similar to: Deferred Default Marker

The package coxme depends heavily on bdsmatrix, to the point of needing access to some of its C calls. The kinship package (in progress) uses the R level functions in bdsmatrix, but not the C calls. That is, I don't want to always export the symbols. For testing I can use an explicit dyn.load('somepath/bsdmatrix.so', local=F). How do I incorporate such a dependency in the

Hi Im using the kinship package to draw a pedigree. On my data set this works fine but when i add indivudals to the pedigree i keep getting an error i hope someone can help me! This is the code im using: Data<-read.table("Tree.txt", header=T, sep=",") attach(Data) ped<-pedigree(id, dadid, momid, sex, aff) par(xpd=T) plot.pedigree(ped) This is my data looks like

Dear All, I am in the somewhat unfortunate position of having to reproduce the results previously obtained from (non-metric?) MDS on a "kinship" matrix using Statistica. A kinship matrix measures affinity between groups, and has its maximum values on the diagonal. Apparently, starting with a nxn kinship matrix, all it was needed to do was to feed it to Statistica flagging that the

I wish to make modifications to the plot.pedigree function in the kinship package. My attempts to contact the maintainer have been unsuccessful, but my question is general, so specifics of the kinship package might not be an issue. My first attempt was to make a new function Plot.pedigree in the .GlobalEnv which mostly achieved what I wanted to. However, I'm sure that's not the tidiest

Hello, I was hoping someone could answer a question for me that may either be statistical or script related. I don't come from a statistics background, so I am not positive if I am using the correct nomenclature or even the correct procedure. Is it possible to model "random coefficients" in a mixed effects cox-regression using coxme from the Kinship package? For example, using

Dear All, I have problem installing the 'kinship' package. I used the 'install.packages' from R command line and had no problem installing other packages before. Here is what I get: * Installing *source* package 'kinship' ... ** libs gcc -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/usr/local/include -fno-common -g -O2 -c agfit6b.c -o agfit6b.o

Hi Folks, Has anyone got a compiled binary of the package 'plm' and/or of the package 'kinship' for Debian Etch? I'm asking because I'd like to install 'plm', but have failed because it depends on 'kinship', and 'kinship' refuses to compile on my Debian Etch. The underlying reason is the Debian refuses to allow me to install the development

Hello, I like to use the package "kinship" (R version 2.2.0). After loading this package the operator %*% doesn't work. Example: R> library(kinship) R> a <- cbind(1:2,rnorm(2)) R> a%*%a Error message: Fehler in a %*% a : keine anwendbare Methode f侟r "%*%" The Message in English: Error in a %*% a: no applicable message for "%*%". What can I do?

I am making the question clear. Please help. > Dear R experts > > I was using kinship package to fit mixed model with kinship matrix. > The package looks like lme4, but I could find a way to extract p-value > out of it. I need to extract is as I need to analyse large number of > variables (> 10000). > > Please help me: > > require(kinship) > > #Generating

Hi,I use the 'lmekin' model of the 'kinship' package of R in order to estimate heritability. I want to estimate the confidence interval of the variance coefficient and so I should use a bootstrap simulation. The pedigree file has 1386 subjects so I create a kinship matrix [1386*1386].This is the code of R I use: kfit2 <- lmekin(IT~1+AGE +(1|ID), dati1,

Hello, I'm looking for a method to estimate narrow sense heritability of traits in a RIL population. Papers I've checked either use either SAS or SPSS or do not give any details at all. I've found some reference to using variance components in ANOVA, using the kinship or wgaim packages, but I don't have a clue as to how to do any of this. Is there any way fro a very R illiterate

I've been looking at the kinship package which looks as though it might be appropriate for my purposes. What I can't find is any reference to the data that is used in the example code. A dataframe called d10 with column names, upn, dadid, momid, sex and affect is required. One can get an idea of what sort of values should be in most columns from the description in the pedigree function,

Hi folks, Wish y'all a Happy New Year 2010! I need some help with the following: Say I have lots of data sets, on which I have to apply a certain function on the same set of columns in each of the data set. Let's take, for ex, the typical data set is: df1 <- as.data.frame(cbind(rnorm(10),rnorm(10))) names(df1)[1] <- "A" names(df1)[2] <- "B" There are many

Can we do Cholesky Decompositon in R for any matrix --------------------------------- [[alternative HTML version deleted]]

Hi, I seem to be facing a strange problem when I use Sweave for creating a LaTeX document of the R lme() output --- The EPS and PDF figure files get created, but are empty. I have attached a reproducible example below (taken from the R lme() help example). ------------------------------------------------------------------------------------ \documentclass[a4paper,10pt]{article}

I have library in development with a function that works when called from the top level, but fails under R CMD check. The paricular line of failure is rsum <- rowSums(kmat>0) where kmat is a dsCMatrix object. I'm currently stumped and looking for some ideas. I've created a stripped down library "ktest" that has only 3 functions: pedigree.R to create a pedigree or

Hello, All, GWAF 1.2 R.Version() is below. system(lme.batch.imputed( phenfile = 'phenfile.csv', genfile = 'CARe_imputed_release.0.fhsR.gz', pedfile='pedfile.csv', phen='phen1', covar=c('covar1','covar2'), kinmat='imputed_fhs.kinship.RData', outfile='imputed.FHS.IBC.GWAF.LME.output.0.txt' )) Gives the error messages: Error in

I'm currently packaging up some of the kinship matrix routines more formally, these are used in coxme when dealing with family correlation structures. One of my test programs exercises error conditions, i.e., it purposely feeds particular types of invalid pedigree data in to see if the right error message results. So there are comment-action pairs # the next line should generate a

Hello, Apologies in advance if this is a stupid question. I am running R on Ubuntu 9. R version 2.9.2 (2009-08-24) I am trying to work with plm. I think the library is installed, as I can do > library(plm) Loading required package: kinship Loading required package: survival Loading required package: splines Loading required package: nlme Loading required package: lattice [1] "kinship

Hello! I am building a package, which includes also one Fortran subroutine, which works fine if I compile it as a shared library and load it into R via dyn.load(). However, when I launch R CMD check it doesn't stop with checking examples. It's just doing and doing ... I pasted the whole output from R CMD check. Does anyone have any suggestions? I'm still using R 2.0.1.