release candidate for poppr version 2.5.0

poppr 2.5.0 release candidate

This is a pre-release of poppr version 2.5.0.

It contains a major bug fix for those who deal with polyploid data and Bruvo's distance with either genome addition or genome loss corrections (details below). We have ensured that all the new functionality is tested accurately, but nevertheless, if you run into any major bugs or otherwise unexpected results, please open an issue at https://github.com/grunwaldlab/poppr/issues

Attached are the windows (poppr_2.5.0.zip) and OSX (poppr_2.5.0.tgz) binaries. You can install them by using:

# For OSX users
install.packages("https://github.com/grunwaldlab/poppr/releases/download/v.2.5.0rc/poppr_2.5.0rc.tgz", repos = NULL)

# For Windows users
install.packages("https://github.com/grunwaldlab/poppr/releases/download/v.2.5.0rc/poppr_2.5.0rc.zip", repos = NULL)

or you can use devtools (Requires a C compiler):

if (!require("devtools") install.packages("devtools", repos = "https://cran.rstudio.com")
devtools::install_github("grunwaldlab/poppr@v.2.5.0rc")

---

ALGORITHMIC CHANGE

• Identified in #139, Bruvo's
  distance will now consider all possible combinations of ordered alleles in the
  calculation under the genome addition and loss models for missing data. This
  will affect those who have polyploid data that contain more than one missing
  allele at any genotype

  To facilitate comparison, the global option old.bruvo.model, has been created.
  By default it is set to FALSE, indicating that poppr should use the ordered
  allele combinations. If the user wants to use the method considering unorderd
  allele combinations, they can set options(old.bruvo.model = TRUE)

  It must be repeated that this does not affect haploid or diploid comparisons,
  those that use the infinite alleles model, or those who do not have more than
  one missing allele at any genotype.

DEPRECATION

• The warning for a short repeat length vector for Bruvo's distance is
  deprecated and will become an error in the future

MISC

• The internal plotting function for mlg.table now uses tidy evaluation for
  dplyr versions > 0.5.0
• The package reshape2 was removed from imports and replaced with base functions
  (see #144 for details)

NEW IMPORTS

• Due to the migration to dplyr version 0.7.0, poppr now imports the "!!"
  operator from the rlang package