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

Documentation for package ‘PopGenReport’ version 2.1

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