[R] Difference between prcomp and cmdscale

I'm looking for someone to explain the difference between these procedures. The function prcomp() does principal components anaylsis, and the function cmdscale() does classical multi-dimensional scaling (also called principal coordinates analysis). My confusion stems from the fact that they give

Re: [R] Difference between prcomp and cmdscale

should that confuse you? Have you tried reading some of the literature on these methods? There's plenty about them on the Net (Wiki's often a goodish place to start)---and even in R, if you're prepared to look ;). BestR, Mark. michael watson (IAH-C) wrote: I'm looking for someone to explain

Re: [R] open .r files with double-click

Hmmm. Possibly your best bet is to create a batch file, runr.bat or something, and associate .r files with that. The batch file would be something like: C:/Program Files/R/R-2.5.0/bin/Rgui.exe --no-save %1 (I think thats how you reference arguments in dos...) -Original Message-

[R] Suppressing the large amount of white space in heatmap.2 in gplots

Hi OK, quick question - I can suppress the calculation and drawing of the column dendrogram by using Colv=FALSE and dendrogram=row, but that leaves me with a large amount of white space at the top of the plot where the dendrogram would have been drawn... Is there a way of getting rid of that?

Re: [R] How to load a big txt file

Erm... Is that a typo? Are we really talking 23800 rows and 49 columns? Because that doesn't seem that many -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of ssls sddd Sent: 07 June 2007 10:48 To: r-help@stat.math.ethz.ch Subject: Re: [R] How to load a

Re: [R] Averaging across rows columns

Check out rowMeans to average over replicate columns first, ie: means - data.frame(t1=rowMeans(a[,1:3]), t2=rowMeans(a[,4:6]), etc) Then, if you want to aggregate every 14 rows: aggregate(means, by=list(rows=rep(1:(nrow(means)/14), each=14)), mean) Or

Re: [R] R help

Yes, but you need to be a bit more specific... When it comes to graphs and drawing lines, there isn't much R can't do... -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of scott flemming Sent: 06 June 2007 04:49 To: r-help@stat.math.ethz.ch Subject: [R] R

Re: [R] Linear Discriminant Analysis

Region and Name are effectively the same variable cor(olive[,4:11]) will also show you that there are strong correlations between some of the variables - this is something you might want to avoid From: [EMAIL PROTECTED] on behalf of Soare Marcian-Alin

Re: [R] sizing and saving graphics in R

There is also the functions pdf(), jpeg(), bmp() and png() -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Murray Pung Sent: 31 May 2007 01:22 To: Felicity Jones Cc: r-help@stat.math.ethz.ch Subject: Re: [R] sizing and saving graphics in R I use the

[R] A matrix with mixed character and numerical columns

Is it possible to have one? I have a data.frame with two character columns and 6 numerical columns. I converted to a matrix as I needed to use the col() and row() functions. However, if I convert the data.frame to a matrix, using as.matrix, the numerical columns get converted to characters, and

Re: [R] Where is CRAN mirror address stored?

chooseCRANmirror() -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Vladimir Eremeev Sent: 31 May 2007 12:14 To: r-help@stat.math.ethz.ch Subject: [R] Where is CRAN mirror address stored? When I update.packages(), R shows the dialog window, listing CRAN

Re: [R] A matrix with mixed character and numerical columns

Message- From: Petr PIKAL [mailto:[EMAIL PROTECTED] Sent: 31 May 2007 12:57 To: michael watson (IAH-C) Cc: r-help@stat.math.ethz.ch Subject: Odp: [R] A matrix with mixed character and numerical columns Hi [EMAIL PROTECTED] napsal dne 31.05.2007 12:48:11: Is it possible to have one? I have

Re: [R] A matrix with mixed character and numerical columns

OK, where is the best place to post these to to get them incorporated in R? -Original Message- From: Petr PIKAL [mailto:[EMAIL PROTECTED] Sent: 31 May 2007 14:23 To: michael watson (IAH-C) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] A matrix with mixed character and numerical columns

[R] Help me understand colours on linux

Hi Here is my sessionInfo(): Version 2.3.1 (2006-06-01) i686-redhat-linux-gnu attached base packages: [1] methods stats graphics grDevices utils datasets [7] base I have a function that is trying to draw rectangles using 136 different colours, and I get the following error:

Re: [R] matrix in data.frame

Have you thought of using a list? a - matrix(1:10, nrow=2) b - 1:5 x - list(a=a, b=b) x $a [,1] [,2] [,3] [,4] [,5] [1,]13579 [2,]2468 10 $b [1] 1 2 3 4 5 x$a [,1] [,2] [,3] [,4] [,5] [1,]13579 [2,]2468

Re: [R] opinions please: text editors and reporting/Sweave?

