Re: [R] Density plot in ggplot2

Hi, small modifications to your code will do the trick Here everything is ok, except few points : 1. I want to remove the name of y-axis, which is by default density. Here I put ylab(), however although for x-axis it is working, for y-axis it is not. Is there any specific formula for that?

[R] selecting vector elements using matrices and combining the results

I've been scratching my head over this one for too long. I'm hoping someone out there can solve this riddle. I have two vectors of characters, v1 and v2, both of length L, and two matrices of logicals, m1 and m2, both of dimension N*L. The first matrix of logicals corresponds to the first

Re: [R] character vector - numeric matrix ??

Hi, On Jul 28, 2009, at 1:13 PM, kathie wrote: Dear R users... I'd like to change this character vector, zz, zz - c(12,56,89) to the following numeric matrix. [,1] [,2] [1,]12 [2,]56 [3,]89 Actually, zz vector has a long length. Any comments will be greatly

Re: [R] Searching for specific values in a matrix

Yes this is working quite well. Basically, I am comparing data obtained from GIS to data obtained from R. It's turning out that the latitude and longitude values from GIS are not matching exactly those obtained in R, and therefore I am trying to find the variance in the data. On Tue, Jul 28,

Re: [R] Searching for specific values in a matrix

all right thank you! this was big help. On Tue, Jul 28, 2009 at 2:22 AM, Martin Maechler maech...@stat.math.ethz.ch wrote: BertG == Bert Gunter gunter.ber...@gene.com on Mon, 27 Jul 2009 15:30:08 -0700 writes: BertG Nothing wrong with rolling your own, but see BertG ?all.equal

[R] Moving axis-labels

Hi, This is hopefully quite a straightforward quandary. I have made a simple R plot but the values on my x-axis are sufficiently large enough that they interfere my x-axis label. How can I shunt the x-axis label further away from the x-axis? Thanks Jim -- JS Walker

Re: [R] Skew-Normal Linear Mixed Model (SNLMM)

See sn.em in the sn package. Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Raphael Fraser Sent: Tuesday, July 28, 2009 9:22 AM To: r-help@r-project.org Subject: [R] Skew-Normal

Re: [R] Searching for specific values in a matrix

quick question, i am trying to get an interval of values now with this code by toggling the tolerance limit. is there any way i can modify this code to find values which are within limits of BOTH latitude and longitude? currently i have to pick one or the other. On Tue, Jul 28, 2009 at 9:29 AM,

Re: [R] Difficulty Increasing R memory on Windows 32-Bit

Dan Fleder wrote: I'm having difficulty increasing the memory R can access above 2Gb and wasn't able to resolve this from the R Windows FAQ. For reference, I'm running Windows XP, 32bit, Service Pack 2 on a machine with 4GB RAM. Following the FAQ, I set the --max-mem-size flag to 2800Mb.

[R] Cell size in heatmap

Dear all, Is it possible to adjust the size of the cells in the heatmap generated by R? I have a heatmap with many rows. Because of this, the size of the cells is very small and the labels of the rows overlap. I have to shrink the labels, but this makes them hardly readable. Any suggestions how

[R] Multiple lmer runs using 2 'for' loops

Dear Mark and the R list, I apologise greatly for not having thanked you earlier for your help with my last mail, which involved trying to sort out variance components using two methods: a direct looped lmer, and a two-step analysis involving regressions of AFLP markers on lmer residuals for

Re: [R] character vector - numeric matrix ??

Dear Kathie, Try also: t(sapply(zz, function(x) as.numeric( strsplit(x, )[[1]] ))) If you want to delete the column names, then res - t(sapply(zz, function(x) as.numeric( strsplit(x, )[[1]] ))) dimnames(res) - NULL res should do it. HTH, Jorge On Tue, Jul 28, 2009 at 1:13 PM, kathie

Re: [R] selecting vector elements using matrices and combining the results

Hi, On Jul 28, 2009, at 12:48 PM, Jean V Adams wrote: I've been scratching my head over this one for too long. I'm hoping someone out there can solve this riddle. I have two vectors of characters, v1 and v2, both of length L, and two matrices of logicals, m1 and m2, both of dimension N*L.

