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.

AuthorKevin Keenan <kkeenan02@qub.ac.uk>
Date of publication2016-12-09 08:03:21
MaintainerKevin Keenan <kkeenan02@qub.ac.uk>
LicenseGPL (>= 2)
Version1.9.89
http://diversityinlife.weebly.com/

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

Functions

allCount Man page
AR Man page
arHex Man page
arp2gen Man page
arSample Man page
basicStats Man page
bigDivPart Man page
bigPreDiv Man page
bsFun Man page
bsHetCalc Man page
chiCalc Man page
corPlotter Man page
diffCalc Man page
diffCalcHarm Man page
divBasic Man page
divMigrate Man page
divMigrateOnline Man page
divMigrateOnline_test Man page
divPart Man page
divRatio Man page
divSimCo Man page
expHet Man page
fastDivPart Man page
fileReader Man page
fstWC Man page
genos2mat Man page
glbWCcpp Man page
gpSampler Man page
haploDiv Man page
Hex Man page
hweFun Man page
hweTab Man page
inCalc Man page
inFunc Man page
multiplot Man page
myTab Man page
obsHet Man page
plotter Man page
polyIn Man page
pre.divLowMemory Man page
pwDivCalc Man page
pwHCalc Man page
pwHt Man page
pwTabMerge Man page
pwWCcpp Man page
rarefactor Man page
readGenepop Man page
readGenepopX Man page
regroup Man page
rgp Man page
snp2gen Man page
SNPs Man page
statCalc Man page
Tab Man page
tabMerge Man page
varFunc Man page
writeBoot Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.