Have you tried R2HTML, or is HTML not what you're looking for? -Original Message- From: [EMAIL PROTECTED] on behalf of Tim Howard Sent: Wed 30/05/2007 9:43 PM To: r-help@stat.math.ethz.ch Subject: [R] opinions please: text editors and reporting/Sweave? dear all - I currently use

Re: [R] Running R in Bash and R GUI

There are two things that occur. Firstly, I normally have to unset no_proxy: % unset no_proxy; R Secondly, if for some reason http_proxy isn't being seen in R, you can use the Sys.putenv() function within R to manipulate the environment -Original Message- From: [EMAIL PROTECTED]

Re: [R] Fonts do not display properly on Red Hat

: 23 May 2007 11:40 To: michael watson (IAH-C) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Fonts do not display properly on Red Hat Are you using a UTF-8 locale? (You know, there are good reasons why the posting guide asks for sessionInfo() output.) If so, the problem is probably with the non

Re: [R] how to change font size in HTML output

You could always modify the .css file that R2HTML outputs... the default is R2HTML.css From: [EMAIL PROTECTED] on behalf of Bos, Roger Sent: Thu 24/05/2007 2:58 PM To: r-help@stat.math.ethz.ch Subject: [R] how to change font size in HTML output I have not

[R] Fonts do not display properly on Red Hat

Hi I'm using R version 2.3.1 on Red Hat Enterprise Server 3. When I run a simple: plot(1:10,1:10) The plot comes out great, but the fonts are displayed wrongly: http://coxpress.sourceforge.net/test.jpg I realise this is probably not an R problem per se, but before I go messing about with

[R] Fonts do not display properly on Red Hat

Hi I'm using R version 2.3.1 on Red Hat Enterprise Server 3. When I run a simple: plot(1:10,1:10) The plot comes out great, but the fonts are displayed wrongly: http://coxpress.sourceforge.net/test.jpg I realise this is probably not an R problem per se, but before I go messing about with

[R] Including data when building an R package in windows

I've done this before, but when I tried the same thing this time, it didn't work. I'm using R 2.4.1 on windows. I have 6 data frames that I want to include in a package I am building. Instead of making users issue six different data(...) commands, I want to wrap them all up in one file so

Re: [R] Including data when building an R package in windows

I forgot to mention. After using package.skeleton(), I replaced the six .rda files with a single .Rdata file that contained all six data frames. -Original Message- From: [EMAIL PROTECTED] on behalf of michael watson (IAH-C) Sent: Wed 09/05/2007 10:58 AM To: r-help@stat.math.ethz.ch

Re: [R] Including data when building an R package in windows

Turns out calling the file DetectiV.rda (rather than .Rdata) fixed it. Odd. -Original Message- From: michael watson (IAH-C) Sent: Wed 09/05/2007 11:09 AM To: michael watson (IAH-C); r-help@stat.math.ethz.ch Subject: RE: [R] Including data when building an R package in windows I forgot

Re: [R] Google Custom Search Engine for R

I always just google for the terms I want and then add R-help to the search, which limits it to the R-help mailing list. It's quite effective. From: [EMAIL PROTECTED] on behalf of Matthew Keller Sent: Fri 23/02/2007 3:51 PM To: Sérgio Nunes Cc:

[R] Sorting a data frame when you don't know the columns

Hi Sorry to ask such a well oiled question, but even with multiple google hits I don't think this has been answered very well. It's all well and good doing a sort of a data frame on multiple columns when you know in advance which columns you want to sort on, but what about when the names of

Re: [R] Sorting a data frame when you don't know the columns

Thanks guys, sorted now :) From: Peter Dalgaard [mailto:[EMAIL PROTECTED] Sent: Tue 28/11/2006 11:05 AM To: Gabor Grothendieck Cc: michael watson (IAH-C); r-help@stat.math.ethz.ch Subject: Re: [R] Sorting a data frame when you don't know the columns Gabor

Re: [R] Colour-coded Editor for R Code

Tinn-R From: [EMAIL PROTECTED] on behalf of Jon Minton Sent: Mon 06/11/2006 9:11 AM To: R-help@stat.math.ethz.ch Subject: [R] Colour-coded Editor for R Code Do any of you know any simple programming editors for R scripts which offer basic colour-coding and

[R] Finding out about objects and classes

When R help simply states something like: Value: An object of class 'loess'. How do I find out more about that class? Shouldn't there be a link in the help file or something? ATB Mick __ R-help@stat.math.ethz.ch mailing list

[R] Faster alternative to by?

