diveRsity: A Comprehensive, General Purpose Population Genetics Analysis Package
Version 1.9.90

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. Also calculates F-statistics from Weir and Cockerham (1984). Various plotting features are provided, as well as Chi-square tests of genetic heterogeneity. 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.

Browse man pages Browse package API and functions Browse package files

AuthorKevin Keenan <kkeenan02@qub.ac.uk>
Date of publication2017-04-04 10:59:38 UTC
MaintainerKevin Keenan <kkeenan02@qub.ac.uk>
LicenseGPL (>= 2)
Version1.9.90
URL http://diversityinlife.weebly.com/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("diveRsity")

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...
Big_data: Example infile for diveRsity package
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
corPlot: A function to plot the relationship between Gst, G'st, Theta,...
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...
diffPlot: A function to plot pairwise statistics calculated by divPart.
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...
divOnline: A function to launch a web app version of 'diveRsity' from...
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
fstOnly: A minimal function for the calculate of Weir & Cockerham's...
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
microPlexer: Launches a 'shiny' app for the arrangement of microsatellite...
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...
pop_stats: Example pop_stats data frame for use in the function...
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
Test_data: Example infile for diveRsity package
varFunc: C++ level function for global total and sub-population...
writeBoot: Generate bootstrap pairwise matrices per locus

Functions

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

Files

inst
inst/CITATION
inst/microPlexer
inst/microPlexer/ui.R
inst/microPlexer/server.R
inst/diveRsity-online
inst/diveRsity-online/ui.R
inst/diveRsity-online/server.R
inst/doc
inst/doc/diveRsity.pdf
inst/doc/diveRsity.Rnw
inst/doc/diveRsity.R
src
src/diffCalcHarm.cpp
src/pwHt.cpp
src/expHet.cpp
src/pwHetCalcCpp.cpp
src/pwWC.cpp
src/registerDynamicSymbol.c
src/hweTab.cpp
src/tabMerge.cpp
src/genos2mat.cpp
src/glbWC.cpp
src/varFunc.cpp
src/pwTabMerge.cpp
src/Tab.cpp
src/myTab.cpp
src/bsHetCalc.cpp
src/obsHet.cpp
src/allCount.cpp
src/RcppExports.cpp
NAMESPACE
data
data/SNPs.rda
data/pop_stats.rda
data/Test_data.rda
data/Big_data.rda
R
R/diffCalc.R
R/hweFun.R
R/divMigrateOnline_test.R
R/gpSampler.R
R/divOnline.R
R/writeBoot.R
R/polyIn.R
R/rarefactor.R
R/corPlot.R
R/haploDiv.R
R/divRatio.R
R/divSimCo.R
R/statCalc.R
R/fstWC.R
R/divPart.R
R/fastDivPart.R
R/fileReader.R
R/chiCalc.R
R/snp2gen.R
R/preBigDiv.R
R/corPlotter.R
R/fstOnly.R
R/multiplot.R
R/arp2gen.R
R/plotter.R
R/microPlexer.R
R/RcppExports.R
R/divBasic.R
R/pre.divLowMemory.R
R/diffPlot.R
R/readGenepop.R
R/arSample.R
R/basicStats.R
R/pwDivCalc.R
R/divMigrateOnline.R
R/inCalc.R
R/rgp.R
R/bigDivPart.R
R/readGenepopX.R
R/regroup.R
R/divMigrate.R
vignettes
vignettes/dirTree.png
vignettes/in_res.RData
vignettes/Rlogo_3.png
vignettes/IN_plot.png
vignettes/microplexer.png
vignettes/diveRsity.Rnw
vignettes/divMS.bib
vignettes/diversity_partition_out.png
vignettes/pw_plot.png
vignettes/pairwise_plots.png
vignettes/microPlexer-1.png
vignettes/pairwise_comp.png
vignettes/IN_res.png
vignettes/MEE.bst
vignettes/gst_vs_nalleles.png
vignettes/titlepage.tex
vignettes/locus_plots.png
vignettes/corPlot.png
vignettes/div_res.RData
vignettes/pw_interplot.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/microPlexer.rd
man/fstOnly.rd
man/divMigrateOnline_test.Rd
man/obsHet.Rd
man/myTab.Rd
man/chiCalc.Rd
man/Hex.Rd
man/Test_data.rd
man/statCalc.Rd
man/readGenepop.Rd
man/pwDivCalc.Rd
man/basicStats.Rd
man/tabMerge.Rd
man/AR.Rd
man/expHet.Rd
man/pre.divLowMemory.Rd
man/divMigrateOnline.Rd
man/arHex.Rd
man/readGenepopX.Rd
man/allCount.Rd
man/glbWCcpp.Rd
man/divMigrate.Rd
man/diffCalcHarm.Rd
man/diffCalc.Rd
man/hweFun.Rd
man/divSimCo.Rd
man/haploDiv.Rd
man/divRatio.Rd
man/inFunc.Rd
man/corPlot.rd
man/SNPs.Rd
man/corPlotter.Rd
man/fstWC.Rd
man/divPart.Rd
man/pwTabMerge.Rd
man/bsFun.Rd
man/arp2gen.Rd
man/diffPlot.rd
man/gpSampler.Rd
man/varFunc.Rd
man/plotter.Rd
man/fastDivPart.Rd
man/snp2gen.Rd
man/rarefactor.Rd
man/pwHCalc.Rd
man/polyIn.Rd
man/fileReader.Rd
man/regroup.Rd
man/arSample.Rd
man/multiplot.Rd
man/genos2mat.Rd
man/divOnline.rd
man/pwWCcpp.Rd
man/Tab.Rd
man/hweTab.Rd
man/rgp.Rd
man/writeBoot.Rd
man/inCalc.Rd
man/pwHt.Rd
man/bigDivPart.Rd
man/pop_stats.rd
man/divBasic.Rd
man/Big_data.rd
man/bigPreDiv.Rd
man/bsHetCalc.Rd
diveRsity documentation built on May 19, 2017, 11:19 a.m.