diveRsity: A Comprehensive, General Purpose Population Genetics Analysis Package

Allows the calculation of both genetic diversity partition statistics, genetic differentiation statistics, and locus informativeness for ancestry assignment. It also provides users with various option to calculate bootstrapped 95\% confidence intervals both across loci, for pairwise population comparisons, and to plot these results interactively. Parallel computing capabilities and pairwise results without bootstrapping are provided. Weir and Cockerham's 1984 F-statistics are also calculated. Various plotting features are also provided, as well as Chi-square tests of genetic heterogeneity are also provided. Functionality for the calculation of various diversity parameters is possible for RAD-seq derived SNP data sets containing thousands of marker loci. A shiny application for the development of microsatellite multiplexes is also available.

Author
Kevin Keenan <kkeenan02@qub.ac.uk>
Date of publication
2015-11-22 15:50:56
Maintainer
Kevin Keenan <kkeenan02@qub.ac.uk>
License
GPL (>= 2)
Version
1.9.89
URLs

View on CRAN

Man pages

allCount
C++ level observed heterozyosity calculation
AR
Count alleles per locus
arHex
Bootstrapped allelic richness and heterozygosity
arp2gen
Fast and simple conversion of arlequin (.arp) genotype files...
arSample
Resample based calculation of allelic richness
basicStats
Claculate basic descriptive population parameters from a...
bigDivPart
Genetic differentiation statistics and their estimators for...
bigPreDiv
Memory efficient diversity statistic calculations
bsFun
divMigrate bootstrap routine
bsHetCalc
C++ level observed heterozyosity calculation
chiCalc
Testing sample independence from genotype counts
corPlotter
An internal function for plotting the relationship between...
diffCalc
A faster function for calculating genetic differentiation...
diffCalcHarm
C++ level function for global total and sub-population...
divBasic
A function to calculate basic population parameters such as...
divMigrate
An experimental function for the detection of directional...
divMigrateOnline
An experimental function for the detection of directional...
divMigrateOnline_test
An experimental function for the detection of directional...
divPart
Genetic differentiation statistics and their estimators
divRatio
Calculates the standardised diversity ratios relative to a...
divSimCo
Similarity coefficients for co-dominant diploid genenotype...
expHet
C++ level observed heterozyosity calculation
fastDivPart
Genetic differentiation statistics and their estimators
fileReader
Genepop and arlequin file conversion to data.frame
fstWC
Calculation of Weir and Cockerham's F-stats
genos2mat
Convert genos loci into presance absence matrices
glbWCcpp
C++ level function for Weir & Cockerham F-stats
gpSampler
Randomly sample a genepop file
haploDiv
A function, allowing the calculation of Weir & Cockerham's...
Hex
Calculates expected heterozygosity for 'divRatio'
hweFun
C++ level function for global total and sub-population...
hweTab
C++ level observed heterozyosity calculation
inCalc
A function to calculate locus informative for the inference...
inFunc
Internal calculation of Rosenberg et al's In
multiplot
Winston Chang's multiplot function for arranging ggplots into...
myTab
C++ level allele frequency calculation
obsHet
C++ level observed heterozyosity calculation
plotter
Internal interactive plot generation
polyIn
A function for calculating informativeness for the inference...
pre.divLowMemory
Internal differentiation calculations
pwDivCalc
Pairwise diversity calculations for directional migration
pwHCalc
C++ level calculation of total and sub-population...
pwHt
Pairwise directional differentiation heterozygosity...
pwTabMerge
C++ level function for generating pairwise hsums for fst...
pwWCcpp
C++ level function for pairwise Weir & Cockerham F-stats
rarefactor
Rarefaction method for allelic richness
readGenepop
A function to calculate allele frequencies from genepop...
readGenepopX
Internal genepop file reader
regroup
regroup individuals in a genepop file according to an index
rgp
Efficient genepop reader
snp2gen
Conversion function for SNP nucleotide genotype matrix to a...
SNPs
Example input format for 'snp2gp' function
statCalc
Internal differentiation calculator
Tab
C++ level allele frequency calculation
tabMerge
C++ level function for combining pw hsums
varFunc
C++ level function for global total and sub-population...
writeBoot
Generate bootstrap pairwise matrices per locus

