A Simple Framework to Analyse Population and Landscape Genetic Data

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Documentation for package ‘PopGenReport’ version 3.1

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addline Function to add lines to landscape
addpoly Function to add a polygon to a landscape
allel.rich Calculates the allelic richness for a genind object
allele.dist Counts and visualises allele frequencies across loci and subpopulations
bilby Bilby data set
costdistances Calculates cost distances for a given landscape (resistance matrix)
emigration Function to execute emigration on a pops object
gd.kosman Individual genetic distance calculation based on Kosman & Leonhard 2005
gd.smouse Individual genetic distance calculation based on Smouse and Peakall 1999
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 null alleles
opt.landgen Function for optimising a landscape genetic analysis based on resistance layers
p2p Function to calculate dispersal distances based on cost distances
pairwise.fstb Calculates pairwise fsts using a genind object (very fast)
pairwise.propShared Calculates proportion of shared alleles per pairs of populations
popgenreport This is the main function of the package. It analyses an object of class 'genind' and then creates a report containing the results of the analysis. There are several routines that can be optionally included in the analysis and there are multiple output options including a PDF with the report, R-code and an object ('fname.results') containing all of the results, which can be used for further analyses.
pops2genind Function converts pops to a genind object
possums A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]
read.genetable Function to convert textfiles into a genind object (the format required for popgenreport)
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
wassermann Partial Mantel tests on costdistance matrices