Re: [R] New to R, Curious about Project Idea

2012-01-12 Thread Antonio Rodriges
Phil, You should look onto sp package which is the base for any other spatial packages in R http://cran.r-project.org/web/packages/sp/index.html Also notice Reverse depends section where you can find a lot of useful packages for spatial operations and analysis. For loading shape files,

[R] problems with method ken.sto in package soil.spec: subscript out of bounds

2012-01-12 Thread Martin Guetlein
Hi All, I would like to use Kennard-Stone algorithm for splitting a dataset. mydata - read.csv(url(http://www.ats.ucla.edu/stat/r/dae/binary.csv )) library(soil.spec) ken.sto(mydata,per.n=0.3) Error in ken.sto(mydata, per.n = 0.3) : subscript out of bounds I found that other people run into

Re: [R] kruskal wallis post hoc?

2012-01-12 Thread Tal Galili
Hi Iasonas , This is a stat question and not an R question. But the general answer is that it could happen :) The R question would have been if their is a Tukey HSD for kruskel.test, the answer is yes: http://stats.stackexchange.com/questions/17342/is-there-a-nonparametric-equivalent-of-tukey-hsd

Re: [R] problems with glht for ancova

2012-01-12 Thread gaiarrido
I answer myself, perhaps it can be useful to anyone. The problem is that I tried to run a psot hoc test before i get the minimal model by deleting the interaction, if I do it: ancova2-aov(log(peso)~edadysexo+log(lcc)) anova(ancova,ancova2) Res.DfRSS Df Sum of Sq F Pr(F) 1509

Re: [R] kruskal wallis post hoc?

2012-01-12 Thread gaiarrido
Try to use kruskalmc in the package pgirmess I give one of my results kruskal.test(rojos~mes) Kruskal-Wallis chi-squared = 132.3091, df = 3, p-value 2.2e-16 kruskalmc(rojos~mes) Multiple comparison test after Kruskal-Wallis p.value: 0.05 Comparisons obs.dif critical.dif

Re: [R] Restricting R session

2012-01-12 Thread Uwe Ligges
On 11.01.2012 21:13, Antonio Rodriges wrote: Thank you, Uwe, below are my comments In particular, how to prohibit some set of functions, for example, from base package? You can't: R is free software. This does not imply it must be inflexible and unsuitable for cloud services The

Re: [R] problems with glht for ancova

2012-01-12 Thread gaiarrido
Thanks very much - Mario Garrido Escudero PhD student Dpto. de Biología Animal, Ecología, Parasitología, Edafología y Qca. Agrícola Universidad de Salamanca -- View this message in context: http://r.789695.n4.nabble.com/problems-with-glht-for-ancova-tp4284908p4288227.html Sent from the R

Re: [R] cannot get tweets from twitteR

2012-01-12 Thread Uwe Ligges
1. Please reply to your former messages (to keep it in the same thread) and quote them. 2. You may want to ask the maintainers of the two projects. I doubt you will find too many users who are using both of them at the same time. Uwe Ligges On 12.01.2012 05:39, Sachinthaka Abeywardana wrote:

Re: [R] kruskal wallis post hoc?

2012-01-12 Thread Iasonas Lamprianou
Thank you for the result, I will have a look at the link.   Dr. Iasonas Lamprianou Department of Social and Political Sciences University of Cyprus From: Tal Galili tal.gal...@gmail.com To: Iasonas Lamprianou lampria...@yahoo.com Cc: r-help@r-project.org

Re: [R] Rpad.org down? Searching latest R-Reference card

2012-01-12 Thread Jonas Stein
i'd like to update my R-Reference card and commit some edits, but i could not get the source from rpad.org R Reference Card is dead? No! Long live the R Reference Card. ;-) Tom Short granted to the public domain 2004-11-07 and got permission to include material from Emmanuel Paradis (R for

Re: [R] R for windows 64 bit

2012-01-12 Thread Manta
Dear all, I know this may have been already discussed, but I could not find a solution. I am using R 13.2 64 bit on a 64 bit machine dual core. I'm fitting a Cox proportional model to a matrix 1e06x7. Before starting the model fitting I set memory.size(max=1) and I do a clean of the garbage

Re: [R] Vegan(ordistep) error: Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed

2012-01-12 Thread Jari Oksanen
Nevil Amos nevil.amos at gmail.com writes: Whilst the constrained proportion was 0 in the example below I am getting the error in cases where this is not so. See new output pasted below Nevil, This still sounds like the same problem. I can't reproduce your problem, but I could construct a

