All functions |
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Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data |
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Phytophthora infestans data from Mexico and South America. |
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Phytophthora ramorum data from OR Forests and Nurseries (OR and CA) |
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Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects. |
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Calculate dissimilarity or Euclidean distance for genlight objects |
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Bootstrap the index of association |
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Create a tree using Bruvo's Distance with non-parametric bootstrapping. |
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Bruvo's distance for microsatellites |
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Create minimum spanning network of selected populations using Bruvo's distance. |
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Remove potential bias caused by cloned genotypes in genind or genclone object. |
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Switch between genind and genclone objects. |
Predict cutoff thresholds for use with mlg.filter |
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Calculate a distance matrix based on relative dissimilarity |
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Perform a bootstrap analysis on diversity statistics |
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Perform bootstrap statistics, calculate, and plot confidence intervals. |
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Produce a table of diversity statistics |
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Utilize all algorithms of mlg.filter |
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Find and fix inconsistent repeat lengths |
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GENclone and SNPclone classes |
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Calculate Genetic Distance for a genind or genclone object. |
Export data from genind objects to genalex formatted \*.csv files. |
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Produce a genotype accumulation curve |
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Get a file name and path and store them in a list. |
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Display a greyscale gradient adjusted to specific parameters |
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Index of Association |
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Create minimum spanning networks interactively |
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Check for samples that are incomparable due to missing data |
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Create a table summarizing missing data or ploidy information of a genind or genclone object |
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Remove all non-phylogentically informative loci |
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Check for validity of a genclone or snpclone object |
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Create a table of summary statistics per locus. |
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Split samples from a genind object into pseudo-haplotypes |
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Treat missing data |
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Create counts, vectors, and matrices of multilocus genotypes. |
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MLG definitions based on genetic distance |
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Access and manipulate multilocus lineages. |
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Define custom multilocus lineages |
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Reset multilocus lineages |
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Peach brown rot pathogen *Monilinia fructicola* |
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Convert an old genclone object to a new genclone object |
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Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance |
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Genotype Probability |
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Plot minimum spanning networks produced in poppr. |
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The poppr R package |
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Produce a basic summary table for population genetic analyses. |
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Process a list of files with poppr |
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Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects. |
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Create a minimum spanning network of selected populations using a distance matrix. |
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Determines whether openMP is support on this system. |
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Subset data by population |
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Tabulate alleles the occur in only one population. |
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Probability of encountering a genotype more than once by chance |
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Correcting rare allele frequencies |
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Importing data from genalex formatted \*.csv files. |
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Recode polyploid microsatellite data for use in frequency based statistics. |
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Round Robin Allele Frequencies |
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Round Robin Multilocus Genotypes |
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Calculate random samples of the index of association for genlight objects. |
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Shuffle individuals in a |
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Create a snpclone object from a genlight object. |
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Test repeat length consistency. |
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Calculate windows of the index of association for genlight objects. |