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poppr version 1.1.2
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@zkamvar zkamvar released this 29 Jul 15:35
v.1.1.2
32f5e03

This release fixes bugs present in poppr version 1.1.0 and 1.1.1.

Below are the features added in version 1.1 relative to 1.0

poppr 1.1

NEW FEATURES

  • Polyploids with ambiguous genotypes are now supported in poppr. See documentation for recode_polyploids for details.
  • Calculations of Bruvo's distance now features correction for partial missing data utilizing genome addition and genome loss models as presented in Bruvo et al. 2004.
  • diss.dist now has options to return raw distances and a matrix instead of a dist object.
  • read.genalex now has the option to import as a genclone object. This is the default action.
  • poppr.all will be able to analyze lists of genind or genclone objects.
  • ia now has the argument valuereturn which will return the sampled data.
  • [bruvo,poppr].msn functions now give the user the choice to show the graph.
  • bruvo.boot has a cleaner plot style.

NEW DATA CLASSES

  • The genclone object is a new extension of the genind object from adegenet. This object contains slots containing population hierarchies and multilocus genotype definitions and will work with all analyses in adegenet and poppr.

NEW FUNCTIONS

  • [get,set,name,split,add]hierarchy - functions that will manipulate the hierarchy slot in a genclone object utilizing hierarchical formulae as arguments for simplification.
  • setpop will set the population of a genclone object utilizing model formulae regarding the hierarchy slot.
  • as.genclone will automatically convert genind objects to genclone objects.
  • is.genclone checks the validity of genclone objects.
  • poppr.amova will run amova on any hierarchical level. This also includes the feature to run amova on clone censored data sets. It utilizes the ade4 version of amova.
  • info_table will calculate missing data per population per locus or ploidy per individual per locus and gives the user the option to visualize this as a heatmap.
  • locus_table will calculate diversity and evenness statistics over all loci in a genind or genclone object.
  • *.dist functions will calculate Nei's distance, Rogers' Distance, Edwards' Distance, Reynolds' Distance, and Provestis' Distance.
  • aboot will allow the user to create bootstrapped dendrograms for ANY distance that can be calculated on genind or genpop objects.
  • plot_poppr_msn will plot minimum spanning networks produced with poppr.
  • private_alleles will give information about the presence of private alleles within a genind or genclone object.
  • recode_polyploids will take in a polyploid genind/genclone object (with missing alleles coded as extra zero-value allele) and recode them to have frequencies relative to the observed number of alleles.
  • genotype_curve will create a genotype accumulation curve for increasing number of loci.
  • mlg.id will return a list indicating the samples belonging to a specific multilocus genotype.

NEW DATA SETS

  • Pinf - a data set of 86 isolates from different populations of the late blight pathogen, Phytophthora infestans. Provided by Erica Goss
  • monpop - a large data set of 694 Monilinia fructicola isolates from a single orchard over three years. Provided by Sydney E. Everhart

NEW CAR

  • Not really.

NAMESPACE CHANGES

  • poppr no longer depends on pegas.
  • ade4 and reshape2 are now explicitly required.

IMPROVEMENTS

  • default shuffling algorithm has been implemented in C to increase speed.
  • output of the mlg functions are now represented as integers to decrease their size in memory.
  • mlg.matrix is now calculated faster utilizing R's internal tabulating capabilities.
  • The function poppr will no longer return rounded results, but rather is printed with three significant digits.

MISC

  • Added unit tests.
  • The poppr user manual has been shortened to only include instructions on data manipulation.
  • A new vignette, "Algorithms and Equations" gives algorithmic details for calculations performed in poppr.
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