similar to: Errors checking a library

Professor Ripley thanks for this. Very much appreciated. The original subject line reflected my late-night conviction that the answer might involve passing a strange list to do.call(). Anyway, package magic is broken (only in R-devel, I might add) because I have a function called "%eq%". R-2.0.0 CMD check is stopping (I think) because it interprets the "%" as a

Hi When I use plot(hclust(dist..)...)...) etc to create a dendrogram of a hierarchial cluster analysis, I end up with a vertical tree. What do I need to do to get a horizontal tree? Also, my users are used to seeing trees who's leaves all "end" at the same place (eg. Like in minitab). Is this possible in R? Thanks Mick Michael Watson Head of Informatics Institute for Animal

Hi Thanks once again for your help, I do appreciate it..... however.... Here is what I get with your test.... (under tcsh - i normally use bash, but I will keep everything the same) users/mwatson> env http_proxy=http://wwwcache.bbsrc.ac.uk:8080/ R >options(internet.info=0) >update.packages() trying URL `http://cran.r-project.org/src/contrib/PACKAGES' unable to connect to

Quite a simple one really! When I run boxplot(), the labels on the X axis are horizontal, and I want them vertical. So I did: par(las=3) boxplot(...) And my labels just aren't there anymore.... Any help???

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 lame asking this. Any suggestions? Mick

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. So I click Save, and am met with a "Save As" dialogue box with the default file called

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 > is.data.frame(submin[,display.gname]) [1] FALSE >

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

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 Infected, Not Vaccinated, Lesions - 4 measurements Uninfected, Not Vaccinated, No Lesions - 3 measurements

Hi I have a complicated plot which has a potentially large legend. What I want to do is actually create the legend in a new window. Has anyone done this before? I'd like to be able to create a window with just the legend in it, and have it so the window is just the right size etc. I'm sure someone must have done this already? If not, any tips would be welcome. Thanks Mick

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 this into is a matrix with the names (cat000_a01 etc) as row names, the first element of each of

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 for each of the 12 variables, so that, for each row, I have 12 means. A grouping variable

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 <- data.frame(c1=c(1,1,1),c2=c(2,2,NA)) df[is.na(df)] <- 0 df df <- data.frame(c1=c(1,1,1),c2=c(2,2,2)) df[is.na(df)] <-

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 element of the list counting the rows, to find the maximum.... BUT I can't help thinking there's

Hi I can't get R to connect to the internet. I am running R 1.7.1 on Windows XP and whenever I try to download packages etc from within R using the internet, it fails. OK so I am behind a firewall and use a proxy server.... SO, if I go to my MS-DOS prompt and type: RGui.exe --internet2 everything works.... BUT i can't set up a shortcut for this as Windows (I hate Windows) complains

OK, I really am struggling with this one! Forgive me if I am being stupid.... I am running R 1.7.1 on Suse Linux 8.1. I connect to the internet through a proxy so I have: IAHC-LINUX03:~ # echo $http_proxy wwwcache.bbsrc.ac.uk:8080 IAHC-LINUX03:~ # echo $HTTP_PROXY wwwcache.bbsrc.ac.uk:8080 just in case ;-) SO, i go into R and I get: >

Hi I have seen a few posts to this list regarding problems accessing the x11() device over cgi - namely, when trying to create a graphic using the jpeg() function, everything is fine from the command line but it won't work over cgi, producing the error: "Unable to open connection to X11 display" Has anyone actually solved this particular problem satisfactorily? Please reply

Hi First a simple question to do with plot(). How do I change the x-axis labels on a plot? For example, I am plotting each row of a matrix, and I want each row to be a line on my graph. Simple really. Eg: plot(sg[1,], type="l") When I do this, the x-axis is labelled 1:38, as I have 38 columns in my matrix. When I do: plot(sg[1,order(sg[1,])], type="l") Ideally I would

Hi Now a more theoretical question. I have two correlation matrices - one of a set of variables under a particular condition, the other of the same set of variables under a different condition. Is there a statistical test I can use to see if these correlation matrices are "different"? Thanks Mick

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 give me the first data frame, pos[2] will give me the second etc... Kind of basic