Files in this package

diveRsity
diveRsity/inst
diveRsity/inst/CITATION
diveRsity/inst/microPlexer
diveRsity/inst/microPlexer/ui.R
diveRsity/inst/microPlexer/server.R
diveRsity/inst/diveRsity-online
diveRsity/inst/diveRsity-online/ui.R
diveRsity/inst/diveRsity-online/server.R
diveRsity/inst/doc
diveRsity/inst/doc/diveRsity.pdf
diveRsity/inst/doc/diveRsity.Rnw
diveRsity/inst/doc/diveRsity.R
diveRsity/src
diveRsity/src/diffCalcHarm.cpp
diveRsity/src/pwHt.cpp
diveRsity/src/expHet.cpp
diveRsity/src/pwHetCalcCpp.cpp
diveRsity/src/pwWC.cpp
diveRsity/src/hweTab.cpp
diveRsity/src/tabMerge.cpp
diveRsity/src/genos2mat.cpp
diveRsity/src/glbWC.cpp
diveRsity/src/varFunc.cpp
diveRsity/src/pwTabMerge.cpp
diveRsity/src/Tab.cpp
diveRsity/src/myTab.cpp
diveRsity/src/bsHetCalc.cpp
diveRsity/src/obsHet.cpp
diveRsity/src/allCount.cpp
diveRsity/src/RcppExports.cpp
diveRsity/NAMESPACE
diveRsity/data
diveRsity/data/SNPs.rda
diveRsity/data/pop_stats.rda
diveRsity/data/Test_data.rda
diveRsity/data/Big_data.rda
diveRsity/R
diveRsity/R/diffCalc.R
diveRsity/R/hweFun.R
diveRsity/R/divMigrateOnline_test.R
diveRsity/R/gpSampler.R
diveRsity/R/divOnline.R
diveRsity/R/writeBoot.R
diveRsity/R/polyIn.R
diveRsity/R/rarefactor.R
diveRsity/R/corPlot.R
diveRsity/R/haploDiv.R
diveRsity/R/divRatio.R
diveRsity/R/divSimCo.R
diveRsity/R/statCalc.R
diveRsity/R/fstWC.R
diveRsity/R/divPart.R
diveRsity/R/fastDivPart.R
diveRsity/R/fileReader.R
diveRsity/R/chiCalc.R
diveRsity/R/snp2gen.R
diveRsity/R/preBigDiv.R
diveRsity/R/corPlotter.R
diveRsity/R/fstOnly.R
diveRsity/R/multiplot.R
diveRsity/R/arp2gen.R
diveRsity/R/plotter.R
diveRsity/R/microPlexer.R
diveRsity/R/RcppExports.R
diveRsity/R/divBasic.R
diveRsity/R/pre.divLowMemory.R
diveRsity/R/diffPlot.R
diveRsity/R/readGenepop.R
diveRsity/R/arSample.R
diveRsity/R/basicStats.R
diveRsity/R/pwDivCalc.R
diveRsity/R/divMigrateOnline.R
diveRsity/R/inCalc.R
diveRsity/R/rgp.R
diveRsity/R/bigDivPart.R
diveRsity/R/readGenepopX.R
diveRsity/R/regroup.R
diveRsity/R/divMigrate.R
diveRsity/vignettes
diveRsity/vignettes/dirTree.png
diveRsity/vignettes/in_res.RData
diveRsity/vignettes/Rlogo_3.png
diveRsity/vignettes/IN_plot.png
diveRsity/vignettes/microplexer.png
diveRsity/vignettes/diveRsity.Rnw
diveRsity/vignettes/divMS.bib
diveRsity/vignettes/diversity_partition_out.png
diveRsity/vignettes/pw_plot.png
diveRsity/vignettes/pairwise_plots.png
diveRsity/vignettes/microPlexer-1.png
diveRsity/vignettes/pairwise_comp.png
diveRsity/vignettes/IN_res.png
diveRsity/vignettes/MEE.bst
diveRsity/vignettes/gst_vs_nalleles.png
diveRsity/vignettes/titlepage.tex
diveRsity/vignettes/locus_plots.png
diveRsity/vignettes/corPlot.png
diveRsity/vignettes/div_res.RData
diveRsity/vignettes/pw_interplot.png
diveRsity/MD5
diveRsity/build
diveRsity/build/vignette.rds
diveRsity/DESCRIPTION
diveRsity/man
diveRsity/man/microPlexer.rd
diveRsity/man/fstOnly.rd
diveRsity/man/divMigrateOnline_test.Rd
diveRsity/man/obsHet.Rd
diveRsity/man/myTab.Rd
diveRsity/man/chiCalc.Rd
diveRsity/man/Hex.Rd
diveRsity/man/Test_data.rd
diveRsity/man/statCalc.Rd
diveRsity/man/readGenepop.Rd
diveRsity/man/pwDivCalc.Rd
diveRsity/man/basicStats.Rd
diveRsity/man/tabMerge.Rd
diveRsity/man/AR.Rd
diveRsity/man/expHet.Rd
diveRsity/man/pre.divLowMemory.Rd
diveRsity/man/divMigrateOnline.Rd
diveRsity/man/arHex.Rd
diveRsity/man/readGenepopX.Rd
diveRsity/man/allCount.Rd
diveRsity/man/glbWCcpp.Rd
diveRsity/man/divMigrate.Rd
diveRsity/man/diffCalcHarm.Rd
diveRsity/man/diffCalc.Rd
diveRsity/man/hweFun.Rd
diveRsity/man/divSimCo.Rd
diveRsity/man/haploDiv.Rd
diveRsity/man/divRatio.Rd
diveRsity/man/inFunc.Rd
diveRsity/man/corPlot.rd
diveRsity/man/SNPs.Rd
diveRsity/man/corPlotter.Rd
diveRsity/man/fstWC.Rd
diveRsity/man/divPart.Rd
diveRsity/man/pwTabMerge.Rd
diveRsity/man/bsFun.Rd
diveRsity/man/arp2gen.Rd
diveRsity/man/diffPlot.rd
diveRsity/man/gpSampler.Rd
diveRsity/man/varFunc.Rd
diveRsity/man/plotter.Rd
diveRsity/man/fastDivPart.Rd
diveRsity/man/snp2gen.Rd
diveRsity/man/rarefactor.Rd
diveRsity/man/pwHCalc.Rd
diveRsity/man/polyIn.Rd
diveRsity/man/fileReader.Rd
diveRsity/man/regroup.Rd
diveRsity/man/arSample.Rd
diveRsity/man/multiplot.Rd
diveRsity/man/genos2mat.Rd
diveRsity/man/divOnline.rd
diveRsity/man/pwWCcpp.Rd
diveRsity/man/Tab.Rd
diveRsity/man/hweTab.Rd
diveRsity/man/rgp.Rd
diveRsity/man/writeBoot.Rd
diveRsity/man/inCalc.Rd
diveRsity/man/pwHt.Rd
diveRsity/man/bigDivPart.Rd
diveRsity/man/pop_stats.rd
diveRsity/man/divBasic.Rd
diveRsity/man/Big_data.rd
diveRsity/man/bigPreDiv.Rd
diveRsity/man/bsHetCalc.Rd