poppr version 2.5.0

Version 2.5.0 of poppr contains very important bug fixes for read.genalex() and all functions that use Bruvo's distance (see details).

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
• jack.ia() is deprecated in favor of resample.ia() for clarity.

BUG FIX

• A bug in read.genalex() where removed samples would have incorrect strata
  labels was fixed. Thanks to Hernán Dario Capador-Barreto for identifying it.
  See #147

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