GENLIB: Genealogical Data Analysis
Version 1.0.4

Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.

AuthorLouis Houde [aut], Jean-Francois Lefebvre [aut], Valery Roy-Lagace [aut], Sebastien Lemieux [aut], Michael J. Fromberger [ctb], Marie-Helene Roy-Gagnon [cre]
Date of publication2015-04-21 07:54:37
MaintainerMarie-Helene Roy-Gagnon <mroygagn@uottawa.ca>
LicenseGPL (>= 2)
Version1.0.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("GENLIB")

Popular man pages

gen.climbPAR: Internal function used by gen.findMRCA
gen.findMRCA: Finding most recent common ancestors, MRCAs
gen.gc: Genetic contribution of ancestors
gen.graph: Pedigree graphical tool
gen.max: Maximum number of generations
gen.min: Minimum number of generations
gen.simuProb: Gene dropping simulations - Probabilities
See all...

All man pages Function index File listing

Man pages

gen.branching: Genealogy subset
gen.children: Get id numbers of children
gen.climbPAR: Internal function used by gen.findMRCA
gen.completeness: Completeness
gen.completenessVar: Variance of completeness index
gen.depth: Genealogy depth
genea140: Genealogical information for 140 individuals from the Quebec...
geneaJi: Highly inbred pedigree
gen.f: Inbreeding coefficient
gen.fCI: Average inbreeding coefficient confidence interval
gen.findDistance: Minimum genetic distance between two individuals
gen.findFounders: Find common founder ancestors
gen.find.Min.Distance.MRCA: Finds the minimum distances between pairs of individuals...
gen.findMRCA: Finding most recent common ancestors, MRCAs
gen.founder: Get founder id numbers
gen.gc: Genetic contribution of ancestors
gen.genealogy: Create object of class GLgen
gen.genout: Create pedigree data
gen.getAncestorsPAR: Internal function used by gen.findMRCA
gen.getFoundersPAR: Internal function used by gen.findFounders
gen.graph: Pedigree graphical tool
gen.half.founder: Get half-founder id numbers
gen.implex: Genealogical implex
gen.implexVar: Variance of genealogical implex
GenlibR-package: Genealogical Data Analysis
gen.lineages: Create object of class GLgen for maternal or paternal...
gen.max: Maximum number of generations
gen.mean: Mean number of generations
gen.meangendepth: Expected Genealogical Depth
gen.meangendepthVar: Variance of genealogical depth
gen.min: Minimum number of generations
gen.nochildren: Number of children
gen.noind: Number of individuals
gen.nomen: Number of men
gen.nowomen: Number of women
gen.occ: Ancestor occurences
gen.parent: Get id numbers of parents
gen.phi: Kinship coefficient
gen.phiCI: Average kinship confidence interval
gen.phiMean: Average kinship
gen.phiOver: Kinship above threshold
gen.pro: Get proband id numbers
gen.rec: Ancestors coverage
gen.sibship: Get id numbers of siblings
gen.simuProb: Gene dropping simulations - Probabilities
gen.simuSample: Gene dropping simulations - Sample
gen.simuSampleFreq: Gene dropping simulations - Frequencies
gen.simuSet: Gene dropping simulations with specified transmission...
GLCGMatrixGroupSingle-class: Classes '"GLmultiPhiGroup"' '"GLmultiPhiGroupSingle"'...
GLgen-class: Class '"GLgen"'
GLgroupe-class: Class '"GLgroup"'
GLmultiList-class: Class '"GLmultiList"'
GLmultiVector-class: Classes '"GLmultiVector"' '"GLmultiArray4"' '"GLmultiMatrix"'...
pop140: Population of origin of the 140 Quebec samples