Hi I have a data.frame, two columns, 12304 rows. Both columns are factors. I want to do an equivalent of an SQL group by statement, and count the number of rows in the data frame for each unique value of the second column. I have: countl - by(mapped, mapped$col2, nrow) Now, mapped$col2 has

[R] Plotting lines and points on the second plot when using gap.plot in plotrix

Hi My question is simple - the gap.plot function in the plotrix package allows users to draw graphs that have a broken axis. However, I want to then add a line to the second plot, but can't. Eg: twogrp-c(rnorm(10)+4,rnorm(10)+20) gap.plot(twogrp,rnorm(20),gap.bounds=c(8,16),gap.axis=x,xlab=X

Re: [R] Plotting lines and points on the second plot when usinggap.plot in plotrix

I've answered my own question, the x-values of the line/points I want to plot must be adjusted by the gap size Thanks Mick -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: 19 July 2006 11:58 To: r-help@stat.math.ethz.ch

Re: [R] Generating random normal distribution with mean 0 and standarddeviation 1

See rnorm() -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Neuro LeSuperHéros Sent: 14 July 2006 13:15 To: r-help@stat.math.ethz.ch Subject: [R] Generating random normal distribution with mean 0 and standarddeviation 1 Hello, This must be really

Re: [R] FW: How to create a new package?

?package.skeleton -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Gabor Grothendieck Sent: 01 June 2006 12:20 To: Rita Sousa Cc: r-help@stat.math.ethz.ch Subject: Re: [R] FW: How to create a new package? The minimum is to create a DESCRIPTION file,

Re: [R] FW: How to create a new package?

In that case, I have found the following useful: http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: 01 June 2006 12:43 To: michael watson (IAH-C) Cc: Gabor Grothendieck; Rita Sousa; r-help@stat.math.ethz.ch

[R] lapply and list attributes

Hi I have a list that has attributes: attributes(lis[2]) $names [1] 150096_at I want to use those attributes in a function and then use lapply to apply that function to every element of the list, eg for simplicity's sake: my.fun - function(x) { attributes(x) } Then l2 - lapply(lis,

[R] Identifying or searching for labels in a hclust/dendrogram/heatmap

Hi Sorry if this is in the help :-S I've looked at example(dendrogram) and though it gives some indication of what I want, it doesn't do all. OK, so here is what I want to do: draw a tree, and then have an action, on user-click, to either draw a sub tree or a plot of the data. I also want

Re: [R] Identifying or searching for labels in a hclust/dendrogram/heatmap

Hi Sean Thanks for the help, but I really wanted to do this in R :) Any suggestions? Mick From: Sean Davis [mailto:[EMAIL PROTECTED] Sent: Thu 09/03/2006 1:01 PM To: michael watson (IAH-C); r-help Subject: Re: [R] Identifying or searching for labels

Re: [R] Boxplot Help Needed

You can always use points() mat - matrix(rnorm(360),nrow=10) boxplot(mat~col(mat)) means - apply(mat,2, mean) points(1:36,means,pch=X,col=red) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Sumanta Basak Sent: 07 March 2006 09:55 To:

[R] Averaging over columns

Hi I've been reading the help for by and aggregate but can't get my head round how to do this. I have a data frame - the first three columns are replicate measurements, then the next 3 are replicates etc up to 36 (so 12 variables with 3 replicate measurements each). I want to compute the mean

[R] Problems with heatmap.2 in the gregmisc package

Hi Sorry to revisit an old problem, I seemed to solve this in 2004, only for it to resurface :-S I am trying to plot a heatmap, and I don't want the columns of my matrix re-ordered. The function doesn't seem to behave as the help would have you believe: a - matrix(rnorm(100),nr=20) a.d -

Re: [R] lines() and recycled colours

Hi Lines behaves as the help() says it does: plot(0:1,0:1,type=n) lines(runif(11),runif(11),col=c(red,green), type=h) Mick -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Robin Hankin Sent: 28 February 2006 09:31 To: RHelp Subject: [R] lines() and

Re: [R] Sorting a dataframe by one column?