Re: [R] R package for Hierarchical Modelling of Multinomial Logistic Regression

See the Bayesian Task View http://cran.r-project.org/web/views/Bayesian.html which will lead you to the arm and bayesm packages, among others. hth, Kingsford On Tue, Jul 28, 2009 at 1:54 AM, nikolay12nikola...@gmail.com wrote: Hello, I need to implement a hierarchical model for Bayesian

Re: [R] selecting vector elements using matrices and combining the results

Try this: lapply(1:3, function(i) cbind(v1, v2)[cbind(col(m1)[i,], (m1+2*m2)[i,])]) [[1]] [1] A b D f [[2]] [1] C E [[3]] [1] D e On Tue, Jul 28, 2009 at 12:48 PM, Jean V Adamsjvad...@usgs.gov wrote: I've been scratching my head over this one for too long.  I'm hoping someone out there can

Re: [R] Moving axis-labels

You can use par(mgp=c(...)) to change where the axis labels are placed by default, but this affects both the x and y axis. Another alternative is to not plot the x axis label (xlab=''), then use the title or mtext function you can manually place the axis label where you want it. Also look at

Re: [R] Multiple lmer runs using 2 'for' loops

I need estimates of how much variance is explained by each marker in each family, which is the end point of this exercise- and the significance of variance explained by each marker- which is why am trying to print 'anova' results for each run of the lmer. -- But these will just be

Re: [R] Superscripts and rounding

I'm anything but an expert in R however if I'm labeling a graph axis with a superscript I have tended to use: plot (x , y , xlab = expression (label^2)) But when you try to have more than one superscript it fails. Assuming you are in a UTF8 location (Western Europe) you could try: plot (x

Re: [R] selecting vector elements using matrices and combining the results

Here is a slight simplification: nr - nrow(m1); nc - ncol(m1) lapply(1:nr, function(i) cbind(v1, v2)[cbind(1:nc, (m1+2*m2)[i,])]) On Tue, Jul 28, 2009 at 1:36 PM, Gabor Grothendieckggrothendi...@gmail.com wrote: Try this: lapply(1:3, function(i) cbind(v1, v2)[cbind(col(m1)[i,],

[R] Summarising Data for Forrest Plots

I tried to post this a few times last week and it seems to have got stuck somehow so I'm trying from a different email in the hope that works. If somehow this has appeared on the list 20 tiems and I never saw any of them I apologize ;-) I'm basically an R-newbie. But I am VERY computer

[R] selecting vector elements using matrices and combining the results

(I'm resending this, because there seemed to be a problem with my previous attempt.) I've been scratching my head over this one for too long. I'm hoping someone out there can solve this riddle. I have two vectors of characters, v1 and v2, both of length L, and two matrices of logicals, m1

Re: [R] Confirmatory factor analysis problems using sem package (works in Amos)

Thanks John. Can I ask under what function you call optim/nlm? I cannot see how this is done by examining sem. Thanks, -Solomon -Original Message- From: John Fox [mailto:j...@mcmaster.ca] Sent: Monday, July 27, 2009 6:23 PM To: 'Solomon Messing' Cc: r-help@r-project.org Subject:

[R] R Codes for fitting Logistic Regression for Multivaraite Data

Hi It would be a great help if someone can direct me to access some existing R codes for fitting Logistic regression models for Multivariate data. I want to find some Robust Estimates (M) for these models. Thanks a lot Best Regards Nimal [[alternative HTML version deleted]]

Re: [R] formatting in r

I'm not really clear on what you want here. First I guess, is the question of where those results are coming from? To 'print' or output to another format depends on what you have and how you want to print it. At the very simplest is ?sink, after that is ?write.table and after that you

[R] different names for new files in a for loop

Hi, I have an excel file with 10 columns and I am trying to create new excel files each with columns 1, 2, and columns 3-10. Does anyone know how to change the name of the file in a for loop so that the first new file will have columns 1, 2, 3 with a name and then the next file will have

[R] R-help IRC chat?

