similar to: R-help Digest, Vol 54, Issue 30

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

A bit late, but you might like to look at http://www.qimr.edu.au/davidD/polyr.R Regarding the original posters queries: You can analyse polychoric correlations as if they were Pearson correlations using standard software (eg sem), and this usually doesn't do too badly, or go to AWLS (Browne) in LISREL etc, or ML analysis of the full multidimensional contingency table using programs such as

This is a bit late, but: > About two years ago there was a thread about this which suggested that at > that time nobody had these coefficients ready to go. > (a) has anyone in the meanwhile programmed them? http://www.qimr.edu.au/davidD/R/polyr.R > (d) I appreciate this last item is not strictly an R question, but my > intention is to use these as input into the sem package for

I have encountered the same problem with sshd -i (under Mandrake linux 6.1) as that described by Ben L Perkins, this time with 2.1.1p4: ... Last login: Mon Jul 17 12:04:50 2000 from orpheus.qimr.edu.au -bash: ?oe90: command not found -bash: glorious: command not found -bash: ?]r90: command not found -bash: marshall4: command not found Connection to orpheus.qimr.edu.au closed. log: Jul 17

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

Hi. I just noticed the paper by Morales and Nocedal Remark on "Algorithm 778: L-BFGS-B: Fortran Subroutines for Large-Scale Bound Constrained Optimization". TOMS 2011; 38(1): 7 http://www.ece.northwestern.edu/~morales/PSfiles/acm-remark.pdf which describes a couple of improvements (speed and accuracy) to the original Netlib code which AFAICT is that still used by optim() via f2c.

I don't know of any R package that can match all the functionality of LEM eg fitting equality constraints to model parameters a la LISREL. WRT dumping tables, I would have thought that as.data.frame.table does pretty much what you want, [not tested] newtab <- as.data.frame(table(a,b,c)) cat("dim\n") for(i in seq(1, ncol(newtab)-1) { cat(nlevels(newtab[,1]," ") }

Hi. I don't know if this a bug or just annoying to me: > x <- c(1,2,3,NA) > table(x, exclude=NULL) x 1 2 3 <NA> 1 1 1 1 > table(factor(x), exclude=NULL) 1 2 3 1 1 1 I don't think many people use factor(x, exclude=NULL): it is not the default handling of character data by read.table(). Cheers, David Duffy. -- | David Duffy (MBBS PhD)

> Date: Mon, 20 Feb 2006 16:43:55 -0600 > From: Aldi Kraja <aldi at wustl.edu> > > Hi, > Using package gclus in R, I have created some graphs that show the > trends within subgroups of data and correlations among 9 variables (v1-v9). > Being interested for more details on these data I have produced also the > var-covar matrices. > Question: From a pair of two

On Fri, 16 Jan 2009, r-help-request at r-project.org wrote: > Date: Thu, 15 Jan 2009 13:29:03 +0100 > From: Pablo G Goicoechea <pgoikoetxea at neiker.net> > Subject: Re: [R] How to create a chromosome location map by locus ID > To: Sake <tlep.nav.ekas at hccnet.nl> > Cc: r-help at r-project.org > Message-ID: <496F2C0F.3040304 at neiker.net> > Content-Type:

On Mon, 8 Nov 2004 ssim at lic.co.nz wrote: > > Is there an add-on package in R for QTL interval mapping for outbred > population, eg. Haley-Knott regression method ? > > Stella I believe Karl Broman's R/QTL (http://biosun01.biostat.jhsph.edu/~kbroman/software/) and Brian Yandell's bim (http://www.stat.wisc.edu/~yandell/qtl/software/), Richard Mott's happyR

I couldn't resist adding a more literal answer unback <- function(x) { chars <- unlist(strsplit(deparse(x),"")) chars <- chars[-c(1,length(chars))] paste(gsub("\\\\","/",chars),collapse="") } unback("\n") | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph:

I couldn't resist adding a more literal answer unback <- function(x) { chars <- unlist(strsplit(deparse(x),"")) chars <- chars[-c(1,length(chars))] paste(gsub("\\\\","/",chars),collapse="") } unback("\n") | David Duffy (MBBS PhD) ,-_|\ | email: davidD at qimr.edu.au ph:

Tony Rossini wrote: > > For various reasons, I spent part of my time today looking at sample > size and power calculation tools (don't ask, don't tell...). This > seems to be one area that R is incredibly weak in (well, nearly all > stat packages, except perhaps specialized tools and SAS); sure, there > are a number of functions in various packages: > >

C?dric Finet wrote: > > I thank you for your answer but I do not understand yet why the Fisher?s exact > test does not work. And why is a "negative key". > > C?dric Finet > Running the original TOMS643 fortran code (R uses an f2c translation of this) says: FEXACT ERROR: 30 Stack length exceeded in f3xact. This problem should not occur. The integer hash key is

Newsgroup members, I appreciate the help on this topic. David Duffy provided a solution (below) that was quite helpful, and came close to what I needed. It did a great job creating two vectors of dichotomous variables with a known correlation (what I referred to as a phi-coefficient). My situation is a bit more complicated and I'm not sure it is easily solved. The problem is that I must

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

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 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 <-