You mean like this? a-1:10 b-(a-5)^2 d-data.frame(a,b) d[order(d$b),] ?? -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of mtb954 mtb954 Sent: 24 February 2006 13:55 To: r-help@stat.math.ethz.ch Subject: [R] Sorting a dataframe by one column? Given the

[R] Bug in setting GUI to SDI mode?

Hi I did a google search on this and came up with nothing. OK, in the latest release of R for windows, I want to change the gui to SDI mode. Edit - GUI preferences Choose SDI Apply I get the message about properties not being able to be changed on a running console, and that I need to save.

Re: [R] Bug in setting GUI to SDI mode?

Woops! RTFM for me :( Thanks everyone for your help. Mick -Original Message- From: Liaw, Andy [mailto:[EMAIL PROTECTED] Sent: 23 February 2006 13:57 To: michael watson (IAH-C); r-help@stat.math.ethz.ch Subject: RE: [R] Bug in setting GUI to SDI mode? The file needs to be in R_HOME

[R] Changing the x-axis labels in plot()

Hi Hopefully this one isn't in the manual or I am about to get shot :-S One of my colleagues wants a slightly strange graph. We basically have a data matrix, and she wants to plot, for each row, the values in the row as points on the graph. The following code draws the graph just fine:

Re: [R] Discriminant Function Analysis

Thanks for the answers Uwe! So this is a common problem in biology - few number of cases and many, many variables (genes, proteins, metabolites, etc etc)! Under these conditions, is discriminant function analysis not an ideal method to use then? Are there alternatives? 1) First problem, I

Re: [R] R under suse linux 9.3

I've been successfully using R on SuSe linux for the last 2 years and I use the rpm :-) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Ernesto Jardim Sent: 07 July 2005 10:48 Cc: r-help@stat.math.ethz.ch Subject: Re: [R] R under suse linux 9.3 Peter

[R] Discriminant Function Analysis

Dear All This is more of a statistics question than a question about help for R, so forgive me. I am using lda from the MASS package to perform linear discriminant function analysis. I have 14 cases belonging to two groups and have measured each of 37 variables. I want to find those variables

RE: [R] Running R from Perl program

Well, after reviewing all the available options about 2 years ago, I decided on the traditional perl option of opening up a pipe to R from within perl and simply firing commands at it. This worked for me because all I wanted to do was create images. If you want to get back the results of an

[R] Wilcoxon paired signed rank test and continuity correction

Hi I am applying the wilcoxon paired signed rank test to many sub-groups of a data frame using by() and wilcox.test, and sometimes the test uses continuity correction and sometimes it doesn't. What I want to know is: 1) what is continuity correction? The docs say: correct: a logical

[R] Anova - interpretation of the interaction term

Hi So carrying on my use of analysis of variance to check for the effects of two factors. It's made simpler by the fact that both my factors have only two levels each, creating four unique groups. I have a highly significant interaction term. In the context of the experiment, this makes sense.

RE: [R] Anova - adjusted or sequential sums of squares?

drop1(model, .~., test=F) Many thanks Mick -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: 20 April 2005 16:35 To: michael watson (IAH-C) Cc: Liaw, Andy; r-help@stat.math.ethz.ch Subject: RE: [R] Anova - adjusted or sequential sums of squares? On Wed, 20 Apr

[R] Anova - adjusted or sequential sums of squares?

Hi I am performing an analysis of variance with two factors, each with two levels. I have differing numbers of observations in each of the four combinations, but all four combinations *are* present (2 of the factor combinations have 3 observations, 1 has 4 and 1 has 5) I have used both

RE: [R] Anova - adjusted or sequential sums of squares?

the answer is no. I guess I could use drop1() to get from the type I to the type III in R... -Original Message- From: Liaw, Andy [mailto:[EMAIL PROTECTED] Sent: 20 April 2005 15:05 To: michael watson (IAH-C); r-help@stat.math.ethz.ch Subject: RE: [R] Anova - adjusted or sequential sums

RE: [R] problem with RODBC

the row number specified is 1 less than in the actual excel file At a guess I'd say this is because the row 1 in excel is taken as the column heads for the data in R __ R-help@stat.math.ethz.ch mailing list

RE: [R] Anova - adjusted or sequential sums of squares?

