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)
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