[R] error message in R 2.1.14 installation

2012-01-12 Thread carol white
Hi, I tried to install R.2.14.1 but when running ./configure command, I got the following error message configure: error: --with-readline=yes (default) and headers/libs are not available All checking prior to this error message passed without any problem (see below). Cheers, Carol

Re: [R] error message in R 2.1.14 installation

2012-01-12 Thread peter dalgaard
On Jan 12, 2012, at 13:03 , carol white wrote: Hi, I tried to install R.2.14.1 but when running ./configure command, I got the following error message configure: error: --with-readline=yes (default) and headers/libs are not available All checking prior to this error message passed

Re: [R] error message in R 2.1.14 installation

2012-01-12 Thread carol white
The OS is fedora 10. It's also a 32-bit architecture. Best, - Original Message - From: peter dalgaard pda...@gmail.com To: carol white wht_...@yahoo.com Cc: r-h...@stat.math.ethz.ch r-h...@stat.math.ethz.ch Sent: Thursday, January 12, 2012 1:27 PM Subject: Re: [R] error message in R

Re: [R] R for windows 64 bit

2012-01-12 Thread Uwe Ligges
1. Please cite the former part of the thread. 2. We need a reproducible example that shows the standstill situation. 3. I doubt you can provide 2: it probably just looks like standstill, but is the slow memory access for virtual memory. Therefore: a) upgrade your R (13.2 is an invalid version

Re: [R] error message in R 2.1.14 installation

2012-01-12 Thread Marc Schwartz
As Peter noted, you would need to install the readline-devel RPM and this is covered in the manual he referenced. Thus, via the command line, as root, you would want to use: yum install readline-devel and that should resolve your problem. In addition, Fedora 10 is around 3 years old and is

Re: [R] error message in R 2.1.14 installation

2012-01-12 Thread peter dalgaard
On Jan 12, 2012, at 13:38 , carol white wrote: The OS is fedora 10. It's also a 32-bit architecture. 10? Aren't they at 15 or 16 by now? I guess you need yum install readline-devel or thereabouts. Best, - Original Message - From: peter dalgaard pda...@gmail.com To:

Re: [R] kruskal wallis post hoc?

2012-01-12 Thread Frank Harrell
The Kruskal-Wallis test is a special case of the proportional odds ordinal logistic model. You can get any contrast you want by testing regression coefficients. In a couple of weeks the rms package's contrast function will allow for individual confidence intervals of effects that together have

Re: [R] R for windows 64 bit

2012-01-12 Thread Manta
Dear Uwe, many thanks for your message. To reply to your questions, as you imagined I cannot provide a reproducible example. In addition, I cannot expand the memory, as I'm working on a virtual desktop. At any rate, the program is really on 'standstill' as the memory usage is flat and does not

[R] data manipulation

2012-01-12 Thread Rinde
Hi all, I'm trying to do some data manipulation using R, but I'm a bit stuck. I have to warn you, I'm a real R noob. I have for example this file: V1 V2 V3 V4 V5V6 1:156706559

[R] defmacro installation issue

2012-01-12 Thread ikuzar
Hi everybody, I want to use macro in my R code. But defmacro was not in my libraries. So I installed it : install.packages(gtools) Installing package(s) into ‘C:/Program Files/R/R-2.13.2/library’ (as ‘lib’ is unspecified) essai de l'URL

[R] glht (multicomparisons) with an interaction factor

2012-01-12 Thread gaiarrido
Hi, i was working with this model mq-glm(rojos~edadysexo*zona*estacion,quasipoisson) and i get this minimal adequate model anova(mq5,test=F) Df Deviance Resid. Df Resid. DevFPr(F) NULL518 64799 edadysexo

[R] posting for r-help

2012-01-12 Thread rbuxton
Hi there I have a post I would like to put on the 95% confidence intercal with glm thread. Thank-you so much! I am wondering first of all if anyone knows how to calculate confidence intervals for a GLMM? I use the lme4 library. Also, I am wondering how to predict a model mean and confidence

Re: [R] RGL- Drawing Circle

2012-01-12 Thread gli
thanks for the help, Duncan. but when you said study some geometry, do you mean the rgl package pdf reference mannual or other documents? please clarify. i am a total beginner on rgl. graham -- View this message in context:

Re: [R] defmacro installation issue

2012-01-12 Thread R. Michael Weylandt
Works for me. Did you actually load the library or just install it? Try this: library(gtools) example(defmacro) Michael On Thu, Jan 12, 2012 at 6:18 AM, ikuzar raz...@hotmail.fr wrote: Hi everybody, I want to use macro in my R code. But defmacro was not in my libraries. So I installed it :

Re: [R] RGL- Drawing Circle

2012-01-12 Thread Uwe Ligges
On 12.01.2012 13:21, gli wrote: thanks for the help, Duncan. but when you said study some geometry, He meant basic school maths, I suppose. Uwe do you mean the rgl package pdf reference mannual or other documents? please clarify. i am a total beginner on rgl. graham -- View this

Re: [R] defmacro installation issue

2012-01-12 Thread Uwe Ligges
You have to load the gtools package via library() or require() before you can make use of the function. Uwe Ligges On 12.01.2012 12:18, ikuzar wrote: Hi everybody, I want to use macro in my R code. But defmacro was not in my libraries. So I installed it : install.packages(gtools)

[R] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread Michael
Hi all, I have an array of 1 x 200 x 200 numbers... which is a time-series of 200x200 2D data... The 1st dimension is the time index. Is there a way to make a movie out of these data - i.e. playback 1 frames(200x200) at a playback rate per second? Thanks a lot! [[alternative

Re: [R] [R-SIG-Finance] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread G See
Michael, Please don't cross post to both lists. If it doesn't have to do with finance, don't send it it r-sig-finance. Thanks, Garrett On Thu, Jan 12, 2012 at 8:38 AM, Michael comtech@gmail.com wrote: Hi all, I have an array of 1 x 200 x 200 numbers... which is a time-series of

Re: [R] general question on Spotfire

2012-01-12 Thread Terry Therneau
John, Spotfire is a menu driven data exploration tool, very popular here with biologists who found that their previous Excel based approach doesn't cut it for large data sets. When TIBCO wanted to expand the tool with further quantitative features they made (I think) a bright decision to

Re: [R] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread Sarah Goslee
[deleted the annoying cross-posting] On Thu, Jan 12, 2012 at 9:38 AM, Michael comtech@gmail.com wrote: Hi all, I have an array of 1 x 200 x 200 numbers... which is a time-series of 200x200 2D data... The 1st dimension is the time index. Is there a way to make a movie out of these

Re: [R] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread Michael
I usually display each 200x200 data as a heatmap... And now I only need to make a movie out of them... I don't have ImageMagick (not admin)... Any more pointers? Thanks a lot! On Thu, Jan 12, 2012 at 8:46 AM, Sarah Goslee sarah.gos...@gmail.comwrote: [deleted the annoying cross-posting]

Re: [R] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread Michael
Basically I wanted to find an equivalent of the following Matlab command in R: http://www.mathworks.com/help/toolbox/images/ref/immovie.html On Thu, Jan 12, 2012 at 8:46 AM, Sarah Goslee sarah.gos...@gmail.comwrote: [deleted the annoying cross-posting] On Thu, Jan 12, 2012 at 9:38 AM,

[R] R codes for Intervention Time Series Analysis

2012-01-12 Thread OMANE-ADJEPONG Maurice
Dear everyone, I need R codes to fit an Intervention Time Series Model for two separate policies for a single observed time series. Please, I have prior knowledge of how to fit the impact parameter(omega) but I no not the codes for the decay parameter(delta). Can someone help me?

Re: [R] R for windows 64 bit

2012-01-12 Thread R. Michael Weylandt michael.weyla...@gmail.com
Perhaps clearing unneeded objects our of your workspace with rm() might save a little memory but it's hard to say if that actually helps. Michael On Jan 12, 2012, at 8:11 AM, Manta mantin...@libero.it wrote: Dear Uwe, many thanks for your message. To reply to your questions, as you

Re: [R] Accomplishing a loop on multiple columns

2012-01-12 Thread Nerak
I just saw a little mistake in my last post: Totally in the end, last line of the last loop, results$depth[,u] [t-1] should be results$newdepth[,u] [t-1]. My apologies. for (u in 1:91) { results$newdepth [,u]- results$depth [,u] for (t in 2:60) { results$newdepth[,u][t] - results$newdepth[,u]

[R] Function accepted by optim but not mle2 (?)