which order I specify the factors. It's this reason that I have been given for using the so-called type III adjusted sums of squares... Mick -Original Message- From: Douglas Bates [mailto:[EMAIL PROTECTED] Sent: 20 April 2005 15:07 To: michael watson (IAH-C) Cc: r-help@stat.math.ethz.ch

[R] Order of boxes in boxplot()

Hi Sorry for such an inane question - how do I control the order in which the boxes are plotted using boxplot() when I pass it a formula and a data.frame? It seems that the groups are plotted in alphabetical order... I want to change this Many thanks Mick

RE: [R] Help with three-way anova

do I interpret that? Many thanks Mick -Original Message- From: Federico Calboli [mailto:[EMAIL PROTECTED] Sent: 05 April 2005 16:33 To: michael watson (IAH-C) Cc: r-help Subject: Re: [R] Help with three-way anova On Tue, 2005-04-05 at 15:51 +0100, michael watson (IAH-C) wrote: So

RE: [R] Help with three-way anova

out what contrasts matrix I need to use... Many thanks for your help Mick -Original Message- From: Federico Calboli [mailto:[EMAIL PROTECTED] Sent: 06 April 2005 10:15 To: michael watson (IAH-C) Cc: r-help Subject: RE: [R] Help with three-way anova On Wed, 2005-04-06 at 09:11 +0100

RE: [R] Help with three-way anova

-Original Message- From: John Fox [mailto:[EMAIL PROTECTED] Sent: 06 April 2005 12:52 To: michael watson (IAH-C) Cc: 'r-help'; [EMAIL PROTECTED] Subject: RE: [R] Help with three-way anova Dear Mick, For a three-way ANOVA, the difference between aov() and lm() is mostly in the print and summary

[R] Help with three-way anova

Hi I have data from 12 subjects. The measurement is log(expression) of a particular gene and can be assumed to be normally distributed. The 12 subjects are divided into the following groups: Infected, Vaccinated, Lesions - 3 measurements Infected, Vaccintaed, No Lesions - 2 measurements

[R] A vector or array of data frames

Hi A simple question again, but I can't find it by google-ing R-help. Quite simply, I want to read in the contents of a number of files, using read.table, and assign the results to elements of a vector/array/list/whatever. I want it so that, if my vector/array/whatever is pos, that pos[1] will

[R] Converting a list to a matrix - I still don't think I have it right

Hi We have touched on this before, but I don't think I quite got it right. So I have a list, each element of which is a a vector of 2 numbers: l2 $cat000_a01 [1] 0.3429944 4.5138244 $cat000_a02 [1] 0.1929336 4.3064944 $cat000_a03 [1] -0.2607796 4.1551591 What I actually want to convert

RE: [R] Making a Package

I follow the guide here and it never fails: http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html So if I have the MyPackage directory, that was created with package.skeleton and subsequently edited, I will cd to the directory that contains the MyPackage directory and: R CMD INSTALL

[R] Setting x-axis labels in plot()

Hi This draws the (kind of) plot I want: plot(InsectSprays[,2:1]) But how do I make it label the x-axis with A, B, C, D etc instead of 1:6? Mick __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

RE: [R] NA's in if statement

Some careful use of is.na() may help. Either by using it to remove NA values or as part of the if statement. Or: my.wdir - na.omit(dat$wdir) for(i in 1:length(my.wdir)) { #etc -Original Message- From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent:

[R] Using a number as a name to access a list

Hi Dumb question time again, for which I apologise. I have a variable that contains the following numerical text 04010. This is the name to access a list: as.list(KEGGPATHID2NAME)$04010 [1] MAPK signaling pathway Marvellous! Except I want to do that when 04010 is assigned to a variable

[R] RE: Using a number as a name to access a list

The answer of course is parse()! Thank you and good night! M -Original Message- From: michael watson (IAH-C) Sent: 10 February 2005 13:36 To: r-help@stat.math.ethz.ch Subject: Using a number as a name to access a list Hi Dumb question time again, for which I apologise. I have

[R] Mantel Ranomization test

Hi I found this post from 2001 (https://stat.ethz.ch/pipermail/r-help/2001-April/011073.html) and was just wondering if this has been updated and included in an R package yet? Cheers Mick __ R-help@stat.math.ethz.ch mailing list