Just throwing the idea around: Maybe it would be a good to have an IRC chat forum for R on Freenode? There are several devoted to programming (c, c++, lisp etc). It would be a good addition to a mailing list. -- View this message in context:

Re: [R] dumping data objects

While .deparseOpts(control=S_compatible) dump(foo) did not work as I had expected, dump(foo,control=S_compatible) did work OK. Bill Meeker William Q. Meeker Department of Statistics 2109 Snedecor Hall Iowa State University Ames, Iowa 50011 Phone: 515-294-5336 Fax: 515-294-4040 Home

Re: [R] Confirmatory factor analysis problems using sem package (works in Amos)

Dear Solomon, You should get a copy of the source package from CRAN. nlm() [not currently optim()] is called in sem:::sem.default. Regards, John -Original Message- From: Solomon Messing [mailto:mess...@stanford.edu] Sent: July-28-09 2:38 PM To: 'John Fox' Cc: r-help@r-project.org

[R] Check functions in package

Hi, I run R on a server via SSH, over a terminal. After loading a specific package, how do I know what functions are in that package? Is there any way to list or display them? tia. -- View this message in context: http://www.nabble.com/Check-functions-in-package-tp24707084p24707084.html Sent

Re: [R] different names for new files in a for loop

Hi, On Jul 28, 2009, at 3:43 PM, Yash Gandhi wrote: Hi, I have an excel file with 10 columns and I am trying to create new excel files each with columns 1, 2, and columns 3-10. Does anyone know how to change the name of the file in a for loop so that the first new file will have columns

Re: [R] Superscripts and rounding

I am in Canada and it worked!! as:\some text\UB2 the round did not work. i also tried nsmall - to specify number of digits to the right to the decimal to no avail. i will keep trying and post if something does work. Polwart Calum (County Durham and Darlington NHS Foundation Trust)

Re: [R] Check functions in package

Hi, On Jul 28, 2009, at 4:16 PM, voidobscura wrote: Hi, I run R on a server via SSH, over a terminal. After loading a specific package, how do I know what functions are in that package? Is there any way to list or display them? Here's one way. Let's say I load the glmnet package, at

Re: [R] character vector - numeric matrix ??

If your entire dataset looks like your example, try: do.call(rbind, sapply(zz, strsplit, split=)) Note that strsplit() requires a character vector as its first parameter. -Brian J. Koch Data Manager Decision Development Inc www.decisiondevelopment.com -Original Message- From:

[R] Looping through R objects

Hi all, I have 13 csv files and I want to assign each csv file to one object, i.e., bc1 - read.csv(1.csv,header=TRUE,sep=) bc2 - read.csv(2.csv,header=TRUE,sep=) bc3 ... So I want to create 13 objects. How could I automate this with a for loop? for (i in c(1:13)) ... Any ideas? Thanks, Vivek

Re: [R] Check functions in package

Hi, You can use help to view the available help files with the package. E.g. for survival package help(package=survival) Cheers, Paul voidobscura wrote: Hi, I run R on a server via SSH, over a terminal. After loading a specific package, how do I know what functions are in that package? Is

Re: [R] Check functions in package

Steve Lianoglou wrote: On Jul 28, 2009, at 4:16 PM, voidobscura wrote: Hi, I run R on a server via SSH, over a terminal. After loading a specific package, how do I know what functions are in that package? Is there any way to list or display them? Here's one way. Let's say I load the

Re: [R] Looping through R objects

Hi, On Jul 28, 2009, at 4:54 PM, Vivek Ayer wrote: Hi all, I have 13 csv files and I want to assign each csv file to one object, i.e., bc1 - read.csv(1.csv,header=TRUE,sep=) bc2 - read.csv(2.csv,header=TRUE,sep=) bc3 ... So I want to create 13 objects. How could I automate this with a

Re: [R] Check functions in package

a couple more options: ls(package:glmnet) [1] coef.glmnet glmnet jerr nonzeroCoef plot.glmnet [6] plotCoefpredict.elnet predict.glmnet predict.lognet predict.multnet [11] print.glmnet # or ls(pos = 2) [1] coef.glmnet glmnet jerr nonzeroCoef

Re: [R] Superscripts and rounding

I receive the error message below - but i agree with you it should work? In fact i don't care if it rounds it can just cut the number at 4 decimal places. Error: unexpected symbol in: sub = sprintf('Seasonal station with natural streamflow - Lat: %s Lon: %s Gross Area %s km\UB2 - Effective

Re: [R] Superscripts and rounding

So the issue is something to do with the [['xxx']] construction of your data. Can you explain what thats' all about - as it errors all over the shop when I try using that... You've set me on a mission to find the answer! So I'd really like to recreate a little bit of your data here, and

[R] Make my plots bigger and reduce white space around panels?

