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

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 <http://www.popgenreport.org/>.

Install the latest version of this package by entering the following in R:
install.packages("PopGenReport")
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
https://github.com/green-striped-gecko/PopGenReport

View on CRAN

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

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

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.