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
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 spatial meta-population for 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)
pairwise.propShared     Calculates proportion of shared alleles per
                        pairs of populations
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 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.
pops2genind             Function converts pops to a genind object
possums                 A genlight object created via the
                        read.genetable functions [possum data set from
                        Sarre et al. 2015]
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 a time-forward popgen simulation
spautocor               Spatial autocorrelation following Smouse and
                        Pekall 1999
wassermann              Partial Mantel tests on costdistance matrices