Hi, I have made a plot with panels (attached) using R code (below) and I'd like to increase the size of each panel and decrease the white space, especially the white space between: 1. rows of panels 2. the top panel and its title (which contains info on r2 and N) 3. each panel and its x label.

[R] how to load packages from different location

Dear list: I know this may be an old question. I know how to install the packages to a different directory, for example, /home/zrl/tmp and I know how to load it library(genefilter,lib.loc=/home/zrl/tmp) but I found some package(for example package A) will have to load some other packages as

Re: [R] r2 question

Hi Sarah, From your description it sounds as though you would be best off consulting with a statistician. Without having a clear understanding of the research hypotheses, experimental units, how randomization was performed, the spatial and temporal structure of the experiment, etc, it's not

Re: [R] how to load packages from different location

Very helpful, thank you Phil. -ZRL On Tue, Jul 28, 2009 at 6:06 PM, Phil Spector spec...@stat.berkeley.eduwrote: I'm attaching some slides that address this issue. I hope you find them useful. - Phil Spector

Re: [R] local regression using loess

Bert, Ryan, Alain, You suggestions are very helpful. Thank you. I learned a lot from the discussion. Cindy On Tue, Jul 28, 2009 at 8:53 AM, Ryan rha...@purdue.edu wrote: Bert Gunter gunter.berton at gene.com writes: Actually, loess is much more than an interpolant. I wouldn't even

[R] A hiccup when using anova on gam() fits.

I stumbled across a mild glitch when trying to compare the result of gam() fitting with the result of lm() fitting. The following code demonstrates the problem: library(gam) x - rep(1:10,10) set.seed(42) y - rnorm(100) fit1 - lm(y~x) fit2 - gam(y~lo(x)) fit3 - lm(y~factor(x))

[R] install package from CRAN

Hi, I have a very basic question about install packages from CRAN on unix. I only installed on Windows before. Should I use the command install.package? The error message I got is syntax error near unexpected token `mvtnorm' Is it because I didn't set the path? Which path should I specify?

Re: [R] Looping through R objects

On Jul 28, 2009, at 5:39 PM, Vivek Ayer wrote: That just creates one object and doesn't contain any $ subobjects in it. Here's what I did to figure it out (It's complicated): for(i in c(1:13)) assign (paste (bc,i,sep=),read.csv(paste(i,.csv,sep=),sep=,header=TRUE)) in shorthand: for

Re: [R] install package from CRAN

On Jul 28, 2009, at 8:15 PM, cindy Guo wrote: Hi, I have a very basic question about install packages from CRAN on unix. I only installed on Windows before. Should I use the command install.package? The error message I got is syntax error near unexpected token `mvtnorm' Is it because I

Re: [R] install package from CRAN

Hi, Steve, Thanks for the response. I did the same thing: install.packages('mvtnorm') -bash: syntax error near unexpected token `'mvtnorm'' I think what may cause difference is that I am using a unix cluster of my university, so I am not the administrator. Do I need to set the path? Cindy

Re: [R] install package from CRAN

Hi, On Jul 28, 2009, at 8:36 PM, cindy Guo wrote: Hi, Steve, Thanks for the response. I did the same thing: install.packages('mvtnorm') -bash: syntax error near unexpected token `'mvtnorm'' I think what may cause difference is that I am using a unix cluster of my university, so I am not

[R] Brief Mention of R in New York Times (July 29, 2009)

In an article about the IBM purchase of SPSS, R gets a brief mention as a price pressure on software suppliers. http://www.nytimes.com/2009/07/29/technology/companies/29ibm.html?_r=1hpw The broad consolidation wave in business intelligence software, analysts say, will bring increasing price

[R] Maximizing values in subsetted dataframe

Dear List, I am trying to sub-sample some data by taking a data point every x minutes. The data contains missing values, and I would like to take the sub-sample that maximizes the number of valid points in the sample. I.e. minimizes the number of NA's in the data set. For example, given

Re: [R] install package from CRAN

-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of cindy Guo Sent: Tuesday, July 28, 2009 5:36 PM To: Steve Lianoglou Cc: r-help@r-project.org Subject: Re: [R] install package from CRAN Hi, Steve, Thanks for the response.

