kinship2: Pedigree Functions
Version 1.6.4

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.

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
URL http://r-forge.r-project.org
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("kinship2")

Popular man pages

align.pedigree: Generate plotting information for a pedigree
findAvailAffected: Find a single person to trim from a pedigree whose is...
kinship: Compute a kinship matrix
pedigree: Create pedigree structure
pedigree.legend: Plot a pedigree legend
plot.pedigree: plot pedigrees
sample.ped: Two example pedigrees
See all...

All man pages Function index File listing

Man pages

align.pedigree: Generate plotting information for a pedigree
autohint: Align a pedigree to print well
bitSize: Calculate pedigree bitsize, defined as 2 * # NonFounders - #...
familycheck: Error check for a family classification
findAvailAffected: Find a single person to trim from a pedigree whose is...
findAvailNonInform: Find subjects from a pedigree who are available and...
findUnavailable: Find unavailable subjects in a pedigree
ibdMatrix: Create an IBD matrix
kindepth: Compute the depth of each subject in a pedigree
kinship: Compute a kinship matrix
makefamid: Construct a family id from pedigree information
makekinship: Create a sparse kinship matrix
minnbreast: Minnesota Breast Cancer Study
pedigree: Create pedigree structure
pedigree.legend: Plot a pedigree legend
pedigree.shrink: Trim a pedigree to specified bit size with priority placed on...
pedigree.unrelated: Determine set of maximum number of unrelated available...
plot.pedigree: plot pedigrees
plot.pedigree.shrink: plot pedigree.shrink object that is a shrunk pedigree object
printBanner: Print a nice banner
sample.ped: Two example pedigrees
testped1: testped1

Functions

align.pedigree Man page Source code
alignped1 Source code
alignped2 Source code
alignped3 Source code
alignped4 Source code
as.data.frame.pedigree Man page Source code
autohint Man page Source code
besthint Source code
bitSize Man page Source code
check.hint Source code
descendant.pedigree Source code
dim.pedigree Source code
excludeStrayMarryin Man page Source code
excludeUnavailFounders Man page Source code
familycheck Man page Source code
findAvailAffected Man page Source code
findAvailNonInform Man page Source code
findUnavailable Man page Source code
fscore.pedigree Source code
ibdMatrix Man page Source code
is.disconnected Source code
is.founder Source code
is.parent Source code
kindepth Man page Source code
kinship Man page Source code
kinship.default Man page Source code
kinship.pedigree Man page Source code
kinship.pedigreeList Man page Source code
makefamid Man page Source code
makekinship Man page Source code
minnbreast Man page
minnbreast2 Man page
oldkinship Source code
oldkinship.default Source code
oldkinship.pedigree Source code
oldkinship.pedigreeList Source code
ped2df Source code
pedigree Man page Source code
pedigree.legend Man page Source code
pedigree.shrink Man page Source code
pedigree.trim Man page Source code
pedigree.unrelated Man page Source code
plot.pedigree Man page Source code
plot.pedigree.shrink Man page Source code
print.pedigree Man page Source code
print.pedigree.shrink Man page Source code
print.pedigreeList Source code
printBanner Man page Source code
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
kinship2 documentation built on May 19, 2017, 1:37 p.m.