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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 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...

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 = polygen...

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, there is nothing to run.? The latex itself will fail when it can't find the figures? (I float them), and the...

...s()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > install.packages('kinship2') Installing package into ?/home/therneau/Rlib? (as ?lib? is unspecified) --- Please select a CRAN mirror for use in this session --- ================================================================= ==21606==ERROR: AddressSanitizer: heap-use-after-free on address 0x602000042830 at pc 0x7f9f83...

...N. The wrapper creates all necessary files automatically, and makes it easy to re-run analysis under different models or with subsets of pedigree members/markers. * Power analysis for linkage (implementing the simulation algorithm of SLINK). * Nice pedigree plots produced by importing the kinship2 package. Includes flexible plotting of marker genotypes. * LOD score plots. * Reads and writes ped/map/dat/freq/model files in MERLIN format. * Computation of genotype probability distributions, unconditional or conditional on partial marker data: - For a single marker, the joint genotyp...

...N. The wrapper creates all necessary files automatically, and makes it easy to re-run analysis under different models or with subsets of pedigree members/markers. * Power analysis for linkage (implementing the simulation algorithm of SLINK). * Nice pedigree plots produced by importing the kinship2 package. Includes flexible plotting of marker genotypes. * LOD score plots. * Reads and writes ped/map/dat/freq/model files in MERLIN format. * Computation of genotype probability distributions, unconditional or conditional on partial marker data: - For a single marker, the joint genotyp...

...1000 # fixed number of permutations, 1000 is recommended alpha = 0.05 # type-I error Pval = 0.1 # significance level at first step of mbmdr set.seed(1982) # for reproducibility # loading libraries and code library(kinship2) library(GenABEL) source("mbmdr_gaussian.r") # removing all possible existing files first as a safety measure file.remove("permoutput.txt") file.remove("simulation.raw") file.remove("permuted.txt") file.remove("permchisq.txt") file.remove("raw...