Re: [R] install package from CRAN

Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows before. Should I use the command install.package? | The error message I got is | syntax error near unexpected token `mvtnorm' | Is it because I

Re: [R] formatting in r

If you want to mix alphanumeric and numerics, the 'sprintf' is one way of doing it: u - 140 xbar - 150 alpha - .05 zcrit - 1.6449 zcrit2 - 1.96 zstat - 4 pvalue - 6.334348e-05 cat(sprintf(u xbar alpha zcrit zcrit2 zstat pvalue %.0f %.0f %.2f %.4f %.2f %.0f %e\n, + u, xbar, alpha,

Re: [R] Nonlinear mixed binary regression model

Caio, check the lme4 library. The lmer function allows for fixed and random effects. Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von

[R] cannot allocate a vector with 1920165909 length

Dear Rusers, The error for the following was that it cannot allocate the vector of length 1920165909. a - expand.grid(se1=0:100/100, sp1=0:100/100, se2=0:100/100, sp2=0:100/100, DR=0:100/100) How to solve it? Maybe setwd(dir) can, i am not very sure about it. Any ideas about it?

Re: [R] cannot allocate a vector with 1920165909 length

What are you trying to do? The expand.grid will create an object with 10 billion rows with 5 variables. My guess is that you would need 50G * 8 bytes/word = 400GB just to hold the one object. How much memory do you have on your system? Is there some other approach you can use? You may have

[R] partially sorting?

Dear all, x - matrix(c(1239,10,10,10,10,1234,10,10,10,10,1500,11,11,11,11,1001,11,11,11,11, 1009,11,11,11,11,1344,12,12,12,12,1349,12,12,12,12,1458,13,13,13,13),8,5,byrow = T) x [,1] [,2] [,3] [,4] [,5] [1,] 1239 10 10 10 10 [2,] 1234 10 10 10 10 [3,] 1500

Re: [R] cannot allocate a vector with 1920165909 length

Out of memory? How large is your physical memory? --- On Tue, 7/28/09, zhijie zhang rusers...@gmail.com wrote: From: zhijie zhang rusers...@gmail.com Subject: [R] cannot allocate a vector with 1920165909 length To: r-h...@stat.math.ethz.ch Date: Tuesday, July 28, 2009, 9:49 PM Dear Rusers, The

Re: [R] partially sorting?

Dear Ashley, Try this: x[,1] - sort(x[,1]) x See ?sort for more details. HTH, Jorge On Tue, Jul 28, 2009 at 10:07 PM, ashley2000 ashley.askew2...@gmail.comwrote: Dear all, x - matrix(c(1239,10,10,10,10,1234,10,10,10,10,1500,11,11,11,11,1001,11,11,11,11,

Re: [R] partially sorting?

Is this what you want? You may have to include other columns for other levels of uniqueness: x [,1] [,2] [,3] [,4] [,5] [1,] 1239 10 10 10 10 [2,] 1234 10 10 10 10 [3,] 1500 11 11 11 11 [4,] 1001 11 11 11 11 [5,] 1009 11 11 11 11 [6,] 1344 12 12

Re: [R] install package from CRAN

Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009 at 17:15, cindy Guo wrote: | I have a very basic question about install packages from CRAN on unix. I | only installed on Windows

Re: [R] install package from CRAN

What was the problem- out of curiosity? Stephen Sefick On Tue, Jul 28, 2009 at 9:23 PM, cindy Guocindy.g...@gmail.com wrote: Hi, Thank you for all your replies. I got it work now. Cindy On Tue, Jul 28, 2009 at 6:09 PM, Dirk Eddelbuettel e...@debian.org wrote: Cindy, On 28 July 2009

