09:10 PM, Richard M. Heiberger wrote: l = list(c(1,2), c(3,5,6), c(7)) sapply(l, `[`, 1) Using sapply() works but won't be very efficient if you have a very long list. If you worry about efficiency, you can do the following (using the IRanges package from Bioconductor)

Re: [R] odd, even indices of a vector

2014-07-21 Thread Hervé Pagès
Hi Carol, On 07/21/2014 01:33 PM, carol white wrote: Might be a trivial question but how to identify the odd and even indices of a vector? x = c(1,z,w,2,6,7) el of odd indices= 1,w,6 el of even indices= z,2,7 The easiest way is to subset your vector with c(TRUE, FALSE) to keep only the odd

Re: [R] odd, even indices of a vector

2014-07-21 Thread Bert Gunter
Ms. White: Unless I have seriously misjudged, you really really really need to go through an R tutorial -- An Intro to R ships with R, but there are many on the web -- before posting here further. You do not appear to have made much of an effort to learn even the basics, and I consider it unfair t

Re: [R] 1st el of a list of vectors

2014-07-21 Thread Richard M. Heiberger
l = list(c(1,2), c(3,5,6), c(7)) sapply(l, `[`, 1) On Mon, Jul 21, 2014 at 3:55 PM, carol white wrote: > Hi, > If we have a list of vectors of different lengths, how is it possible to > retrieve the first element of the vectors of the list? > > > l = list(c(1,2), c(3,5,6), c(7)) > > 1,3,7 shoul

Re: [R] odd, even indices of a vector

2014-07-21 Thread Richard M. Heiberger
## these functions assume the argument is integer odd <- function(x) x%%2 != 0 even <- function(x) x%%2 == 0 evenb <- function(x) !odd(x) odd(1:10) even(1:10) evenb(1:10) On Mon, Jul 21, 2014 at 4:33 PM, carol white wrote: > Might be a trivial question but how to identify the odd and even ind

Re: [R] Maximum likelihood estimation (stats4::mle)

2014-07-21 Thread David Winsemius
On Jul 21, 2014, at 12:10 PM, Ronald Kölpin wrote: > Dear R-Community, > > I'm trying to estimate the parameters of a probability distribution > function by maximum likelihood estimation (using the stats4 function > mle()) but can't seem to get it working. > > For each unit of observation I hav

Re: [R] Help with SEM package - model significance

2014-07-21 Thread Bernardo Santos
Hi John, Thanks for your reply (1 month later lol). In fact maybe the point is that I do not understand exactly the role of latent variables (what they are, and how to define them in R) in SEM. Do you have any suggestion of easy basic literature on SEM that can help me with that? Most things I h

[R] odd, even indices of a vector

2014-07-21 Thread carol white
Might be a trivial question but how to identify the odd and even indices of a vector? x = c(1,z,w,2,6,7) el of odd indices= 1,w,6 el of even indices= z,2,7 given the def of odd and even in https://stat.ethz.ch/pipermail/r-help/2010-July/244299.html should a loop be used? for (i in 1: length(

[R] Maximum likelihood estimation (stats4::mle)

2014-07-21 Thread Ronald Kölpin
Dear R-Community, I'm trying to estimate the parameters of a probability distribution function by maximum likelihood estimation (using the stats4 function mle()) but can't seem to get it working. For each unit of observation I have a pair of observations (a, r) which I assume (both) to be log-nor

Re: [R] standard error of survfit.coxph()

2014-07-21 Thread array chip
Dear Terry/All, I was trying to use your explanation of the standard error estimate from survfit.coxph() to verify the standard error estimates for the method of log(log(S)), but couldn't get the estimates correct. Here is an example using the lung dataset: > fit<-coxph(Surv(time,status)~wt.

[R] 1st el of a list of vectors

2014-07-21 Thread carol white
Hi, If we have a list of vectors of different lengths, how is it possible to retrieve the first element of the vectors of the list? l = list(c(1,2), c(3,5,6), c(7)) 1,3,7 should be retrieved Thanks Carol [[alternative HTML version deleted]] __

Re: [R] duplicated rows of a matrix

2014-07-21 Thread carol white
I need that duplicated indicate all row indices (occurences) that are duplicated. In your example, rows 2,3,4,5,8 Thanks. Carol On Monday, July 21, 2014 9:17 PM, William Dunlap wrote: Can you give an example of duplicated() not working on the rows of a matrix? Here is an example where i

Re: [R] standard error of survfit.coxph()

2014-07-21 Thread array chip
Terry, I figured out that variance of log(-log(S)) should be (1/H^2)var(H), not (1/S^2)var(H)! Thanks John e...@mayo.edu>; "r-help@r-project.org" Sent: Monday, July 21, 2014 11:41 AM Subject: Re: standard error of survfit.coxph() Dear Terry, I was try

Re: [R] Application design.

