similar to: Biodem 0.1/orphaning of MAlmig

Hi All, I am trying to build a new R package to submit, but it's failing to create a tex manual: R CMD check Biodem * checking for working latex ... OK * using log directory '/home/greatsage/Fede/R-packages/temp/Biodem.Rcheck' * checking for file 'Biodem/DESCRIPTION' ... OK * checking if this is a source package ... OK * Installing *source* package 'Biodem' ... ** R

[ This was posted to the R-packages list (which I moderate), but definitely doesn't belong there. Martin Maechler ] ------- start of forwarded message ------- From: Federico Calboli <f.calboli at ucl.ac.uk> To: r-packages at stat.math.ethz.ch Subject: how to upload Date: 15 Jul 2004 18:30:26 +0100 Dear All, I just finished a add on lib called Malmig, to calculate Malecot

Hi All, I have a list of matrices: > x [,1] [,2] [1,] 1 4 [2,] 2 5 [3,] 3 6 > y [,1] [,2] [,3] [,4] [,5] [,6] [1,] 18 21 24 27 30 33 [2,] 19 22 25 28 31 34 [3,] 20 23 26 29 32 35 > z =list(x,y) I want to create a second list that is has a subset each matrix in the list subsetting so I get the 2nd and 3rd row of each (and

Hi All, I have the following problem: x = c(1,2) x [1] 1 2 as.matrix(x) [,1] [1,] 1 [2,] 2 BUT, if I add: y = c(3,4) as.matrix(rbind(x,y)) [,1] [,2] x 1 2 y 3 4 It does not transpose. Since I will need as.matrix() for a list of data that is in one or more lines, I need as.matrix to behave in a consisten fashions, so I get as.matrix(x, whatever) [,1] [,2] x 1

Hi All, I am using plot(x, type = 'l') for some plotting, but I would like rounded edges rather than jagged edges in the plot (purely for aestetic reasons). How could I achieve that? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 7594 1602 Fax (+44) 020

Hi All, I am (almost) successfully using apply() to apply a function recursively on a data matrix. The function is question is as.genotype() from the library 'genetics' apply(subset(chr1, names$breed == 'lab'),2,as.genotype,sep ="") Unfortuantely apply puts it's results into a matrix object rather than a data frame, tranforming my factors into numerics and

Hi All, is there a function in R that allows me to work with fractions without transforming them to floats (or whatever) in between? Something that would calculate something like: (1/2 + 1/8) * 1/2 = 5/16 without ever transforming to 0.5 and 0.125? Best, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place,

Hi All, a colleague wants to calculate the Fisher information matrix for a model he wrote (not in R). He can easily get the neg-log-likelihood and the best fit parameters at the minimum. He can also get negLLs for other parameter values too. Given these data, is there a way in R to calculate the Fisher information matrix? Best, Federico -- Federico C. F. Calboli Department of Epidemiology

Hi everyone, I would like to find out when and where exactly I get the following warning in a piece of code I've written: Error in "[<-"(`*tmp*`, iseq, value = numeric(0)) : nothing to replace with The code is a for () loop performing a somewhat trivial calculation, modulated by a number of logical if(){} else(){} conditions, involving the creation of a number of

Hi You could try to find an equivalent representation as a string and try to match those. > (A <- cbind(sample(1:2, 10, rep=TRUE), sample(1:2, 10, rep=TRUE))) [,1] [,2] [1,] 1 2 [2,] 1 2 [3,] 1 2 [4,] 2 2 [5,] 1 1 [6,] 1 2 [7,] 1 2 [8,] 1 1 [9,] 1 2 [10,] 1 1 > (B <- unique(A)) [,1] [,2] [1,] 1 2

Dear All, I am trying to calculate the Hardy-Weinberg Equilibrium p-value for 42 SNPs. I am using the function HWE.exact from the package "genetics". In order not to do a lot of coding "by hand", I have a for loop that goes through each column (each column is one SNP) and gives me the p.value for HWE.exact. Unfortunately some SNP have reached fixation and HWE.exact requires a

Dear All, I saved by mistake the environment I was working in after typing q(), and now I get the annoying message: [Previously saved workspace restored] I have already deleted all the objects in the environment, saving it as an empty environment, so it's just a matter of nitpicking I suppose. The message does not appear if I start R from any other place in the directory tree. I am

Hi All, is there an equivalent of the Unix command 'less' (or 'more'), so I can look at what's inside a data.frame or a matrix without having it printed out on console? I am using R on Debian Linux and Mac OS 10.4.5 Cheers, F -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St Mary's Campus Norfolk Place, London W2 1PG Tel +44

Hi All, I need to write as text files 1000 ish variation of the same data frame, once I permute a row. I would like to use the function write.table() to write the files, and use a loop to do it: for (i in 1:1000){ bb8[2,] = sample(bb8[2,]) write.table(bb8, quote = F, sep = '\t', row.names = F, col.names = F, file = 'whatever?????.txt') } so all the files are called

Hi All, I am looking for references on R as a programming language (apart form the standard R-lang.pdf and the other manuals), reference that would cover _in_depth_ things like loops, code optimisation, debugging tools etc... and is as up-to-date as possible. Can anyone suggest any book or other reference apart from the "green book" and the V&R "S-programming"? Cheers,

Hi Everyone, I would like to add errorbars to a lattice plot. I already have a function that adds error bars to a plot (originally written by George Gilchrist) which takes as arguments the coordinates of the point and then the size of the error bar. I would like to integrate it in my lattice code but I seem to be stumped. I can put the error bar function inside my code as if it were a panel

Hi All, I cannot upgrade r-base and r-recommended because the latest (latest as in it was not listed as 'upgradable' yesterday but today is) r-base-cose is 2.7.1-2hardy0 not hardy1: r-base: Depends: r-base-core (>=2.7.2-1hardy1) but 2.7.1-2hardy0 is to be installed Depends: r-recommended (=2.7.2-1hardy1) but 2.7.1-2hardy0 is to be installed r-base-core: r-recommended:

Hi All, Is there some document/manual about data manipulation within R that I could use as a reference (obviously, aside the R manuals)? The reason I am asking is that I have a number of data frames/matrices containg genetic data. The data is in a character form, as in: V1 V2 V3 V4 V5 1 AA AG AA GG AG 2 AC AA AA GG AG 3 AA AG AA GG AG 4 AA AA AA GG AG 5 AA AA AA GG AA I need, to chop,

Dear All, I'm using apply to do some genetic association analysis along a chromosome, with many thousands markers. For each marker the analysis is the same, so I was planning to use apply(chrom, 2, somefunction) In the specific case I do: my.results = apply(chr, 2, function(x){anova(lrm( cpstc.f ~ x + time.cpstc + age + sex + mri))[1,3]}) This is all good and well in theory, but in

Hello, I am on the latest Ubuntu 10.04 and I am upgrading R. I get the following error: r-base-core-dbg: Depends: r-base-dev (=2.11.1-2lucid0) but 2.11.1-1lucid0 is to be installed If that helps my CRAN mirror is: http://stat.ethz.ch/CRAN/bin/linux/ubuntu lucid/ I did check on the archives for any email concerning the problem, I hope I am not duplicating a thread. Best, F -- Federico