Re: [R] install package from CRAN

Hi, Thank you for asking. Actually I downloaded the tar.gz file as Mark said and used R CMD INSTALL -l . package.tar.gz to install. I didn't know I can download CRAN packages from the internet. I am not a unix person, so I struggled a lot with the commands on unix and directories especially. I

[R] how to initial the R script

hi everyone, I am wondering if I can inintial all of the varibles and vectors at the begining part of my R script to make clear all the meanning defined in another script runned before It is just similiar with the command close all in Matlab or reinit in grads.How can I do? thank you.:)

Re: [R] How to do poisson distribution test like this?

I have gone to have a look at the paper. (http:// www.plantphysiol.org/cgi/content/full/148/3/1189 ) to try to work out what they're actually doing, in the hope that I might be able to figure out their procedure so we can give a more complete answer to the question. Unfortunately, I'm more

Re: [R] How to do poisson distribution test like this?

Corrected links (the originals somehow aquired an extra space, sorry) Paper: http://www.plantphysiol.org/cgi/content/full/148/3/1189 Table I: http://www.plantphysiol.org/cgi/content/full/148/3/1189/TBL1 -- View this message in context:

Re: [R] make one matirx in list after removing duplicated rows

That did not actually deliver the requested results because it bound before it unique-ed. unique(do.call(rbind,z)) [,1] [,2] [1,] 110 [2,]90 [3,] 101 [4,]71 I found it necessary to do a bit more list processing before the rbind: do.call( rbind,

Re: [R] make one matirx in list after removing duplicated rows

You are totally right David! Thank you so much for your correction! Best regards, Jorge On Tue, Jul 28, 2009 at 11:34 PM, David Winsemius wrote: That did not actually deliver the requested results because it bound before it unique-ed. unique(do.call(rbind,z)) [,1] [,2] [1,] 11

[R] Installing lme4 package in Windows Vista

Hi all, I have a problem with package installing in Windows, on my PC machine. The end goal is to be able to use the lme() function. Here's what I did so far: install.packages(lme4) Warning in install.packages(lme4) : argument 'lib' is missing: using

[R] partially sorting?

Dear all, x - matrix(c(1239,10,10,10,10,1234,10,10,10,10,1500,11,11,11,11,1001,11,11,11,11, 1009,11,11,11,11,1344,12,12,12,12,1349,12,12,12,12,1458,13,13,13,13),8,5,byrow = T) x [,1] [,2] [,3] [,4] [,5] [1,] 1239 10 10 10 10 [2,] 1234 10 10 10 10 [3,] 1500

Re: [R] Make my plots bigger and reduce white space around panels?

The plot is attached this time... On Tue, Jul 28, 2009 at 4:47 PM, Mark Na mtb...@gmail.com wrote: Hi, I have made a plot with panels (attached) using R code (below) and I'd like to increase the size of each panel and decrease the white space, especially the white space between: 1. rows

Re: [R] how to initial the R script

Just a guess, since I am not a Matlab user and you have not defined what you mean by inintial all of the varibles and vectors at the begining part of my R script to make clear all the meanning defined other than by analogy with non-R software. Perhaps you want: quit(save=yes) The next

Re: [R] Installing lme4 package in Windows Vista

The function lme() is in the package nmle, ***not*** in lme4. The somewhat analagous (but very different) function in lme4 is lmer(). cheers, Rolf Turner Hi all, I have a problem with package installing in Windows, on my PC machine. The end goal is to be able to

[R] xtable formatting: RED for negative numbers?

I've been experimenting recently with the fantastic Sweave/xtable combination for generating latex. In the xtable vignette, I found this great example of printing a ts object by months. Is there a way to modify this code to generate RED numbers inside xtable for negative results in x.ts?

Re: [R] Installing lme4 package in Windows Vista

After installation of lme4, you need to load it before use it. library(lme4) ?lmer 2009/7/29 Angela Radulescu angela.radule...@gmail.com: Hi all, I have a problem with package installing in Windows, on my PC machine. The end goal is to be able to use the lme() function. Here's what I did so

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