similar to: Major update: paramlink version 0.6-1

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 "[," * pedigree plotting routine

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 "[," * pedigree plotting routine

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],

Dear R developers: I am a PHD candidate student in the school of public health of Peking University and my major is genetic epidemiology. I am learning the FAM-MDR algorithm, which is used to detect the gene-gene and gene-environment interactions in the data of pedigree. The codes were written by Tom Cattaert of the University of Liege. The algorithms and the sample datasets are available at

I had added a vignette to the coxme package and all worked well locally, but it failed at CRAN.???? The issue is that the vignette involves using coxme for pedigree data, it doesn't work without the kinship2 package, and I hadn't put in the necessary "if (require(...." logic. The question is, how do I make the entire vignette conditional? If the package isn't available,

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 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 List, I downloaded R for the first time yesterday, in the hopes that I might deal more effectively with a complex repeated measures experimental design involving inbred strains of laboratory mice. The design below, somewhat simplified, cannot be computed with standard ANOVA, because something called the X'X matrix is too large. The design has the following factors: Between-subject

Package bqtl version 1.0 is now available on CRAN. Description: QTL mapping toolkit for inbred crosses and recombinant inbred lines. Includes maximum likelihood and Bayesian tools. I am keen to have comments about this package including implementation details, additional functionality, and (of course) problems and bugs. Chuck Berry -- Charles C. Berry (858) 534-2098

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 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

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 users, Version 2.1-1 of the sem package, for structural equation modeling, is now on CRAN. Unlike version 2.0-0, which was a major overhaul of the package, version 2.1-1 just sprinkles some syntactic sugar on it, introducing the specifyEquations() and cfa() functions; specifyEquations() supports model specification in equation (rather than path) format, and cfa() facilitates compact

Dear R users, Version 2.1-1 of the sem package, for structural equation modeling, is now on CRAN. Unlike version 2.0-0, which was a major overhaul of the package, version 2.1-1 just sprinkles some syntactic sugar on it, introducing the specifyEquations() and cfa() functions; specifyEquations() supports model specification in equation (rather than path) format, and cfa() facilitates compact

Ron Crump wrote: > 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

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

Hi, You should look at Pinheiro and Bates (2000) Mixed-effects models in S and S-Plus. It describes how to format the correlation matrix to pass to functions lme and gls. Basically, the correlation matrix has to be one of the corStruct classes, probably corSymm for your example. So in the call to lme (or gls if you really have no random effects), use something like:

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

Hola a todos, A partir de los siguientes datos: d <- list(`1` = structure(list(ped = c(1L, 1L, 1L, 1L, 1L, 1L, 1L), id = 1:7, father = c(2L, 0L, 0L, 2L, 2L, 2L, 2L), mother = c(3L, 0L, 0L, 3L, 3L, 3L, 3L), sex = c(2L, 1L, 2L, 2L, 2L, 1L, 2L), affected = c(1L, 2L, 1L, 1L, 2L, 2L, 2L)), row.names = c("1", "2", "3", "4", "5",

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