| aboot | Calculate a dendrogram with bootstrap support using any... |
| Aeut | Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data |
| bitwise.dist | Calculate dissimilarity or Euclidean distance for genlight... |
| bitwise.ia | Calculate the index of association between samples in a... |
| bootgen-class | Bootgen object |
| bootgen-methods | Methods used for the bootgen object. |
| boot.ia | Bootstrap the index of association |
| bruvo.boot | Create a tree using Bruvo's Distance with non-parametric... |
| bruvo.dist | Bruvo's distance for microsatellites |
| bruvomat-class | bruvomat object |
| bruvomat-methods | Methods used for the bruvomat object. |
| bruvo.msn | Create minimum spanning network of selected populations using... |
| clonecorrect | Remove potential bias caused by cloned genotypes in genind or... |
| coercion-methods | Switch between genind and genclone objects. |
| cutoff_predictor | Predict cutoff thresholds for use with mlg.filter |
| diss.dist | Calculate a distance matrix based on relative dissimilarity |
| diversity_boot | Perform a bootstrap analysis on diversity statistics |
| diversity_ci | Perform bootstrap statistics, calculate, and plot confidence... |
| diversity_stats | Produce a table of diversity statistics |
| filter_stats | Utilize all algorithms of mlg.filter |
| fix_replen | Find and fix inconsistent repeat lengths |
| genclone-class | GENclone and SNPclone classes |
| genclone-method | Methods used for the genclone object |
| genetic_distance | Calculate Genetic Distance for a genind or genclone object. |
| genind2genalex | Export data from genind objects to genalex formatted \*.csv... |
| genotype_curve | Produce a genotype accumulation curve |
| getfile | Get a file name and path and store them in a list. |
| grapes-greater-than-grapes | magrittr forward-pipe operator |
| greycurve | Display a greyscale gradient adjusted to specific parameters |
| ia | Index of Association |
| imsn | Create minimum spanning networks interactively |
| incomp | Check for samples that are incomparable due to missing data |
| informloci | Remove all non-phylogentically informative loci |
| info_table | Create a table summarizing missing data or ploidy information... |
| is.clone | Check for validity of a genclone or snpclone object |
| levels-methods | Unique and Duplicated implementations for MLG objects |
| locus_table | Create a table of summary statistics per locus. |
| make_haplotypes-method | Split samples from a genind object into pseudo-haplotypes |
| missingno | Treat missing data |
| mlg | Create counts, vectors, and matrices of multilocus genotypes. |
| MLG-accessors | Accessors for the MLG object |
| MLG-class | MLG class |
| mlg.filter | MLG definitions based on genetic distance |
| MLG-method | Methods used for MLG objects |
| mll.custom | Define custom multilocus lineages |
| mll-method | Access and manipulate multilocus lineages. |
| mll.reset-method | Reset multilocus lineages |
| monpop | Peach brown rot pathogen *Monilinia fructicola* |
| old2new_genclone | Convert an old genclone object to a new genclone object |
| partial_clone | Simulated data illustrating a Minimum Spanning Network based... |
| pgen | Genotype Probability |
| Pinf | Phytophthora infestans data from Mexico and South America. |
| plot_filter_stats | Plot the results of filter_stats |
| plot_poppr_msn | Plot minimum spanning networks produced in poppr. |
| poppr | Produce a basic summary table for population genetic... |
| poppr.all | Process a list of files with poppr |
| poppr.amova | Perform Analysis of Molecular Variance (AMOVA) on genind or... |
| poppr_has_parallel | Determines whether openMP is support on this system. |
| poppr.msn | Create a minimum spanning network of selected populations... |
| poppr-package | The 'poppr' R package |
| poppr.plot | Internal function to plot the results from ia() and poppr() |
| popsub | Subset data by population |
| Pram | Phytophthora ramorum data from OR Forests and Nurseries (OR... |
| private_alleles | Tabulate alleles the occur in only one population. |
| psex | Probability of encountering a genotype more than once by... |
| rare_allele_correction | Correcting rare allele frequencies |
| read.genalex | Importing data from genalex formatted \*.csv files. |
| recode_polyploids | Recode polyploid microsatellite data for use in frequency... |
| rraf | Round Robin Allele Frequencies |
| rrmlg | Round Robin Multilocus Genotypes |
| samp.ia | Calculate random samples of the index of association for... |
| shufflepop | Shuffle individuals in a 'genclone' or 'genind' object... |
| snpclone-coercion-methods | Create a snpclone object from a genlight object. |
| snpclone-method | Methods used for the snpclone object |
| test_replen | Test repeat length consistency. |
| unique-methods | Unique and Duplicated implementations for MLG objects |
| upgma | UPGMA |
| win.ia | Calculate windows of the index of association for genlight... |
