similar to: qr with missing dependent variables

Does anyone know if the survreg function in the survival package can fit numerical covariates ? When I fit a survival model of the form survreg( Surv(time,censored) ~ x ) then x is always treated as a factor even if it is numeric (and even if I try to force it to be numeric using as.numeric(x). Thus, in the particular example I am analysing, a simple numerical covariate becomes a factor

Hi Is there a maximum length for the character string representing a level of a factor? I have a set of several million variables, each a factor of length 19. Each factor level is a character string which in some cases can be many thousands of characters long. I am trying to find out why my analysis fails - I just wanted to rule out the possibility that the internal factor conversion has a

Is there a method to save a large and complex R object (either as a binary or text file) so that it can be loaded and reused at a later time? Specifically, I am creating large lists (several thousand elements), each element of which is either a vector or a matrix (with ~ 2000 rows). The dimensions of the matrices are not all the same. My ideal would be a set of functions of the form obj

Does anyone know a way to do the following: Save a large number of R objects to a file (like load() does) but then read back only a small named subset of them . As far as I can see, load() reads back everything. The context is: I have an application which will generate a large number of large matrices (approx 15000 matrices each of dimension 2000*30). I can generate these matrices using an

Dear all, I am running qtl mapping. I have 75 RI lines with some residual heterogeneous loci. The loci are code A, B or H(heterogeneous). Questions: 1) R/qtl determine the data is F2 intercross. 2) Warning message about strange genotype pattern > library(qtl) > dat=read.cross("csv", file="rqtl_trt.csv") --Read the following data: 75 individuals

I am running Samba on Solaris 2.6 and am connecting to it from Windows NT4.0. Whilst running some Access software the database is initially accessed without problem but part way through processing I get the report that the database file cannot be accessed since it is exclusively opened by another user. I cannot then read the database at all until I log out of Windows then back in. All is

I have a set of data that is not normally distributed and for which I need to build a model. So, I tried the lrm function from the design-package. The first run went well, and I got the following results: Wald Statistics Response: RVCL2PROC.mott Factor Chi-Square d.f. P TTV.mott (Factor+Higher Order Factors) 69.01 4

Hi, For the last few days I have tried utilise your package "pegas" in order to obtain some values for indices like the nuclear diversity and tajimas d value. I have modified my dataset (a text file containing dna sequences) in order to be able to read it in with the tools provided by pegas. Here, I have oriented myself on the description provided by the help-page in read.loci().

#Hello, #I have a question about obtaining results from a loop I have written. #Below is a sample of individual genotypes from a genetic question I am working on called "P.genotype.sample ". P.genotype.sample<-matrix(10,10,10) P.genotype.sample[,1]<-c(2,2,1,5,1,1,5,6,1,3) P.genotype.sample[,2]<-c(6,3,3,6,8,1,6,7,2,3) P.genotype.sample[,3]<-c(2,2,2,3,3,2,2,2,3,3)

Bottom Line Up Front: How does one reshape genetic data from long to wide? I currently have a lot of data. About 180 individuals (some probands/patients, some parents, rare siblings) and SNP data from 6000 loci on each. The standard formats seem to be something along the lines of Famid, pid, fatid, motid, affected, sex, locus1Allele1, locus1Allele2, locus2Allele1, locus2Allele2, etc In other

Hi All, I have a problem trying to get a set of columns recognised as a list and can't work out how to do it despite trawling through the mailing list archives, and docs. A short example... to.convert <- NULL n <- 6 for(x in 1:n){ to.convert <- paste(to.convert, paste((2 * x) -1, (2 * x), sep=":"), sep=",") } to.convert <- gsub("^,", "",

Hi all - I am NEW to R and NEW to any type of programming. I am making heatmaps using the heatmap.2 function within gplots package. At present, when the heatmap is plotted it uses the row identifiers as 1,2,3,4...etc. However, I much rather use my own labels. I was told my another well-versed R programmer to use the follow script: x<-as.matrix(test1[,-1]) ## skip column 1 rownames(x)<-

http://bugzilla.mindrot.org/show_bug.cgi?id=176 Summary: OpenSSH_3.1p1 gives X_ShmAttach error on forwarded X11 channel Product: Portable OpenSSH Version: 3.1p1 Platform: ix86 OS/Version: Linux Status: NEW Severity: normal Priority: P3 Component: sshd AssignedTo:

Hi Iain, It's a simple answer: > For example, if a box on a 128kbps upload connection is > serving a 64Kbps stream (and not audio-on-demand) - is it limited to two > connections Yes it is. > or is icecast somehow more efficient? No - icecast can't work miracles! The underlying technology of the internet (the way it is at present, at least) only allows a packet of

Hello All, Once again thanks for all of the help to date. I am climbing my R learning curve. I've got a few more questions that I hope I can get some guidance on though. I am not sure whether the etiquette is to break up multiple questions or not but I'll keep them together here for now as it may help put the questions in context despite the fact that the post may get a little long.

I am about one step away from heaven on earth. I think only one step! I am using dgc.genetics to run a TDT test on thousands of genetic loci. I have learnt (through the help of others on this mailing list) to send the complex output to useful data frames which in turn allow me to look at the big picture and screen the thousands of loci. Resultdt<-lapply(PGWide[,240:290], tdt) the above

Rers, I have been using the function 'by' in such a manner: by(LogMetric, list(Loci.Number=Loci.Number, Code.Flag=Code.Flag), plot) with par(mfrow=c(5,3)) to produce a single R Graphics: Device with 14 different plots on it as described above in my 'by' statement. Thank you for helping me thus far. A similar command using 'tapply' can be written as well. My

Hi All, I am trying to plot outlier loci in R from data generated by BayesFst. The developers provide the code which I use but I can't seem to get it to work consistently. Sometimes I can get R to generate a plot (without confidence intervals or loci IDs) and other times I cannot even generate P-values using the code supplied. I am wondering if any one has used R to plot the BayesFst

Hi, These are two problems I've never seen when I used xtable() before... R 1.9.1 for Windows XP, xtable version 1.2-3: > final.df Loci Chr Marker Position P.values Deviance DF 1 Idd5 1 D1Mit181 42.6 0.0011 103.21 78 2 Idd6/19/20 6 D6Mit374 66.7 0.0014 104.29 78 3 Idd13 2 D2Mit490 64.5 0.0025 97.83 78 4

Hello R-help community, I have another question about filtering datasets. Please consider the following "toy" data matrix example, called "x" for simplicity. There are 20 different individuals ("ID"), with information about the alleles (A,T, G, C) at six different loci ("Locus1" - "Locus6") for each of these 20 individuals. At any single locus