Functions

Dim Source code
Dim,GLmultiArray4-method Man page
Dim,GLmultiFGroup-method Man page
Dim,GLmultiFGroupSingle-method Man page
Dim,GLmultiMatrix-method Man page
Dim,GLmultiNumber-method Man page
Dim,GLmultiPhiGroup-method Man page
Dim,GLmultiPhiGroupSingle-method Man page
Dim,GLmultiVector-method Man page
GLCGGroup Source code
GLCGMatrixGroupSingle-class Man page
GLFGroup Source code
GLOverGroup2 Source code
GLOverGroup3 Source code
GLOverGroup4 Source code
GLOverNumber1 Source code
GLOverVector2 Source code
GLPhiGroup Source code
GLPriv.completeness3V Source code
GLPriv.entropie3V Source code
GLPriv.implex3V Source code
GLPriv.initDemifon3V Source code
GLPriv.initImp3V Source code
GLPriv.initcomp3V Source code
GLPriv.initfon3V Source code
GLPriv.variance3V Source code
GLPrivCG Source code
GLPrivCGPLUS Source code
GLPrivCGcumul Source code
GLPrivCGgroup Source code
GLPrivCGmoyen Source code
GLPrivCGproduit Source code
GLPrivCGtotal Source code
GLPrivExtCG Source code
GLPrivExtF Source code
GLPrivExtFSINGLE Source code
GLPrivExtPHI Source code
GLPrivExtPHISINGLE Source code
GLPrivOcc Source code
GLapplyCG Source code
GLapplyF Source code
GLapplyGroup Source code
GLapplyPhi Source code
GLapplyPhi.mat Source code
GLgen Source code
GLgen-class Man page
GLgroup Source code
GLgroup-class Man page
GLmulti Source code
GLmultiArray4-class Man page
GLmultiFGroup-class Man page
GLmultiFGroupSingle-class Man page
GLmultiList-class Man page
GLmultiMatrix-class Man page
GLmultiNumber-class Man page
GLmultiPhiGroup-class Man page
GLmultiPhiGroupSingle-class Man page
GLmultiVector-class Man page
GenlibR-package Man page
[,GLCGMatrixGroupSingle,ANY,ANY,ANY-method Man page
[,GLgroup,ANY,ANY,ANY-method Man page
[,GLmultiArray4,ANY,ANY,ANY-method Man page
[,GLmultiFGroup,ANY,ANY,ANY-method Man page
[,GLmultiFGroupSingle,ANY,ANY,ANY-method Man page
[,GLmultiMatrix,ANY,ANY,ANY-method Man page
[,GLmultiNumber,ANY,ANY,ANY-method Man page
[,GLmultiPhiGroup,ANY,ANY,ANY-method Man page
[,GLmultiPhiGroupSingle,ANY,ANY,ANY-method Man page
[,GLmultiVector,ANY,ANY,ANY-method Man page
[<-,GLCGMatrixGroupSingle,ANY,ANY,ANY-method Man page
[<-,GLmultiArray4,ANY,ANY,ANY-method Man page
[<-,GLmultiFGroup,ANY,ANY,ANY-method Man page
[<-,GLmultiFGroupSingle,ANY,ANY,ANY-method Man page
[<-,GLmultiMatrix,ANY,ANY,ANY-method Man page
[<-,GLmultiNumber,ANY,ANY,ANY-method Man page
[<-,GLmultiPhiGroup,ANY,ANY,ANY-method Man page
[<-,GLmultiPhiGroupSingle,ANY,ANY,ANY-method Man page
[<-,GLmultiVector,ANY,ANY,ANY-method Man page
data.sum Source code
depth,GLgen-method Man page
depth,GLmultiArray4-method Man page
depth,GLmultiMatrix-method Man page
depth,GLmultiNumber-method Man page
depth,GLmultiVector-method Man page
error.bar Source code
gen.branching Man page Source code
gen.children Man page Source code
gen.climbPAR Man page Source code
gen.completeness Man page Source code
gen.completenessVar Man page Source code
gen.depth Man page Source code
gen.detectionErreur Source code
gen.etiquetteGenMinuscule Source code
gen.f Man page Source code
gen.fCI Man page Source code
gen.find.Min.Distance.MRCA Man page Source code
gen.findDistance Man page Source code
gen.findFounders Man page Source code
gen.findMRCA Man page Source code
gen.formatage... Source code
gen.founder Man page Source code
gen.gc Man page Source code
gen.genealogy Man page Source code
gen.genout Man page Source code
gen.getAncestorsPAR Man page Source code
gen.getFoundersPAR Man page Source code
gen.graph Man page Source code
gen.half.founder Man page Source code
gen.implex Man page Source code
gen.implex3V Source code
gen.implexVar Man page Source code
gen.initImp3V Source code
gen.isGen3V Source code
gen.lineages Man page Source code
gen.max Man page Source code
gen.mean Man page Source code
gen.meangendepth Man page Source code
gen.meangendepthVar Man page Source code
gen.min Man page Source code
gen.nochildren Man page Source code
gen.noind Man page Source code
gen.nomen Man page Source code
gen.nowomen Man page Source code
gen.occ Man page Source code
gen.parent Man page Source code
gen.phi Man page Source code
gen.phiCI Man page Source code
gen.phiMean Man page Source code
gen.phiOver Man page Source code
gen.pro Man page Source code
gen.rec Man page Source code
gen.sibship Man page Source code
gen.simuProb Man page Source code
gen.simuSample Man page Source code
gen.simuSampleFreq Man page Source code
gen.simuSet Man page Source code
gen.validationAsc Source code
gen.validationGLgen Source code
gen.validationGen Source code
genea140 Man page
geneaJi Man page
genlibDLLC Source code
genlibDLLCall Source code
genlibDLLCall2 Source code
genlibDLLTest Source code
initialize,GLgen-method Man page
initialize,GLgroup-method Man page
is.all.white Source code
length,GLgen-method Man page
pop140 Man page

