search for: kinship

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 matrix was NOT a distance matrix but a kinship one....

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 resources I n...

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 applica...

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...

...he short test case. tmt34% R --vanilla R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 > temp <- matrix(runif(50), ncol=2) > t(temp) %*% temp [,1] [,2] [1,] 7.916016 6.049698 [2,] 6.049698 7.650694 > library(kinship) Loading required package: survival Loading required package: splines Loading required package: nlme Loading required package: lattice > t(temp) %*% temp `__Deferred_Default_Marker__` ----------------------------------------- Within the library is a definition of %*% for bdsmatrix objects, whi...

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 b...

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) > > #Generati...

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...

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...

Hello, I am using the Kinship package to draw a pedigree plot. I am trying to control the spacing between individuals in the pedigree. Currently, it is drawing a pedigree with too little space, so the text is overlapping. I'd like to increase the distance between individuals. According to the documentation, I would expec...

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 random example data id <- 1:100 da...

Hi, I had a problem with the lmekin() in kinship package: lmekin() can not be wrapped into another function library(kinship) #creat an example dataset xx<-rnorm(100) yy<-rnorm(100) id<-1:100 test.dat<-as.data.frame(cbind(xx,yy,id)) rm(xx,yy,id) a<-bdsmatrix(rep(10,10),rep(block,10),dimnames=list(c(1:100),c(1:100))) #100x100 b...

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+A...

...hat 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 lmer from the lme4 package, I can model V1 and V2 as a fixed & random coefficient: Mod1=lmer(y ~ V1 + V2 + V3 + V4 + (1 + V1 + V2|GROUP)) Can I do something like this, though correctly without getting the error ("Error in max(kindex) : object "kindex&q...

Dear Sir/Madam, Since a few day now I try to use the command "polygenic" from the GenAbel package. However, I keep bumping up against an error message: "Error in polygenic(Testo, kin = kinship, data = data1) : dimension of outcome and kinship.matrix do not match". My data exists of 1240 individuals with 74 markers. It mainly consists of small families (2 or more brothers, father and mother; otherwise only the brothers are given). Genotypes are provided for the largest part of th...

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 user to do it? Thanks -- View this message in context: http://r.789695.n4.nabble.com/heritability-estimation-tp3904908p3904908.html Sent from the R help mailing list archive at Nab...

...aricular 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 pedigreeList object, kinship.R with "kinship" methods for the two objects one small compute function called by the others along with the minimal amount of other information such that a call to R --vanilla CMD check ktest gives no errors until the fatal one. There are two test cases. A 3 line one that creat...

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 is loaded" Loading required package: Formula Loading required package: MASS Loading required package: sandwich Loading required package: zoo...

Dear useRs: Announcing the release of kinship2, version 1.2.1, to CRAN. kinship2 is a branch from the original kinship package with some key updates for the pedigree and kinship functions, with some additional functions that work with the pedigree object. Highlights: * pedigree and pedigreeList objects implemented with S3 methods print and...

Dear all, I get an unexpected error when using the mantel.test function in library(ape). Is there something wrong with my matrices? > dmatr<- read.table("obt.Loiselle.kinship.intens02.DIST.matrix.txt",head=F) > kmatr<- read.table("obt.Loiselle.kinship.intens02.KINSHIP.matrix.txt",head=F) > > mantel.test(as.matrix(kmatr), as.matrix(dmatr), nperm = 500, graph = T) Error in var(x, na.rm = na.rm) : `x' is empty > > is.matrix(as.matrix(...