similar to: Re : LOOPS

Hi Everyone, I posted a similar question about a week ago, but haven't gotten any replies -- I'm afraid that's because my previous question was too vague. Let me try again with a more specific question, and I hope someone can help. NOTE, I know I should be using the newer lme4 package, I just haven't had a chance to update my version of R yet, so the question below relates

Hi R community, I am new bird to R and moved recently from SAS. I am no means expert on either but very curious learner. So your help crucial for me to learn R. I have already got positive expression. I was trying to fit a mixed model in animal experiment but stuck at simple point. The following similar example is from SAS mixed model pp 212. # data genetic_evaluation <-

Hi , is it possible to calculate ld-measures D, D', r and perhaps corresponding p-values with r IF THE PHASE IS KNOWN? The genetics - package provides the LD function only for ambigious phase. Thank you very much Bettina Kulle

# Hello, # I have a list with 6 categories and with different numbers of rows. # I would like to change each of them into a unique data frame in order to match # values with other data frames and perform some calculations. # Or I could make each category or list element have the same number of rows and create one large data.frame. # below is a creation of a sample list # I apologize for the

Hello, I am trying to make the switch from SAS, and I have a fairly elemental problem with syntax using the nlme package for analyzing mixed models. There was a previous question on this topic posted to this list, so I apologize for redundancy, but I didn't understand the advice given to that inquiry. The model I want to run has the following factors: Host (fixed) Sire (random) Dam

Hi, I have a dataframe that contains pedigree information; that is individual, sire and dam identities as separate columns. It also has date of birth. These identifiers are not numeric, or not sequential. Obviously, an identifier can appear in one or two columns, depending on whether it was a parent or not. These should be consistent. Not all identifiers appear in the individual column - it is

I have a data frame containing the Id, Mother, Father and Sex from about 10,000 animals in our colony. I am interested in graphing simple family trees for a given subject or small number of subjects. The basic idea is: start with data frame from entire colony and list of index animals. I need to identify all immediate relatives of these index animals and plot the pedigree for them. We're

Dear R helpers I have a table and i need to make new table table1: sire snp1 snp2 snp3 snp4 snp5 snp6 snp7 snp8 snp9 snp10 snp11 snp12 snp13 snp14 snp15 8877 -1 -1 -1 -1 0 0 -1 -1 -1 0 1 1 1 -1 -1 7765 1 1 1 0 0 0 -1 1 1 1 0 0 0 1 0 8766 1 1 -1 0 -1 -1 0 -1 0 -1 -1 -1 0 1 0 6756 0 1 0 -1 1 -1 -1 0 0 0 0 -1 0 1 1 5644 -1 0 1 -1 0 0 0 0 -1 -1 0 0 0 0 1 I have table2 sire

Hi All, I'd like to ask for a few clarifications. I am doing some calculations over some biggish datasets. One has ~ 23000 rows, and 6 columns, the other has ~620000 rows and 6 columns. I am using these datasets to perform a simulation of of haplotype coalescence over a pedigree (the datestes themselves are pedigree information). I created a new dataset (same number of rows as the pedigree

> From: Yuandan Zhang > > If you want to call R from perl, why don't you do a simple > system call like: > > $callR="/usr/loca/bin/R CMD BATCH plotscript.R"; > system ($callR); > > It is not necessary to start X display if anything can be > done in background But the problem is jpeg()/png() are not available unless an X display is available to the

Hi All, Anybody know how to make R emit base64 encoded text in some way that perl can grab it, instead of planting a file on your harddrive when calling JPEG or PNG? I've managed to get these scripts to work and put a file on the harddisk #!/usr/bin/perl -Wall # by jin kee. a simple script to demonstrate # the needed steps to get R to emit a jpeg. use strict; my($callR, $callRold); # need

Hola a todos, me gustaría realizar una consulta asociada a la generación de valores genéticos del pedigreemm en R. Primero generé el archivo de pedigree incluyendo los parentales para posteriormente estimar la varianza aditiva y los valores genéticos para cada individuo, relacionando los individuos por medio de la matriz de parentesco. Me da todo perfecto, el complemento pedigreemm trabaja muy

Estimados Estoy probando una alternativa, la cual no tiene ranef Pero puedo saber cuáles son desde la siguiente matriz, 4 , 5, 6, 7, 8 son hijos de sire1, sire3 y sire4. Obtengo los resultados, pero ¿como puedo tomar los nombres de filas y columnas, sire1, sire2, sire3, 4, 5, 6, 7, y 8, de forma tal de hacer legible el resultado para cada animal? Lógicamente, un listado de números sin decir

Hi, I'm running into a problem subsetting a data frame that I have never encountered before: > dim(chkPd) [1] 3213 6 > df = head(chkPd) > df PN WB Sire Dam MG SEX 601 1001 715349 61710 61702 67 F 969 1001_1 511092 616253 615037 168 F 986 1002_1 511082 616253 623905 168 F 667 1003 715617 61817 61441 67 F

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

-------- Original Message -------- Subject: [AGDG-LIST:405] R Computing Contest Date: Sat, 21 Oct 2006 12:08:13 -0400 From: Larry Schaeffer <lrs at uoguelph.ca> Reply-To: lrs at uoguelph.ca To: Animal Geneticist's Discussion <agdg-list at colostate.edu> For those that are interested only: R Computer Programming Challenge Given: y = Factor A + Factor B + b1(Covariate1) +

Hi, I'm using R for a QTL analysis of SNP data. I was wondering if anyone had any advice on fitting a dominance effect into the following function; > myfun4 function (x) { x <- scan(con, nmax=169) y <- unique(x[which(!is.na(x))]) if(length(y)>1) { summary(lme(Ad ~ x, random= ~1|sire, na.action="na.omit")) } else {print("no.infomation")} } Con is the

Just the sort of newbie question we all hate ;-) I'm a bit stuck with MOH. I think all is done right and I've read everyhing I can find, but whenever * tries to do MOH, all that happens is '-z: No such file or directory' Yes, I am on redHat. Yes I have installed real mpg123. Yes, it does seem to work from the command line. Any suggestions would be greta, I'm sire

I am trying to run a simple nested manova with two levels of nesting, Sires, and Dams within Sires. The goal is to extract the among sires covariance matrix and secondarily, the among Dams within Sires covariance matrix. Both sires and dams are random effects. At present there are four dependent variables, but that may change. This is part of a larger bootstrapping project, so efficiency and