2012-01-12 Thread Medimel
Dear Sir/ Madam, I'm having trouble de-bugging the following - which works perfectly well with optim or optimx - but not with mle2. I'd be really grateful if someone could show me what is wrong. Many thanks in advance. JSC: gompertz- function (x,t=data) { a3-x[1] b3-x[2]

Re: [R] Accomplishing a loop on multiple columns

2012-01-12 Thread Nerak
Many thanks! Never used lists before, but it’s a great solution! It works very well! Although, I have a next question concerning this. I want to know for which value (column) I have the maximal Rsquared. Therefore, I unlist the LIST so that it’s written like a vector. The columns were always

[R] compare means

2012-01-12 Thread kende jan
Dear all,   I would compare two means between cases and controls taking into account that I have  matched 1 case to two controls. How i can do it with R. Thanks in advance  Jan [[alternative HTML version deleted]] __ R-help@r-project.org

[R] strsplit() does not split on .?

2012-01-12 Thread Czerminski, Ryszard
Any ideas what is wrong? strsplit(a.b, .) # generates empty strings with split=. [[1]] [1] strsplit(a b, ) # seems to work fine with split= , and other characters... [[1]] [1] a b R.Version() $platform [1] x86_64-unknown-linux-gnu $arch [1] x86_64 $os [1] linux-gnu $system [1] x86_64,

Re: [R] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread Sarah Goslee
On Thu, Jan 12, 2012 at 9:59 AM, Michael comtech@gmail.com wrote: I usually display each 200x200 data as a heatmap... And now I only need to make a movie out of them... That was the part I was querying: do you need to be able to upload this to YouTube? Embed in a presentation? Look at it

Re: [R] strsplit() does not split on .?

2012-01-12 Thread Sarah Goslee
Reread the help for strsplit: ## Note that 'split' is a regexp! ## If you really want to split on '.', use unlist(strsplit(a.b.c, \\.)) ## [1] a b c ## or unlist(strsplit(a.b.c, ., fixed = TRUE)) For your example: strsplit(a.b, \\.) [[1]] [1] a b In other words,

Re: [R] strsplit() does not split on .?

2012-01-12 Thread Jorge I Velez
Hi Ryszard, Try strsplit(a.b, [.])[[1]] and see Extended Regular Expressions in ?regexp. HTH, Jorge,- On Thu, Jan 12, 2012 at 10:15 AM, Czerminski, Ryszard wrote: Any ideas what is wrong? strsplit(a.b, .) # generates empty strings with split=. [[1]] [1] strsplit(a b, ) # seems

Re: [R] strsplit() does not split on .?

2012-01-12 Thread Czerminski, Ryszard
Because it uses regexp: use split='\\.' to split on . char and read help(strsplit) :) Ryszard -- Confidentiality Notice: This message is private and may contain confidential and proprietary information. If you have

Re: [R] Points inside a polygon

2012-01-12 Thread Justin Haynes
On Wed 11 Jan 2012 08:28:03 PM PST, Hasan Diwan wrote: I have a list of bounds for a series of polygons. I do understand the formula to determine whether point i is within polygon X (X[x1] i[x] X[x2] i[x] X[y1] i[y] X[y2] i[y]), and I can apply this throughout the dataset. However, this

Re: [R] R for windows 64 bit

2012-01-12 Thread Manta
It was already done, as I reduced the dataset at the minimum I could. I really need to solve this issue somehow. -- View this message in context: http://r.789695.n4.nabble.com/R-for-windows-64-bit-tp1011346p4289419.html Sent from the R help mailing list archive at Nabble.com.

[R] [R-pkgs] Rook: software and specification for R web applications and servers

2012-01-12 Thread Jeffrey Horner
Dear  useRs, Rook version 1.0-3 has been submitted to CRAN. In the mean time you can get it here: https://github.com/jeffreyhorner/rRack/blob/master/Rook_1.0-3.tar.gz The latest release contains support for deployment with rApache. Please see 3.6.5 and 3.6.6 under section 'Configuring rApache'

Re: [R] R for windows 64 bit

2012-01-12 Thread Marc Schwartz
On Jan 12, 2012, at 9:54 AM, Manta wrote: It was already done, as I reduced the dataset at the minimum I could. I really need to solve this issue somehow. What VM are you using on what underlying OS? Perhaps the VM configuration is limiting memory allocation in some fashion for

Re: [R] how do I make a movie out of a timeseries of 2D data?

2012-01-12 Thread Greg Snow
If you need the animation in a file outside of R (or possibly in R) then look at the animation package. This allows you quite a few options on how to save an animation, some of which depend on outside programs, but options mean that if you don't have one of those programs there are other ways

Re: [R] Function accepted by optim but not mle2 (?)

