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Import/Export
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getfile
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Provides a quick GUI to grab files for import |
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read.genalex
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Read GenAlEx formatted csv files to a genind object |
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genind2genalex
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Converts genind objects to GenAlEx formatted csv files |
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Manipulation
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missingno
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Handles missing data |
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clonecorrect
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Clone censors at a specified population hierarchy |
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informloci
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Detects and removes phylogenetically uninformative loci |
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popsub
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Subsets genind objects by population |
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shufflepop
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Shuffles genotypes at each locus using four different shuffling algorithms (details in Table 3) |
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splitcombine
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Manipulates population hierarchy |
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Analysis
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bruvo.boot
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Produces dendrograms with bootstrap support based on Bruvo’s distance |
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bruvo.dist
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Calculates Bruvo’s distance |
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diss.dist
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Calculates the percent allelic dissimilarity |
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ia
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Calculates the index of association |
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mlg
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Calculates the number of multilocus genotypes |
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mlg.crosspop
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Finds all multilocus genotypes that cross populations |
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mlg.table
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Returns a table of populations by multilocus genotypes |
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mlg.vector
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Returns a vector of a numeric multilocus genotype assignment for each individual |
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poppr
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Returns a diversity table by population |
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poppr.all
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Returns a diversity table by population for all compatible files specified |
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Visualization
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greycurve
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Helper to determine the appropriate parameters for adjusting the grey level for msn functions |
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bruvo.msn
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Produces minimum spanning networks based off Bruvo’s distance colored by population |
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poppr.msn
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Produces a minimum spanning network for any pairwise distance matrix related to the data |