2014-07-21 Thread Richard M. Heiberger
Since your boss is Excel based, you might want to give the appearance of staying in that environment. Take a look at RExcel and RWord, both at rcom.univie.ac.at RExcel is a seamless integration of Excel and R. See the book R through Excel that Erich Neuwirth (the author of RExcel) and I wrote. ht

[R] Application design.

2014-07-21 Thread John McKown
I'm designing an R based application for my boss. It's not much, but it might save him some time. What it will be doing is reading data from an MS-SQL database and creating a number of graphs. At present, he must log into one server to run a vendor application to display the data in a grid. He then

Re: [R] Help with SEM package - model significance

2014-07-21 Thread John Fox
Dear Bernado, This isn't really a suitable topic to pursue on the r-help list, so I'll just comment briefly: On Mon, 21 Jul 2014 17:34:52 -0700 Bernardo Santos wrote: > Hi John, > > Thanks for your reply (1 month later lol). > In fact maybe the point is that I do not understand exactly the r

Re: [R] Semi Markov warnings ( for dummies)

2014-07-21 Thread Rolf Turner
If you are going to drive a car you should learn to drive. Read the basic intro material for R. Where does the function "readdata" come from? The syntax you use (having an assignment inside the function call) is let us say unorthodox and highly inadvisable. Since you got an error reading

Re: [R] roxygen2

2014-07-21 Thread Brian Diggs
On 7/20/2014 12:50 AM, Kevin Kunzmann wrote: Hi, I have developed a package and would like to switch documentation to roxygen2 from manual :) However >roxygen2::roxygenize() First time using roxygen2 4.0. Upgrading automatically... Loading required package: nleqnslv Error in

Re: [R] Include plotting symbals pch 16 and 17 into captions / text in pdf graph

2014-07-21 Thread David Winsemius
It's a hack but this works: cairo_pdf("utftext.pdf", family="Calibri") plot(0:1,0:1, type="n") points(0.2, 1, pch=16) mtext( text = "pch=16 (\U25CF)", side = 3, at = 0.2, line = 1, ) points(0.8, 1, pch=17); points(0.85, 1.1, pch=17, xpd=TRUE) # par(xpd=TRUE) lets p

Re: [R] duplicated rows of a matrix

2014-07-21 Thread William Dunlap
duplicated(x), for vector or matrix x, flags any value (row for matrices) previously seen in x. To flag all duplicated values (rows for matrices) you can use the following allDups() function. allDups <- function(x) duplicated(x) | duplicated(x, fromLast=TRUE) > In your example, rows 2,3,4,5,8

[R] anova.lme

2014-07-21 Thread Robert Lynch
I would like to know the sum of squares for each term in my model. I used the following call to fit the model fit.courseCross <- lme(fixed= zGrade ~ Rep + ISE +P7APrior+Female+White+HSGPA+MATH+Years+Course+Course*P7APrior , random= ~1|SID, data = Master.complet

Re: [R] duplicated rows of a matrix

2014-07-21 Thread William Dunlap
Can you give an example of duplicated() not working on the rows of a matrix? Here is an example where it does work: > m <- cbind(c(a=1,b=2,c=3,d=2,e=3,f=4,g=1,h=1), c(11,13,11,13,11,13,13,11)) > class(m) [1] "matrix" > m [,1] [,2] a1 11 b2 13 c3 11 d2 13 e3 11 f

Re: [R] standard error of survfit.coxph()

2014-07-21 Thread array chip
Dear Terry, I was trying to use your explanation of the standard error estimate from survfit.coxph() to verify the standard error estimates for the method of log(log(S)), but couldn't get the estimates correct. Here is an example using the lung dataset: > fit<-coxph(Surv(time,status)~wt.loss,l

[R] Error message for corAR1()

2014-07-21 Thread Wilson, Jenny
Hi, I am trying to answer the see if density.km (response) is affected by Direction (continuous, integer), Layer (nominal with 12 levels) and direction (nominal with 8 levels). There is an interaction between Layer and Direction. Platform.field is a list of 9 different platforms and is being t

[R] deviance as a goodness of fit in GLM

2014-07-21 Thread Samantha PameLa
Good day everybody, I'm a marine biologist student, working on my bachelor thesis and I'm stucked with a statistical doubt in the process, I hope someone here could help me. My thesis aims to understand which biological and environmental factors influences the male aggressive rate of male

[R] duplicated rows of a matrix

2014-07-21 Thread carol white
Hi, is it possible to find the duplicated rows of a matrix without a loop or i have to loop over the rows? duplicated doesn't seem to be helpful Thanks Carol [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://st

[R] Estimation of Zero Inflated Over dispersed Beta Binomial Using glamADMB()

