PopGenReport: A simple way to analyse and visualize population genetic data


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Documentation for package ‘PopGenReport’ version 2.1

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PopGen-package Analysing population genetic data within a standardised framework
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
fric.raster a simulated friction map
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
landgen A simulated genind data set with spatial coordinates
landgenreport Create a landscape genetic report
lgrMMRR Multiple Matrix Regression with Randomization analysis
null.all Checks for the presence of and determine the frequency of null alleles
PopGen Analysing population genetic data within a standardised framework
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 multip 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.
read.genetable Function to convert textfiles into a genind object (the format required for popgenreport)
spautocor Spatial autocorrelation following Smouse and Pekall 1999
wassermann Partial Mantel tests on costdistance matrices