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A B C D E F G I J L M N O P R S T W
| poppr-package | The 'poppr' R package |
| aboot | Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects. |
| Aeut | Oomycete root rot pathogen *Aphanomyces euteiches* AFLP data |
| amova | Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects. |
| as.genambig | Switch between genind and genclone objects. |
| as.genambig-method | Switch between genind and genclone objects. |
| as.genclone | Switch between genind and genclone objects. |
| as.genclone-method | Switch between genind and genclone objects. |
| as.snpclone | Create a snpclone object from a genlight object. |
| as.snpclone-method | Create a snpclone object from a genlight object. |
| bitwise.dist | Calculate dissimilarity or Euclidean distance for genlight objects |
| boot.ia | Bootstrap the index of association |
| bootgen2genind | Switch between genind and genclone objects. |
| bootgen2genind-method | Switch between genind and genclone objects. |
| bootstrap | Calculate a dendrogram with bootstrap support using any distance applicable to genind or genclone objects. |
| bruvo.boot | Create a tree using Bruvo's Distance with non-parametric bootstrapping. |
| bruvo.dist | Bruvo's distance for microsatellites |
| bruvo.msn | Create minimum spanning network of selected populations using Bruvo's distance. |
| clonecorrect | Remove potential bias caused by cloned genotypes in genind or genclone object. |
| 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 intervals. |
| diversity_stats | Produce a table of diversity statistics |
| edwards.dist | Calculate Genetic Distance for a genind or genclone object. |
| filter_stats | Utilize all algorithms of mlg.filter |
| fix_replen | Find and fix inconsistent repeat lengths |
| genclone | GENclone and SNPclone classes |
| genclone-class | GENclone and SNPclone classes |
| genclone2genind | Switch between genind and genclone objects. |
| genclone2genind-method | Switch between genind and genclone objects. |
| genind2genalex | Export data from genind objects to genalex formatted \*.csv files. |
| genotype_curve | Produce a genotype accumulation curve |
| getfile | Get a file name and path and store them in a list. |
| 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 of a genind or genclone object |
| is.clone | Check for validity of a genclone or snpclone object |
| is.genclone | Check for validity of a genclone or snpclone object |
| is.snpclone | Check for validity of a genclone or snpclone object |
| jack.ia | Index of Association |
| locus_table | Create a table of summary statistics per locus. |
| make_haplotypes | Split samples from a genind object into pseudo-haplotypes |
| 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.crosspop | Create counts, vectors, and matrices of multilocus genotypes. |
| mlg.filter | MLG definitions based on genetic distance |
| mlg.filter-method | MLG definitions based on genetic distance |
| mlg.filter<- | MLG definitions based on genetic distance |
| mlg.filter<--method | MLG definitions based on genetic distance |
| mlg.id | Create counts, vectors, and matrices of multilocus genotypes. |
| mlg.table | Create counts, vectors, and matrices of multilocus genotypes. |
| mlg.vector | Create counts, vectors, and matrices of multilocus genotypes. |
| mll | Access and manipulate multilocus lineages. |
| mll-method | Access and manipulate multilocus lineages. |
| mll.custom | Define custom multilocus lineages |
| mll.custom-method | Define custom multilocus lineages |
| mll.custom<- | Define custom multilocus lineages |
| mll.custom<--method | Define custom multilocus lineages |
| mll.levels | Define custom multilocus lineages |
| mll.levels-method | Define custom multilocus lineages |
| mll.levels<- | Define custom multilocus lineages |
| mll.levels<--method | Define custom multilocus lineages |
| mll.reset | Reset multilocus lineages |
| mll.reset-method | Reset multilocus lineages |
| mll<- | Access and manipulate multilocus lineages. |
| mll<--method | Access and manipulate multilocus lineages. |
| monpop | Peach brown rot pathogen *Monilinia fructicola* |
| msn.bruvo | Create minimum spanning network of selected populations using Bruvo's distance. |
| msn.poppr | Create a minimum spanning network of selected populations using a distance matrix. |
| nei.dist | Calculate Genetic Distance for a genind or genclone object. |
| nmll | Access and manipulate multilocus lineages. |
| nmll-method | Access and manipulate multilocus lineages. |
| old2new_genclone | Convert an old genclone object to a new genclone object |
| old_partial_clone | Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance |
| old_Pinf | Phytophthora infestans data from Mexico and South America. |
| pair.ia | Index of Association |
| partial_clone | Simulated data illustrating a Minimum Spanning Network based on Bruvo's Distance |
| pgen | Genotype Probability |
| Pinf | Phytophthora infestans data from Mexico and South America. |
| plot_poppr_msn | Plot minimum spanning networks produced in poppr. |
| poppr | Produce a basic summary table for population genetic analyses. |
| poppr.all | Process a list of files with poppr |
| poppr.amova | Perform Analysis of Molecular Variance (AMOVA) on genind or genclone objects. |
| poppr.msn | Create a minimum spanning network of selected populations using a distance matrix. |
| poppr_has_parallel | Determines whether openMP is support on this system. |
| popsub | Subset data by population |
| Pram | Phytophthora ramorum data from OR Forests and Nurseries (OR and CA) |
| prevosti.dist | Calculate Genetic Distance for a genind or genclone object. |
| private_alleles | Tabulate alleles the occur in only one population. |
| provesti.dist | Calculate Genetic Distance for a genind or genclone object. |
| psex | Probability of encountering a genotype more than once by chance |
| 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 based statistics. |
| resample.ia | Index of Association |
| reynolds.dist | Calculate Genetic Distance for a genind or genclone object. |
| rogers.dist | Calculate Genetic Distance for a genind or genclone object. |
| rraf | Round Robin Allele Frequencies |
| rrmlg | Round Robin Multilocus Genotypes |
| samp.ia | Calculate random samples of the index of association for genlight objects. |
| shufflepop | Shuffle individuals in a 'genclone' or 'genind' object independently over each locus. |
| snpclone | GENclone and SNPclone classes |
| snpclone-class | GENclone and SNPclone classes |
| test_replen | Test repeat length consistency. |
| win.ia | Calculate windows of the index of association for genlight objects. |