PopGenReport: A Simple Framework to Analyse Population and Landscape Genetic Data
Version 3.0.0

Provides beginner friendly framework to analyse population genetic data. Based on 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit .

Browse man pages Browse package API and functions Browse package files

AuthorBernd Gruber [aut, cre], Aaron Adamack [aut]
Date of publication2017-02-01 08:34:41
MaintainerBernd Gruber <bernd.gruber@canberra.edu.au>
LicenseGPL
Version3.0.0
URL https://github.com/green-striped-gecko/PopGenReport
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PopGenReport")

Man pages

addline: Function to add lines to landscape
addpoly: Function to add a polygon to a landscape
allele.dist: Counts and visualises allele frequencies across loci and...
allel.rich: Calculates the allelic richness for a genind object
bilby: Bilby data set
costdistances: Calculates cost distances for a given landscape (resistance...
emigration: Function to execute emigration on a pops object
gd.kosman: Individual genetic distance calculation based on Kosman &...
gd.smouse: Individual genetic distance calculation based on Smouse and...
genleastcost: Least-cost path analysis based on a friction matrix
init.popgensim: Initialise a spatial meta-population for a popgen simulation
landgen: A simulated genind data set with spatial coordinates
landgenreport: Create a landscape genetic report
lgrMMRR: Multiple Matrix Regression with Randomization analysis
mutation: Function to execute mutation on a pop data.frame
null.all: Checks for the presence of and determine the frequency of...
opt.landgen: Function for optimising a landscape genetic analysis based on...
p2p: Function to calculate dispersal distances based on cost...
pairwise.fstb: Calculates pairwise fsts using a genind object (very fast)
pairwise.propShared: Calculates proportion of shared alleles per pairs of...
popgenreport: This is the main function of the package. It analyses an...
pops2genind: Function converts pops to a genind object
possums: A genlight object created via the read.genetable functions...
read.genetable: Function to convert textfiles into a genind object (the...
reproduction: Function to execute reproduction on a pop data.frame
run.popgensim: Run a time-forward popgen simulation
spautocor: Spatial autocorrelation following Smouse and Pekall 1999
treeScrub: A raster file [proportion of treeScrub per cell in Hawke Bay,...
wassermann: Partial Mantel tests on costdistance matrices

Functions

addline Man page Source code
addpoly Man page Source code
allel.rich Man page Source code
allele.dist Man page Source code
bilby Man page
costdistances Man page Source code
emigration Man page Source code
fric.raster Man page
gd.kosman Man page Source code
gd.smouse Man page Source code
genleastcost Man page Source code
init.popgensim Man page Source code
landgen Man page
landgenreport Man page Source code
lgrMMRR Man page Source code
mutation Man page Source code
null.all Man page Source code
opt.landgen Man page Source code
p2p Man page Source code
pairwise.fstb Man page Source code
pairwise.propShared Man page Source code
popgenreport Man page Source code
pops2genind Man page Source code
possums Man page
read.genetable Man page Source code
reproduction Man page Source code
run.popgensim Man page Source code
spautocor Man page Source code
treeScrub Man page
wassermann Man page Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/platypus1c.csv
inst/extdata/nancycoords.csv
inst/extdata/platypus2c.csv
inst/extdata/tiger.csv
inst/doc
inst/doc/PopGenReportIntroduction.Rnw
inst/doc/Tutorial_optimizer.pdf
inst/doc/Tutorial_landgenreport.pdf
inst/doc/Tutorial_landgenreport.rnw
inst/doc/Tutorial_optimizer.Rnw
inst/doc/PopGenReportIntroduction.pdf
inst/swchunks
inst/swchunks/allele.dist.snw
inst/swchunks/pmantel.snw
inst/swchunks/footer.snw
inst/swchunks/gd.kosman.snw
inst/swchunks/gd.smouse.snw
inst/swchunks/null.all.snw
inst/swchunks/hwe.snw
inst/swchunks/custom.snw
inst/swchunks/header.snw
inst/swchunks/locihz.snw
inst/swchunks/differ.stats.snw
inst/swchunks/counts.snw
inst/swchunks/allel.rich.snw
inst/swchunks/required.snw
inst/swchunks/pcoa.snw
inst/swchunks/spautocor.snw
inst/swchunks/map.snw
inst/swchunks/fst.snw
NAMESPACE
data
data/treeScrub.rda
data/landgen.rda
data/fric.raster.rda
data/possums.rda
data/bilby.rda
R
R/popdynfun.r
R/opt.landgen.r
R/popgenreport.r
R/wassermann.r
R/gd.smouse.r
R/null.all.r
R/datasets.r
R/spautocor.r
R/pairwise.propShared.r
R/lgrMMRR.r
R/gd.kosman.r
R/allel.rich.r
R/landgenreport.r
R/allele.dist.r
R/genleastcost.r
R/read.genetable.r
R/costdistances.r
vignettes
vignettes/PopGenReportIntroduction.Rnw
vignettes/figures
vignettes/figures/Tutorial_optimizer.pdf
vignettes/figures/Tutorial_landgenreport_create.Rnw
vignettes/figures/Tutorial_landgenreport.pdf
vignettes/figures/createpdfs.R
vignettes/figures/PopGenReportIntroduction.pdf
vignettes/Tutorial_landgenreport.rnw
vignettes/Tutorial_optimizer.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/addpoly.Rd
man/pops2genind.Rd
man/addline.Rd
man/reproduction.Rd
man/spautocor.Rd
man/landgen.Rd
man/gd.kosman.Rd
man/pairwise.propShared.Rd
man/mutation.Rd
man/possums.Rd
man/costdistances.Rd
man/lgrMMRR.Rd
man/init.popgensim.Rd
man/landgenreport.Rd
man/read.genetable.Rd
man/wassermann.Rd
man/treeScrub.Rd
man/emigration.Rd
man/p2p.Rd
man/run.popgensim.Rd
man/allele.dist.Rd
man/gd.smouse.Rd
man/null.all.Rd
man/bilby.Rd
man/pairwise.fstb.Rd
man/opt.landgen.Rd
man/allel.rich.Rd
man/popgenreport.Rd
man/genleastcost.Rd
PopGenReport documentation built on May 19, 2017, 7:30 p.m.