Files

src
src/hashtable.h
src/genlibDLL.h
src/Makevars
src/apparentement.cpp
src/statanal.cpp
src/statanal.h
src/probsimul.h
src/genphi.h
src/genphi.cpp
src/outilsalloc.h
src/fondateur.h
src/base.h
src/apparentement.h
src/mpi.h
src/logtab.h
src/mpajout.c
src/exception.h
src/mpi-types.h
src/mpi-config.h
src/mplogic.h
src/mpi.c
src/consanguinite.h
src/outils.cpp
src/userInterface.h
src/hal.cpp
src/interface.h
src/outilanal.h
src/consanguinite.cpp
src/congen.h
src/mplogic.c
src/md5.cpp
src/congen.cpp
src/hal.h
src/fondateur.cpp
src/cbignum.h
src/outils.h
src/probsimul.cpp
src/Makevars.win
src/interface.cpp
src/userInterface.cpp
src/md5.h
src/outilanal.cpp
src/basemt.h
src/exception.cpp
NAMESPACE
data
data/genea140.rda
data/pop140.rda
data/geneaJi.rda
R
R/classes_methodes.R
R/fonctionsSimul.R
R/genlibDLL.R
R/fonctionsBase.R
R/fonctionsPAR.R
R/fonctionsPriv.R
R/fonctionsGraph.R
R/fonctionsStat.R
MD5
DESCRIPTION
man
man/pop140.Rd
man/gen.branching.Rd
man/gen.getFoundersPAR.Rd
man/gen.fCI.Rd
man/gen.founder.Rd
man/gen.phiOver.Rd
man/gen.find.Min.Distance.MRCA.Rd
man/GLmultiList-class.Rd
man/gen.implexVar.Rd
man/gen.nowomen.Rd
man/gen.meangendepth.Rd
man/gen.simuSampleFreq.Rd
man/gen.mean.Rd
man/GLCGMatrixGroupSingle-class.Rd
man/gen.findDistance.Rd
man/gen.genout.Rd
man/gen.noind.Rd
man/gen.genealogy.Rd
man/gen.meangendepthVar.Rd
man/gen.occ.Rd
man/gen.simuProb.Rd
man/gen.simuSet.Rd
man/GenlibR-package.Rd
man/gen.completenessVar.Rd
man/gen.half.founder.Rd
man/geneaJi.Rd
man/gen.f.Rd
man/gen.climbPAR.Rd
man/GLgen-class.Rd
man/gen.max.Rd
man/genea140.Rd
man/gen.findFounders.Rd
man/gen.rec.Rd
man/gen.parent.Rd
man/gen.implex.Rd
man/gen.completeness.Rd
man/gen.depth.Rd
man/gen.phiCI.Rd
man/gen.graph.Rd
man/gen.phi.Rd
man/gen.sibship.Rd
man/gen.findMRCA.Rd
man/gen.lineages.Rd
man/gen.nomen.Rd
man/gen.getAncestorsPAR.Rd
man/gen.children.Rd
man/gen.nochildren.Rd
man/gen.gc.Rd
man/GLmultiVector-class.Rd
man/gen.min.Rd
man/gen.simuSample.Rd
man/gen.phiMean.Rd
man/GLgroupe-class.Rd
man/gen.pro.Rd
GENLIB documentation built on May 19, 2017, 2:17 p.m.

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