2012-01-12 Thread Jeff Newmiller
What is wrong is that you define and use parameters and global data inconsistently in your functions. v - 6 f - function( x ) { x^2 } g - function( x ) { v^3 } f(v) # right answer g(v) # right answer, accidentally f(5) # works as expected g(5) # surprise You need to go through your functions

[R] parallel computation in plyr 1.7

2012-01-12 Thread Aditya Bhagwat
Dear all, I have a question regarding the possibility of parallel computation in plyr version 1.7. The help files of the following functions mention the argument '.parallel': ddply, aaply, llply, daply, adply, dlply, alply, ldply, laply However, the help files of the following functions do

Re: [R] Function accepted by optim but not mle2 (?)

2012-01-12 Thread Ben Bolker
Medimel medimelenglish at gmail.com writes: Dear Sir/ Madam, I'm having trouble de-bugging the following - which works perfectly well with optim or optimx - but not with mle2. I'd be really grateful if someone could show me what is wrong. Many thanks in advance. JSC: mle2 is

Re: [R] general question on Spotfire

2012-01-12 Thread Frank Harrell
As a slight aside, Tibco/Spotfire originally planned to provide a capability to load R packages into S-Plus. This always seemed to me to be a hard thing to do, and if my understanding is correct, this proved to be too difficult to do in S-Plus, at least for large packages such as mine. Frank

[R] How can I prevent solve.QP from printing the solution progress ?

2012-01-12 Thread Uzuner, Tolga I
Dear R Users, How can I prevent solve.Qp from printing the solution progress ? Thanks in advance, Tolga This email is confidential and subject to important disclaimers and conditions including on offers for the purchase or sale of securities, accuracy and completeness of information, viruses,

[R] is there an equivalent for #ifdef (C langage) in R

2012-01-12 Thread ikuzar
Hi, I'd like to know if there is an equivalent for #ifdef (Clangage) in R. I 'd like to do something like: useDebug = defmacro(DEBUG, expr=(DEBUG==1)) if(useDebug(0)){ #Here I do not use debug mode make_addition = function(a, b) { c=a+b plot(c) return(c) }

[R] help request

2012-01-12 Thread OMANE-ADJEPONG Maurice
Good day everyone, I am using the data below to fit Intervention Time Series model for two policies introduced in 2002 (54th data point) and 2003 (55th data point) respectively. Please can anyone give me a complete R code for modeling the two step functions? I have already modeled the

[R] [R-pkgs] haplo.stats version 1.5.2

2012-01-12 Thread Sinnwell, Jason P.
haplo.stats, version 1.5.2, is now available on CRAN. Below I provide the description and link to our software page where you can also find the updated user manual. The most notable updates for this version were to make the haplo.glm fitted object work more like the glm object; other changes are

[R] Add color to Boxplot by value

2012-01-12 Thread KWyshak
I have a boxplot of Production run rates per 10 minute intervals and I would like to color code them by the average (i.e. 15ppm = green, 9ppm = red, everything else yellow). Is there a way to do this? http://r.789695.n4.nabble.com/file/n4289381/RunRateBoxWhisker.png -- View this message in

[R] using list= to force evaluation before execution

2012-01-12 Thread Aditya Bhagwat
Dear all, I have noticed that the expression 'list =' is sometimes used to tell R to evaluate something before executing it. Two examples: rm(list=ls()) a = 3 myVarName = 'a' save(list=myVarName, file=...) I was wondering whether there is any documentation on this way of using list. Which is

Re: [R] using list= to force evaluation before execution

2012-01-12 Thread jim holtman
Read the documentation for those two commands and you will see that 'list' is just a parameter to the function. It would have been called 'xyz' and worked the same. The is nothing special about 'list =' in this context; it is just naming a parameter to the function. On Thu, Jan 12, 2012 at

[R] relative frequency plot using ggplot or other function

2012-01-12 Thread Mary Kindall
Hi I have a data frame in the following form. There are two groups and for each 'width' relative frequency for group1 and group2 is given. How to plot this in R using ggplot or other package. Width relativeFrequency1 relativeFrequency2 1 100 0.0006388783 0.02265428 2 200

Re: [R] using list= to force evaluation before execution

2012-01-12 Thread R. Michael Weylandt michael.weyla...@gmail.com
Nope - you misunderstand entirely. Both of those functions have an argument named list and the code you quote is just the standard way of using a named argument. It could just as well read rm(salmon = ls()) but that would be absurd. The list argument gets its name from the fact it (usually)

[R] how do I find previous version of a package?

