To cite citation("poppr"). When referring to
genind vignette("how_to_migrate", "poppr") for more details on
major changes and how to deal with them.
Many new features in function(data type) - Descriptionmlg.table)
}getfile(x) - Provides a quick GUI to grab files for importread.genalex(x) - Reads GenAlEx formatted csv files to a genind objectgenind2genalex(m) - Converts genind objects to GenAlEx formatted csv filesgenclone2genind(m) - Removes the @mlg slot from genclone objectsas.genclone(m) - Converts genind objects to genclone objectsmissingno(m) - Handles missing dataclonecorrect(m | s) - Clone-censors at a specified population hierarchyinformloci(m) - Detects and removes phylogenetically uninformative locipopsub(m | s) - Subsets genind objects by populationshufflepop(m) - Shuffles genotypes at each locus using four different shuffling algorithmsrecode_polyploids(m|x) - Recodes polyploid data sets with missing alleles imported as "0"bruvo.dist(m) - Bruvo's distance (see also:fix_replen)diss.dist(m) - Absolute genetic distance (see prevosti.dist)nei.dist(m | x) - Nei's 1978 genetic distancerogers.dist(m | x) - Rogers' euclidean distancereynolds.dist(m | x) - Reynolds' coancestry distanceedwards.dist(m | x) - Edwards' angular distanceprevosti.dist(m | x) - Prevosti's absolute genetic distancebitwise.dist(s) - Calculates fast pairwise distances for genlight objects.aboot(m | s | x) - Creates a bootstrapped dendrogram for any distance measurebruvo.boot(m) - Produces dendrograms with bootstrap support based on Bruvo's distancediversity_boot(x) - Generates boostrap distributions of diversity statistics for multilocus genotypesdiversity_ci(m | s | x) - Generates confidence intervals for multilocus genotype diversity.mlg(m | s) - Calculates the number of multilocus genotypesmll(m | s) - Displays the current multilocus lineages (genotypes) defined.nmll(m | s) - Same asmlg.mlg.crosspop(m | s) - Finds all multilocus genotypes that cross populationsmlg.table(m | s) - Returns a table of populations by multilocus genotypesmlg.vector(m | s) - Returns a vector of a numeric multilocus genotype assignment for each individualmlg.id(m | s) - Finds all individuals associated with a single multilocus genotypemlg.filter(m | s) - Collapses MLGs by genetic distancefilter_stats(m | s) - Calculates mlg.filter for all algorithms and plotscutoff_predictor(x) - Predicts cutoff threshold from mlg.filter.mll.custom(m | s) - Allows for the custom definition of multilocus lineagesmll.levels(m | s) - Allows the user to change levels of custom MLLs.mll.reset(m | s) - Reset multilocus lineages.diversity_stats(x) - Creates a table of diversity indices for multilocus genotypes.poppr.amova(m) - Analysis of Molecular Variance (as implemented in ade4)ia(m) - Calculates the index of associationpair.ia(m) - Calculates the index of association for all loci pairs.win.ia(s) - Index of association windows for genlight objects.samp.ia(s) - Index of association on random subsets of loci for genlight objects.poppr(m | x) - Returns a diversity table by populationpoppr.all(m | x) - Returns a diversity table by population for all compatible files specifiedprivate_alleles(m) - Tabulates the occurrences of alleles that only occur in one population.locus_table(m) - Creates a table of summary statistics per locus.rrmlg(m | x) - Round-robin multilocus genotype estimates.rraf(m) - Round-robin allele frequency estimates.pgen(m) - Probability of genotypes.psex(m) - Probability of observing a genotype more than once.imsn(m | s) - Interactive construction and visualization of minimum spanning networksplot_poppr_msn(m | s | x) - Plots minimum spanning networks produced in poppr with scale bar and legendgreycurve(x) - Helper to determine the appropriate parameters for adjusting the grey level for msn functionsbruvo.msn(m) - Produces minimum spanning networks based off Bruvo's distance colored by populationpoppr.msn(m | s | x) - Produces a minimum spanning network for any pairwise distance matrix related to the datainfo_table(m) - Creates a heatmap representing missing data or observed ploidygenotype_curve(m | x) - Creates a series of boxplots to demonstrate how many markers are needed to represent the diversity of your data.Aeut- (AFLP) Oomycete root rot pathogenAphanomyces euteiches(Grünwald and Hoheisel, 2006)monpop- (SSR) Peach brown rot pathogenMonilinia
fructicola(Everhart and Scherm, 2015)partial_clone- (SSR) partially-clonal data simulated via
simuPOP (Peng and Amos, 2008)Pinf- (SSR) Potato late blight pathogenPhytophthora infestans(Goss et. al., 2014)Pram- (SSR) Sudden Oak Death pathogenPhytophthora
ramorum(Kamvar et. al., 2015; Goss et. al., 2009)genind genlight genclone snpclone ?function_name in the R console. Detailed topic explanations
live in the package vignettes:
vignette("how_to_migrate", "poppr")
Data import and manipulation vignette("poppr_manual", "poppr")
Algorithms and Equations vignette("algo", "poppr")
Multilocus Genotype Analysis vignette("mlg", "poppr")
}
Important notes on the changes from poppr version 1 to poppr version 2 are
in Migration from poppr version 1, essential functions for importing
and manipulating data are detailed within the Data import and
manipulation vignette, details on algorithms used in Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for genetic
analysis of populations with clonal, partially clonal, and/or sexual
reproduction. PeerJ 2:e281
Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of
genome-wide population genetic data with emphasis on clonality. Front. Genet.
6:208. doi: 10.3389/fgene.2015.00208
--------- Papers referencing data sets ---------
Grunwald, NJ and Hoheisel, G.A. 2006. Hierarchical Analysis of Diversity,
Selfing, and Genetic Differentiation in Populations of the Oomycete
Aphanomyces euteiches. Phytopathology 96:1134-1141 doi:
SE Everhart, H Scherm, (2015) Fine-scale genetic structure of Monilinia
fructicola during brown rot epidemics within individual peach tree canopies.
Phytopathology 105:542-549 doi:
Bo Peng and Christopher Amos (2008) Forward-time simulations of nonrandom mating populations using simuPOP. bioinformatics, 24 (11): 1408-1409.
Goss, Erica M., Javier F. Tabima, David EL Cooke, Silvia Restrepo, William E.
Fry, Gregory A. Forbes, Valerie J. Fieland, Martha Cardenas, and Niklaus J.
Grünwald. (2014) "The Irish potato famine pathogen Phytophthora
infestans originated in central Mexico rather than the Andes." Proceedings
of the National Academy of Sciences 111:8791-8796. doi:
Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald, N.
J. (2015). Spatial and temporal analysis of populations of the sudden oak
death pathogen in Oregon forests. Phytopathology 105:982-989. doi:
Goss, E. M., Larsen, M., Chastagner, G. A., Givens, D. R., and Grünwald, N.
J. 2009. Population genetic analysis infers migration pathways of
Phytophthora ramorum in US nurseries. PLoS Pathog. 5:e1000583. doi: