A Simple Framework to Analyse Population Genetic Data


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Documentation for package ‘PopGenReport’ version 2.2.2

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PopGen-package Analysing population genetic data within a simple framework
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
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
init.popgensim Initialise a pops object fo a 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)
PopGen Analysing population genetic data within a simple 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.
pops2genind Function converts pops to a genind object
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 forward step generations a popgen simulation
spautocor Spatial autocorrelation following Smouse and Pekall 1999
wassermann Partial Mantel tests on costdistance matrices