kinship2: Pedigree Functions

Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.

Install the latest version of this package by entering the following in R:
install.packages("kinship2")
AuthorTerry M Therneau [aut], Schaid Daniel [ctb], Jason Sinnwell [aut, cre], Elizabeth Atkinson [ctb]
Date of publication2015-08-03 21:10:46
MaintainerJason Sinnwell <sinnwell.jason@mayo.edu>
LicenseGPL (>= 2)
Version1.6.4
http://r-forge.r-project.org

View on CRAN

Functions

align.pedigree Man page
as.data.frame.pedigree Man page
autohint Man page
bitSize Man page
excludeStrayMarryin Man page
excludeUnavailFounders Man page
familycheck Man page
findAvailAffected Man page
findAvailNonInform Man page
findUnavailable Man page
ibdMatrix Man page
kindepth Man page
kinship Man page
kinship.default Man page
kinship.pedigree Man page
kinship.pedigreeList Man page
makefamid Man page
makekinship Man page
minnbreast Man page
minnbreast2 Man page
pedigree Man page
pedigree.legend Man page
pedigree.shrink Man page
pedigree.trim Man page
pedigree.unrelated Man page
plot.pedigree Man page
plot.pedigree.shrink Man page
printBanner Man page
print.pedigree Man page
print.pedigree.shrink Man page
sample.ped Man page
testped1 Man page

Files

inst
inst/COPYRIGHT
inst/NEWS.Rd
inst/doc
inst/doc/pedigree.snw
inst/doc/pedigree.pdf
inst/doc/pedigree.R
inst/GPL2.txt
tests
tests/test.pedigree.trim.R
tests/kin1.Rout.save
tests/test.pedigree.legend.R
tests/ped3.txt
tests/subscript.Rout.save
tests/makefam.Rout.save
tests/test.kinX.Rout.save
tests/sampleped1.pdf
tests/ped2.pdf
tests/ped1.pdf
tests/kin1.R tests/monozygote.R tests/failure.R
tests/twin.Rout.save
tests/ped27_71.txt
tests/failure.Rout.save
tests/makefam.R tests/test.kinX.R
tests/test.pedigree.legend.Rout.save
tests/test.pedigree.trim.Rout.save
tests/subscript.R tests/test.pedigree.shrink.R
tests/monozygote.Rout.save
tests/test.pedigree.shrink.Rout.save
tests/test.pedigree.unrelated.R tests/twin.R
tests/test.pedigree.unrelated.Rout.save
NAMESPACE
noweb
noweb/Makefile
noweb/all.toc
noweb/all.log
noweb/plot.Rnw
noweb/noweb.sty
noweb/pedigree.R
noweb/pedigree.shrink.Rnw
noweb/kinship.Rnw
noweb/all.tex
noweb/MAINTAIN.steps
noweb/figure
noweb/figure/pdraw3.s
noweb/figure/pdraw1.s
noweb/figure/pdraw2.s
noweb/all.aux
noweb/pedigree.Rnw
noweb/checks.Rnw
noweb/align2.Rnw
noweb/kinship.R noweb/noweb.R
noweb/align.Rnw
noweb/all.nw
data
data/sample.ped.tab.gz
data/testped1.tab.gz
data/minnbreast.rda
R
R/findUnavailable.R R/alignped1.R R/print.pedigree.R R/as.data.frame.pedigree.R R/makefamid.R R/alignped2.R R/alignped4.R R/besthint.R R/familycheck.R R/pedigree.R R/pedigree.unrelated.R R/pedigree.trim.R R/findAvailNonInform.R R/check.hint.R R/printBanner.R R/fscore.pedigree.R R/makekinship.R R/descendant.pedigree.R R/pedigree.legend.R R/findAvailAffected.R R/plot.pedigree.R R/alignped3.R R/kindepth.R R/pedigree.shrink.minor.R R/plot.pedigree.shrink.R R/bitSize.R R/align.pedigree.R R/ped2df.R R/kinship.R R/autohint.R R/ibdMatrix.R R/print.pedigree.shrink.R R/pedigree.shrink.R
vignettes
vignettes/pedigree.snw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/ibdMatrix.Rd man/findAvailAffected.Rd man/align.pedigree.Rd man/findUnavailable.Rd man/bitSize.Rd man/kindepth.Rd man/testped1.Rd man/pedigree.legend.Rd man/findAvailNonInform.Rd man/kinship.Rd man/pedigree.Rd man/familycheck.Rd man/pedigree.shrink.Rd man/makefamid.Rd man/plot.pedigree.Rd man/printBanner.Rd man/makekinship.Rd man/minnbreast.Rd man/plot.pedigree.shrink.Rd man/autohint.Rd man/sample.ped.Rd man/pedigree.unrelated.Rd

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