introgress: methods for analyzing introgression between divergent lineages

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introgress provides functions for analyzing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. Functions are also provided for maximum likelihood estimation of molecular hybrid index and graphical analysis.

Author
Zachariah Gompert, C. Alex Buerkle
Date of publication
2012-10-29 08:59:02
Maintainer
C. Alex Buerkle <buerkle@uwyo.edu>
License
GPL (>= 2)
Version
1.2.3
URLs

View on CRAN

Man pages

AdmixDataSim1
Admixed Population Genotype Data from Simulation 1
AdmixDataSim2
Admixed Population Genotype Data from Simulation 2
AdmixDom
Admixed Population Dominant Genotype Data from Simulation 1
calc.intersp.het
Calculate Interspecific Heterozygosity
clines.plot
Clines Plot
compare.clines
Compare Clines
composite.clines
Composite Clines Plot
delta
Delta
est.h
Estimate Hybrid Index
fit.c.clines
Fit Co-dominant Clines
fit.invariant.clines
Fit Invariant Clines
fixup.combos.touse
Fix Combos To Use
genomic.clines
Genomic Clines
h.func
Hybrid Index Function
introgress-package
introgress
like.h
Likelihood Hybrid Index
LociD
Dominant Marker Information for Simulation 1
LociDataSim1
Marker Information for Simulation 1
LociDataSim2
Marker Information for Simulation 2
mk.image
Make Image
p1D
Parental Population 1 Dominant Genotype Data from Simulation...
p1DataSim2
Parental Population 1 Dominant Genotype Data from Simulation...
p2D
Parental Population 2 Dominant Genotype Data from Simulation...
p2DataSim2
Parental Population 2 Genotype Data from Simulation 2
per.locus.like
Per Locus Likelihood
prepare.data
Prepare Data
support.limit
Support Limit
s.wrapper
Sign Wrapper
test.combinations
Test Combinations
test.data.objects
Test Data Objects
test.genotypes
Test Genotypes
triangle.plot
Triangle Plot

Files in this package

introgress
introgress/data
introgress/data/p1DataSim2.rda
introgress/data/LociDataSim2.rda
introgress/data/p1D.rda
introgress/data/AdmixDataSim1.rda
introgress/data/p2DataSim2.rda
introgress/data/LociDataSim1.rda
introgress/data/AdmixDataSim2.rda
introgress/data/LociD.rda
introgress/data/AdmixDom.rda
introgress/data/p2D.rda
introgress/NAMESPACE
introgress/man
introgress/man/delta.Rd
introgress/man/AdmixDom.Rd
introgress/man/LociD.Rd
introgress/man/prepare.data.Rd
introgress/man/fit.c.clines.Rd
introgress/man/p2D.Rd
introgress/man/p1D.Rd
introgress/man/fit.invariant.clines.Rd
introgress/man/fixup.combos.touse.Rd
introgress/man/calc.intersp.het.Rd
introgress/man/support.limit.Rd
introgress/man/s.wrapper.Rd
introgress/man/AdmixDataSim2.Rd
introgress/man/LociDataSim1.Rd
introgress/man/like.h.Rd
introgress/man/p1DataSim2.Rd
introgress/man/h.func.Rd
introgress/man/test.data.objects.Rd
introgress/man/genomic.clines.Rd
introgress/man/introgress-package.Rd
introgress/man/p2DataSim2.Rd
introgress/man/est.h.Rd
introgress/man/composite.clines.Rd
introgress/man/LociDataSim2.Rd
introgress/man/per.locus.like.Rd
introgress/man/test.genotypes.Rd
introgress/man/mk.image.Rd
introgress/man/AdmixDataSim1.Rd
introgress/man/compare.clines.Rd
introgress/man/test.combinations.Rd
introgress/man/clines.plot.Rd
introgress/man/triangle.plot.Rd
introgress/DESCRIPTION
introgress/MD5
introgress/R
introgress/R/compare.clines.R
introgress/R/composite.clines.R
introgress/R/triangle.plot.R
introgress/R/per.locus.like.R
introgress/R/calc.intersp.het.R
introgress/R/s.wrapper.R
introgress/R/fixup.combos.touse.R
introgress/R/fit.c.clines.R
introgress/R/test.combinations.R
introgress/R/test.data.objects.R
introgress/R/genomic.clines.R
introgress/R/fit.invariant.clines.R
introgress/R/h.func.R
introgress/R/like.h.R
introgress/R/test.genotypes.R
introgress/R/clines.plot.R
introgress/R/support.limit.R
introgress/R/est.h.R
introgress/R/mk.image.R
introgress/R/prepare.data.R
introgress/R/delta.R