similar to: from character to numeric over multiple columns

Hi All, I would like to ask the following. I have an array of data in an objetct, let's say X. I need to use a for loop on the elements of one or more columns of X and I am having a debate with a colleague about the best memory management. I believe that if I do: col1 = X[,1] col2 = X[,2] ... colx = X[,x] and then for(i in whatever){ do something using col1[i], col2[i] ... colx[i] }

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, 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 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, 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 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

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 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

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, 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

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 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 am confused on how to specify some nesting and interaction terma with lme(). I have a dataset where some flies where selected for accessory gland size, made to mate in presence/absence of another male and the level of some protein measured. Now the complex stuff. The selection has been replicated twice, so that the selection term has got two levels (large and small) with

Hi All, I noticed the following: pip = array(1:6, dim = c(3,2)) dim(pip) [1] 3 2 pup = pip[1,] dim(pup) NULL I bet there is a *good* reason why one row of an array is *dimensionless*, but it's highly inconvenient for my purpose, i.e. to use apply() after an array goes through a number of logical steps and is redimensioned, sometimes to one single row. How do I keep dim(pup) to 1 2?

Hi All, is there any chance of vectorising the two ifelse() statements in the following code: for(i in gp){ new[i,1] = ifelse(srow[i]>0, new[srow[i],zippo[i]], sample(1:100, 1, prob =Y1, rep = T)) new[i,2] = ifelse(drow[i]>0, new[drow[i]>0,zappo[i]], sample(1:100, 1, prob =Y1, rep = T)) } Where I am forced to check if the value of drow and srow are >0 for each line... in

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