2012-01-12 Thread Michael
Hi all, I am installing a package called fields but it's for R version 2.13... I only have R 2.12 on Linux. How do I find the earlier version of fields? Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing

Re: [R] using list= to force evaluation before execution

2012-01-12 Thread Aditya Bhagwat
Oh, indeed. Thanks, Jim and Michael for clarifying, and making me aware of my incorrect inference! Adi On Thu, Jan 12, 2012 at 6:04 PM, R. Michael Weylandt michael.weyla...@gmail.com michael.weyla...@gmail.com wrote: Nope - you misunderstand entirely. Both of those functions have an argument

Re: [R] is there an equivalent for #ifdef (C langage) in R

2012-01-12 Thread William Dunlap
You could put your debug-only code into a function calls like ifDebug(diagnosticPlot(c)) and ifDebug({ tmp - timeConsumingFunction(c) stopifnot(tmp 1.0) }) When you want debug output define ifDebug as ifDebug - function(expr) force(expr) and when you don't want it

Re: [R] how do I find previous version of a package?

2012-01-12 Thread R. Michael Weylandt michael.weyla...@gmail.com
I assume you mean it's not on CRAN. You'll have to build from source. The easiest way to do so is with the type argument to install.packages() Michael On Jan 12, 2012, at 12:05 PM, Michael comtech@gmail.com wrote: Hi all, I am installing a package called fields but it's for R version

Re: [R] [ncdf] programmatically copying a netCDF file

2012-01-12 Thread David William Pierce
Hi Tom, a few answers to your questions: On Mon, Jan 9, 2012 at 3:54 PM, Tom Roche tom_ro...@pobox.com wrote: :-) I guess I should have explained: I need to copy most of a source file, modifying only part, and to write a target file. So my motivation for this thread is, first, to be sure I

Re: [R] relative frequency plot using ggplot or other function

2012-01-12 Thread Justin Haynes
On Thu 12 Jan 2012 09:02:27 AM PST, Mary Kindall wrote: Hi I have a data frame in the following form. There are two groups and for each 'width' relative frequency for group1 and group2 is given. How to plot this in R using ggplot or other package. Width relativeFrequency1

Re: [R] how do I find previous version of a package?

2012-01-12 Thread Michael
http://cran.r-project.org/web/packages/fields/index.html As you can see, it clearly stated that 2.13... I thought in Linux, we default to download and build from the source... using install.packages() ... How do I really build it for 2.12? On Thu, Jan 12, 2012 at 11:12 AM, R. Michael

Re: [R] how do I find previous version of a package?

2012-01-12 Thread Marc Schwartz
You missed the Old Sources link under Downloads: on that page (which most CRAN packages have): http://cran.r-project.org/src/contrib/Archive/fields/ You can then download the appropriate tarball version and install the package locally. HTH, Marc Schwartz On Jan 12, 2012, at 11:17 AM,

Re: [R] relative frequency plot using ggplot or other function

2012-01-12 Thread Mary Kindall
Hi this is exactly what i am looking for but I do not like to draw as histogram instead I want two separate plot for this data. Something like the ones shown in the following link. Please disregard the legends of the following fig.

Re: [R] how do I find previous version of a package?

2012-01-12 Thread R. Michael Weylandt michael.weyla...@gmail.com
Use a version from the archives available on the link you quoted. If you really want the current version, you could try to change the dependency before installation but I imagine the maintainer put it there for good reasons. Of course, the real answer is to update R. Michael PS - If I

Re: [R] Unexpected results using the oneway_test in the coin package

2012-01-12 Thread David Winsemius
The usual way to pose questions about unexpected behavior is to look up the package maintainer's name and email address in the DESCRIPTION file of the package which is accessed with the help function: help(package=coin) You see: Maintainer: Torsten Hothorn torsten.hoth...@r-project.org --

Re: [R] using list= to force evaluation before execution

2012-01-12 Thread David Winsemius
On Jan 12, 2012, at 12:04 PM, R. Michael Weylandt wrote: Nope - you misunderstand entirely. Both of those functions have an argument named list and the code you quote is just the standard way of using a named argument. It could just as well read rm(salmon = ls()) but that would be

Re: [R] kruskal wallis post hoc?