2014-07-21 Thread Rajibul Mian
Dear All, I have been facing problem running the following code by using ---glamADMB()-- glmmadmb(y_zibb~x+factor(z)+g, data= data_mis_model, family = "betabinomial", link = "logit", zeroInflation=T) where "y_zibb" contains zero inflated Beta Binomial response , "x" is a normal random variate "z

[R] Generating nonlinear Poisson time series data

2014-07-21 Thread Kristynn Sullivan
We are attempting to create a short Poisson time series (between 10 and 50 datapoints) for a simulation. We want these time series to have no counts of over 100 and not be zero-inflated. We also are trying generate various nonlinearities, particularly of a cyclic nature. We have been attempting to

[R] Weight, weight - do tell me

2014-07-21 Thread Lenth, Russell V
This is a question only about terminology. Suppose I have data categorized by three factors A, B, and C, with cell means ybar_ijk and cell frequencies n_ijk, where I, j, and k index A, B, and C respectively. And suppose I want to summarize the results for factor A by computing some sort of weig

Re: [R] help with column substaction with a twist

2014-07-21 Thread Greg Snow
Here is another approach in R (blatantly stealing Jim Holtman's code to generate sample data): > set.seed(1) > n <- 100 > test <- data.frame(p = sample(10, n, TRUE) + , b = sample(10, n, TRUE) + ) > test$e <- sample(5, n, TRUE) + test$b # make sure e > b > > tmp1 <

[R] FW: two questions - function help and 32vs64 bit sessions

2014-07-21 Thread Fowler, Mark
-Original Message- From: Fowler, Mark Sent: July 21, 2014 1:56 PM To: 'Duncan Murdoch' Subject: RE: [R] two questions - function help and 32vs64 bit sessions The server doesn't shut down, it just kind of shuts everybody else down. But your mention of TEMPDIR jostled some old memory cell

Re: [R] Survival Analysis with an Historical Control

2014-07-21 Thread Andrews, Chris
Hi Paul, Sorry for the delayed reply. I was away last week. I'm not clear what you want confirmed about your approach. (a) "20.57"- computing the rejection region of the analysis. The formulas implemented at the addresses you gave in your original post are from a reputable source - Lawless (1

Re: [R] two questions - function help and 32vs64 bit sessions

2014-07-21 Thread Duncan Murdoch
On 21/07/2014 9:40 AM, Fowler, Mark wrote: Hi Duncan, I tried your suggestion, but no luck. The first error is no surprise, it just confirms the address is lost. The second line suggests it worked, but it didn't. The session is still remembering the original address. > tools::startDynamicHelp(FA

[R] Semi Markov warnings ( for dummies)

2014-07-21 Thread M.A. Pet
*Hello,* I never worked with R before my supervisor asks me to run a semiMarkov analysis a month ago. After a long struggle, to date, the code works, but I still get some warnings. However, because of my lack of knowledge in R I am not possible to figure out the problems or say anything about the

Re: [R] two questions - function help and 32vs64 bit sessions

2014-07-21 Thread Fowler, Mark
Hi Duncan, I tried your suggestion, but no luck. The first error is no surprise, it just confirms the address is lost. The second line suggests it worked, but it didn't. The session is still remembering the original address. > tools::startDynamicHelp(FALSE) # shut it down Warning message: In file(

[R] Include plotting symbals pch 16 and 17 into captions / text in pdf graph

2014-07-21 Thread Rainer M Krug
Hi I want to include the plotting symbols pch=16 and pch=17 in text in the graph used as labels. This works: --8<---cut here---start->8--- plot(0:1,0:1, type="n") points(0.2, 1, pch=16) mtext( text = "pch=16 (\U25CF)", side = 3, at =

Re: [R] packages across different versions of R

2014-07-21 Thread Prof Brian Ripley
On 21/07/2014 12:24, Charles Thuo wrote: I have just installed R 3.1.1 in a machine where R 3.0.1 is already installed. Is it possible to use packages in the 3.0.1 on the 3.1.1. version as the same are in a single workstation. Perhaps, perhaps not. It depends in part on your platform which

[R] packages across different versions of R

2014-07-21 Thread Charles Thuo
I have just installed R 3.1.1 in a machine where R 3.0.1 is already installed. Is it possible to use packages in the 3.0.1 on the 3.1.1. version as the same are in a single workstation. Charles [[alternative HTML version deleted]] __ R-help@

Re: [R] plotly

2014-07-21 Thread Sarah Goslee
Hi, On Monday, July 21, 2014, Shane Carey wrote: > Hey, > > What version of R is required to use the plotly library? > > I have R version 3.0.1 and it will not allow me to install the devtools > package or the ploty package. > > I have googled and searched to see what version of R I should be ru

[R] plotly

2014-07-21 Thread Shane Carey
Hey, What version of R is required to use the plotly library? I have R version 3.0.1 and it will not allow me to install the devtools package or the ploty package. I have googled and searched to see what version of R I should be running but could not find anything. Thanks -- Shane [[