PopGenReport

Function to add lines to landscape

Function to add a polygon to a landscape

Calculates the allelic richness for a genind object

Counts and visualises allele frequencies across loci and subpopulations

Bilby data set

Calculates cost distances for a given landscape (resistance matrix)

Function to execute emigration on a pops object

Individual genetic distance calculation based on Kosman & Leonhard 2005

Individual genetic distance calculation based on Smouse and Peakall 1999

Least-cost path analysis based on a friction matrix

Initialise a spatial meta-population for a popgen simulation

A simulated genind data set with spatial coordinates

Create a landscape genetic report

Multiple Matrix Regression with Randomization analysis

Function to execute mutation on a pop data.frame

Checks for the presence of and determine the frequency of null alleles

Function for optimising a landscape genetic analysis based on resistance layers

Function to calculate dispersal distances based on cost distances

Calculates pairwise fsts using a genind object (very fast)

Calculates proportion of shared alleles per pairs of populations

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.

Function converts pops to a genind object

A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]

Function to convert textfiles into a genind object (the format required for popgenreport)

Function to execute reproduction on a pop data.frame

Run a time-forward popgen simulation

Spatial autocorrelation following Smouse and Pekall 1999

Partial Mantel tests on costdistance matrices