similar to: kinship package example data

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 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 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 dadid <- c(rep(0, 5), rep(1, 5), rep(3, 5), rep(5, 5), rep(7,

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

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

Hi, I'm using kinship2 to calculate heritabilty, but I would like calculate in GenABEL too. I trying the code: > require(kinship2) > require(GenABEL) > pedig = with(Dados, pedigree(id=IID, dadid=PAT, momid=MAT, sex=SEX, famid=FID, missid=0)) > kmat = kinship(pedig) > (mod1 = polygenic(altura ~ SEX + idade, data=Dados, kin=kmat)) Erro em intI(i, n = d[1],

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 expect the following to be relevant:

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

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

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?

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,

I've finally narrowed down a puzzling problem: here is the 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:

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! 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.

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, 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 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

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 block (n=10) diagonal matrix to indicate the

I've been able to do most things I'd like to using the map package, but I can't figure out how to fill a region without drawing a black outline. I can draw the outline in a specified colour, but as soon as I set fill to TRUE, I get a black outline in addition. My map has a lot of activity on the coastline so I don't want a black line obscuring what I do there. A pale colour to

I have a square matrix wherein a '*' indicates an HSD between the levels indicated by row name and column name. The '.' is simply marking the diagonal. A blank indicates the same group A B C D E F G H I J K L M N A . B . C * * . D * * . E * * * . F * * * .