2012-01-12 Thread peter dalgaard
On Jan 12, 2012, at 14:11 , Frank Harrell wrote: The Kruskal-Wallis test is a special case of the proportional odds ordinal logistic model. Eh? Can you elaborate on that? I would expect that at best it is equivalent to some _test_ in a polr-type model. It is never really clear what the

Re: [R] posting for r-help

2012-01-12 Thread Ben Bolker
rbuxton at mun.ca writes: I have a post I would like to put on the 95% confidence intercal with glm thread. Thank-you so much! Sending it where you did and titling it Re: 95% confidence interval with glm might add it to the same thread, but even if not it will be in roughly the right

Re: [R] relative frequency plot using ggplot or other function

2012-01-12 Thread Justin Haynes
ggplot(dat.melt,aes(x=width,y=value,fill=variable,colour=variable))+geom_density(stat='identity',alpha=0.5) the fill and colour variables can be removed if you want. or ggplot(dat.melt,aes(x=width,y=value,fill=variable))+geom_density(stat='identity',alpha=0.5)+facet_wrap(~variable,ncol=1) same

Re: [R] parallel computation in plyr 1.7

2012-01-12 Thread abhagwat
Additional question: the plyr package mentions that parallel computation can be set up using the parallel computing backend from 'foreach'. Is this limited to executing the following two lines on a UNIX machine (source http://cran.r-project.org/web/packages/doMC/.../gettingstartedMC.pdf

Re: [R] parallel computation in plyr 1.7

2012-01-12 Thread abhagwat
The code below shows that (1) the way to activate the parallel backend indeed is to use 'registerDoMC' (2) the function d_ply does NOT accept the argument parallel, while the function ddply does. Perhaps it is interesting to add this feature to d_ply, l_ply and a_ply too? As a workaround one can

Re: [R] is there an equivalent for #ifdef (C langage) in R

2012-01-12 Thread Thomas Lumley
On Fri, Jan 13, 2012 at 6:12 AM, William Dunlap wdun...@tibco.com wrote: You could put your debug-only code into a function calls like   ifDebug(diagnosticPlot(c)) and   ifDebug({        tmp - timeConsumingFunction(c)        stopifnot(tmp 1.0)   }) When you want debug output define

[R] parLapply within a function

2012-01-12 Thread Katja Hebestreit
Dear R users, I have some problems with the parLapply function from the parallel package: I use parLapply on a pretty big R object without changing the object within the called function. If I execute parLapply alone, everything works fine. It seems that the object resides only once in the

Re: [R] using list= to force evaluation before execution

2012-01-12 Thread R. Michael Weylandt
You are of course correct: I was trying to walk the line between using list in the colloquial sense of a set of things that seems to have motivated the formals of rm() and list in the sense of a VECSXP. In retrospect, I probably shouldn't have relegated that important distinction to a ill-phrased

Re: [R] Add color to Boxplot by value

2012-01-12 Thread Justin Haynes
how bout: dat-data.frame(val=rnorm(100,12,10),x=letters[1:4]) col.val-ddply(dat,.(x),summarise,mean(val)) col.val$breaks-cut(col.val$..1,c(0,9,15,Inf)) dat.merge-merge(dat,col.val) ggplot(dat.merge,aes(x=x,y=val,colour=breaks))+geom_boxplot()+scale_color_manual(values=c('green','yellow','red'))

Re: [R] Restricting R session

2012-01-12 Thread Antonio Rodriges
Thank you, Thomas, More precisely, there are several packages that could provide separate sessions, such as rserve and RApache. Thank you, we tried RServe. RApache is new for me. I've checked it: R access through Apache server. I also found interesting blog http://www.stat.ucla.edu/~jeroen/

Re: [R] Points inside a polygon

2012-01-12 Thread Rolf Turner
On 12/01/12 17:28, Hasan Diwan wrote: I have a list of bounds for a series of polygons. I do understand the formula to determine whether point i is within polygon X (X[x1] i[x] X[x2] i[x] X[y1] i[y] X[y2] i[y]), and I can apply this throughout the dataset. However, this naive algorithm

Re: [R] Restricting R session

2012-01-12 Thread Antonio Rodriges
Uwe, The opposite: It implies it is extremely flexible in the sense a user can do anything the OS allows, e.g by installation of packages that reimplement functions you had prohibited before. I don't see why this is related to cloud services. In a cloud process, again, the user can do as

Re: [R] is there an equivalent for #ifdef (C langage) in R

2012-01-12 Thread Gabor Grothendieck
On Thu, Jan 12, 2012 at 12:12 PM, William Dunlap wdun...@tibco.com wrote: You could put your debug-only code into a function calls like   ifDebug(diagnosticPlot(c)) and   ifDebug({        tmp - timeConsumingFunction(c)        stopifnot(tmp 1.0)   }) When you want debug output define

Re: [R] kruskal wallis post hoc?