[R] How to convert a list to a matrix

Hi Sorry to ask such a basic question. I have a list, each element of which is a vector of two values. What I actually want is a matrix with two columns, and one row per element of the list. Obviously I have tried as.matrix(), and as.vector() but I didn't expect the latter to work. I feel so

RE: [R] Combining two histograms

Sean If you want two bars for each bin then that sounds more like barplot() could be used. I know you can tightly control the distance between bars and the width of the bars, and so with a little coding you could probably use that. Mick -Original Message- From:

RE: [R] Combining two histograms

Something a bit more sohpisticated than this: a - rnorm(2) b - rnorm(2, mean=1.5) ah - hist(a,breaks= seq(-5,6,by=0.2),plot=FALSE) bh - hist(b,breaks= seq(-5,6,by=0.2),plot=FALSE) data - t(cbind(ah$counts,bh$counts)) barplot(data,beside=TRUE, space=rep(0,2*ncol(data)))

RE: [R] Runnning R remotely

This isn't exactly the same as your problem, but I came across access to X11 problems when running R over CGI. I got round it by installing Xvfb (X Virtual Frame Buffer) on the server. Mick -Original Message- From: [EMAIL PROTECTED] on behalf of Laura Quinn

RE: [R] A rude question

Hi I don't know if you are asking the question for the same reasons I did, but recently (and ongoing) we have been required to adopt an internationally recognised standard. Being in the bioinformatics field, where open-source software is the beating heart of cutting edge research, we have

[R] Rd problems when converting DVI version

Hi Running R v2.0 on SuSe linux 8.2. I'm trying to build a package (which built perfectly on Windows...) on Linux, and I ran: R CMD check mypackage I got: * checking mypackage-maual.tex ... ERROR LaTeX errors when creating DVI version This typically indicates Rd problems OK, there are no

RE: [R] Plotting hclust with lot of objects

I think you need to use just: cut You may also want to look at: cutree -Original Message- From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Tue 1/25/2005 6:06 PM To: r-help@stat.math.ethz.ch Cc: Subject:[R] Plotting hclust with lot of objects Hi! I am

RE: [R] lookups and joins

All together now: ?merge :-) -Original Message- From: [EMAIL PROTECTED] on behalf of Paul Sorenson Sent: Mon 1/24/2005 10:34 PM To: r-help@stat.math.ethz.ch Cc: Subject:[R] lookups and joins I have some data coming from SQL sources that I wish to relate in various

[R] Subsetting a data frame by a factor, using the level that occurs the most times

I think that title makes sense... I hope it does... I have a data frame, one of the columns of which is a factor. I want the rows of data that correspond to the level in that factor which occurs the most times. I can get a list by doing: by(data,data$pattern,subset) And go through each

[R] Replacing NAs in a data frame using is.na() fails if there are no NAs

Hi This is a difference between the way matrices and data frames work I guess. I want to replace the NA values in a data frame by 0, and the code works as long as the data frame in question actually includes an NA value. If it doesn't, there is an error: df -

RE: [R] Replacing NAs in a data frame using is.na() fails if there are no NAs

) mat[is.na(mat)] - 0 mat - matrix(c(1,1,1,NA),nrow=2,ncol=2) mat[is.na(mat)] - 0 -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: 14 January 2005 11:57 To: michael watson (IAH-C) Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Replacing NAs in a data frame using

[R] Space between bars in barplot

Hi I am trying to understand the space argument to barplot() and I think it is not working as stated. The docs say: space: the amount of space (as a fraction of the average bar width) left before each bar. Which means that I can pass a vector, the same length as the no. of bars,

RE: [R] Installation of XML library can't find libxml2.dll

PROTECTED] Sent: 10 January 2005 17:47 To: michael watson (IAH-C) Cc: R-help@stat.math.ethz.ch Subject: RE: [R] Installation of XML library can't find libxml2.dll My reading of this is that you may have installed the 'Windows binary' package from the Omegahat site - if so, it would appear

[R] Installation of XML library can't find libxml2.dll

Sorry to ask a (probably) dumb question, but I am trying to install XML package on Windows XP, R 2.0.1, and I get the error: This application has failed to start because libxml2.dll was not found. Re-installing the application may fix this problem library(XML) Error in dyn.load(x,

[R] Installing RCurl on Linux

Hi I'm not having much luck today! Running Suse Linux 8.2, R 2.0.0, trying to install RCurl_0.5-1.tar.gz. Perhaps there's an issue with my C compiler, but I got some errors: IAHC-LINUX03:/usr/users/mwatson # R CMD INSTALL RCurl_0.5-1.tar.gz * Installing *source* package 'RCurl' ... checking