2012-01-12 Thread Frank Harrell
Peter, The score test from the P.O. model for the global null hypothesis (k-1 degrees of freedom for comparing k groups) is almost exactly the Kruskal-Wallis test statistic. For the case where k=2 (Wilcoxon test) the numerator of the score test is exactly the numerator of the

[R] Keep rows where a variable matches one item of a vector

2012-01-12 Thread dadrivr
How do I subset data to only keep those rows of a dataframe where a variable's value matches one item of a vector. For example, how do I keep all of the rows (and all variables) where mydata$id equals one of the values in keepid? See below? mydata - NULL mydata$id - 1:30 mydata$value -

Re: [R] Keep rows where a variable matches one item of a vector

2012-01-12 Thread Sarah Goslee
Hi, On Thu, Jan 12, 2012 at 3:10 PM, dadrivr dadr...@gmail.com wrote: How do I subset data to only keep those rows of a dataframe where a variable's value matches one item of a vector.  For example, how do I keep all of the rows (and all variables) where mydata$id equals one of the values in

Re: [R] remoting ESS/R with tramp

2012-01-12 Thread Tom Roche
Tom Roche Thu, 12 Jan 2012 11:56:25 -0500 * I have access to the cluster [where I want to run R] configured [in .ssh/config] such that I can `ssh t` from commandline. 1 I can open an R file on the cluster with `C-x C-f /t:/home/me/onlyOrigDN2.r` from my laptop, and note the following

Re: [R] strange Sys.Date() side effect

2012-01-12 Thread MacQueen, Don
My best guess is that you are misunderstanding what the c() function does. I'd suggest reading the help page for c, obtained by typing ?c Note that if you supply c() with objects of different types (as you have), the results will probably not be what you wanted. Given what c() does, your output

Re: [R] is there an equivalent for #ifdef (C langage) in R

2012-01-12 Thread Henrik Bengtsson
You could generate an R script using an RSP template 'main.R.rsp' containing: % DEBUG - TRUE % % if (!DEBUG) { %   make_addition = function(a, b) { % } % % if (DEBUG) { %   a = 1   b = 2 % } %   c=a+b   plot(c) % if (!DEBUG) { %        return(c)    } % } % which you can compile into 'main.R'

Re: [R] remoting ESS/R with tramp

2012-01-12 Thread Tom Roche
Tom Roche Thu, 12 Jan 2012 11:56:25 -0500 * I have access to the cluster [where I want to run R] configured [in my linux laptop's .ssh/config] such that I can `ssh t` from commandline. Note also that I'm using keychain

Re: [R] remoting ESS/R with tramp

2012-01-12 Thread poti
-Tom Roche Thu, 12 Jan 2012 11:56:25 -0500 - Starting R from the resulting tramp buffer fails with either of two messages in buffer=*Messages* ... Cannot read history file /scpc:t:/home/me/.Rhistory This is normal. Not a problem. I'm also guessing I might have a configuration problem, too.

[R] how to select column wich median is in this interval [5;6]

2012-01-12 Thread ikuzar
Hello, I have got a data frame df like this : df e1 e2 e3 e4 1 1 11 1 21 2 2 12 2 22 3 3 13 3 23 4 4 14 4 24 5 5 15 5 25 6 6 16 6 26 7 7 17 7 27 8 8 18 8 28 9 9 19 9 29 10 10 20 10 30 where e1 ... e3 are vectors I have to select columns which median is in the

[R] work with a subset of the dataset

2012-01-12 Thread manu79
Hello, I have a big dataset with many variables and I would like to consider only the rows in which there is a specific value of a variable. I make an example for explain what I mean: I have 5 variables describing a person: age, sex, weight, colour of hair, colour of eyes. I have 1000 rows

Re: [R] Problem with Snowball RWeka

2012-01-12 Thread plecto
Thanks! I read your shoer term solution and thanks to it was able to make stemming working in R for Mac OS X. I actually used Sys.setenv(NOAWT=TRUE) instead of Sys.setenv(NOAWT, true), as the latter produces the following error message: Error in Sys.setenv(NOAWT, true) : all arguments must be

[R] GGplot controlling point size across range

2012-01-12 Thread Darran King
Hi all New to R and GGplot2 but loving the potential. I am trying to plot four separate point plots by looping over the data and plotting a different subset each time. When I plot the data as a point plot, the size of the points is determined by the data values used as below qplot(accum_rain,

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