[R] SSOAP and Rcurl with proxy server

Hi I'm trying to use a bioconductor package (KEGGSOAP) which relies on Rcurl and SSOAP. As an example, a function exists: list.organisms function () { orgs - matrix(unlist(.SOAP(KEGGserver, list_organisms, , action = KEGGaction, xmlns = KEGGxmlns), use.names = FALSE),

[R] Replacing all NA values in a matrix

OK, dumb question, and it is probably in the docs somewhere, but after 12 months working with R and quite a while looking at the docs, I still don't know (or have forgotten) how to replace all NA values in a matrix at once with some other value. I can do it column by column using is.na(), but I

RE: [R] Replacing all NA values in a matrix

Doh, replace() does the job just fine. Sheesh, I'm not coping well with work post christmas ;-) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: 05 January 2005 14:26 To: R-help@stat.math.ethz.ch Subject: [R] Replacing all NA

[R] Difference between R CMD build --binary and R CMD INSTALL --build

As the title suggests, when building R packages on Windows, what is the difference between: R CMD build --binary mypack And R CMD INSTALL --build mypack ?? The former is suggested by my previous notes and seems to work, and the latter is suggested by

[R] Where to put example files?

I'm writing an R package which includes some text file parsing functions, and I want to include with my package some example files to be used with those functions. My question is which directory should I put these example files in for the user to access? I have tried demo, example, doc and

[R] Preformatted text in Rd files

A quickie - how do I include preformatted text within the details section of an .Rd file? Thanks Mick __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide!

RE: [R] about colnames

Try colnames(df)[4:6] - c(x,y,z) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: 21 December 2004 09:45 To: [EMAIL PROTECTED] Subject: [R] about colnames Hello sir: If there's a data frame(with name df): a b c d e f 1 10

[R] Creating a vector of colours that are as different from one another as possible

Hi I want to create a vector of colors that are as different from one another as possible. ?rainbow states Conceptually, all of these functions actually use (parts of) a line cut out of the 3-dimensional color space This suggests to me that the resulting colors are all placed on this line

[R] Memory problem with jpeg() and wide jpegs

Hi I have been creating very, very long jpeg images for the last two weeks using jpeg(). All of a sudden, and I mean that, it's stopped working - I've not changed a thing! The error message I get is: jpeg(out.jpg,width=5,height=480, quality=100) Error in devga(paste(jpeg:, quality, :,

RE: [R] Memory problem with jpeg() and wide jpegs

: Mon 12/20/2004 5:37 PM To: Uwe Ligges Cc: michael watson (IAH-C); [EMAIL PROTECTED] Subject:Re: [R] Memory problem with jpeg() and wide jpegs It is also several times greater than the limit of human perception, being several feet long at printing resolutions that need a magnifying

RE: [R] problems with limma

Could you give a bit more detail about your experimental design? You're using affy, so you're working with single channel data - so nzw, akr and bas all have six arrays? -Original Message- From: [EMAIL PROTECTED] on behalf of [EMAIL PROTECTED] Sent: Mon 12/20/2004 8:45 PM To:

[R] If it's not a data.frame, matrix or vector, what is it?

Hi Forgive my ignorance. I am selecting a column of a data.frame using the column name, and I want to know what the resulting column is. My data frame is called submin and the column name is held in a variable called display.gname Eg: is.data.frame(submin) [1] TRUE

[R] Incorrect permissions to edit database package

Hi I am running R 2.0 on Suse Linux 8.2. I get an error message when loading a library: Incorrect permissions to edit the package database, /usr/lib/R/library/liblisting.Rda: save.locLib(locLibList, curLib) However, when I look at that file, the user I am running R as has r and w permissions

RE: [R] R: functions problem

Sometimes it's in function_name.default Eg: barplot function (height, ...) UseMethod(barplot) environment: namespace:graphics barplot.default function (height, width = 1, space = NULL, names.arg = NULL, legend.text = NULL, beside = FALSE, horiz = FALSE, density = NULL, angle = 45,

RE: [R] Create a plot legend in a new window

legend in a new window :-D Mick -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of michael watson (IAH-C) Sent: 09 December 2004 13:57 To: [EMAIL PROTECTED] Subject: RE: [R] Create a plot legend in a new window Following on from this, what I want

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