poppr version 2.3.0

poppr 2.3.0

This version of poppr introduces the function bootgen2genind() that allows you to use aboot() with distance functions that explicitly expect "genind" objects:

aboot(myData, dist = myDist) # fails
aboot(myData, dist = function(x) myDist(bootgen2genind(x))) # works

There are other various bug fixes and improvements, which are listed below.

NEW FUNCTIONS

• The function bootgen2genind() will help users take advantage of
  bootstrapping distance functions from other packages that require genind
  objects. For details, see #112 and
  #111

NEW FEATURES

• There is now a plot parameter for the genotype curve to enable or suppress
  plotting.
• Progress bars are now automatically suppressed when running non-interactively.
  to turn them on when running non-interactively, use
  options(poppr.debug = TRUE).
• The progress bar for ia() and poppr() will now show estimated time. This
  is from dplyr's progress_estimated().

MISC

• The hist argument in the ia() is deprecated in favor of plot.
• The x axis for the genotype_curve() plot is now numeric, allowing you to
  fit a smoothing function over the points without having to use the hack
  geom_smooth(aes(group = 1)). This is thanks to Kara Woo for pointing this
  out on twitter (https://twitter.com/kara_woo/status/783336540407685120).
• The "show" method for genclone objects now delimits populations and strata
  by a comma, avoiding confusion with multi-word population names. Thanks to
  @knausb for the fix in #116.
• Documentation for poppr.amova now contains a note about significance testing
  with the ade4 function randtest.amova.

BUG FIX

• The subsetting methods will now properly handle mlgs when using sample names
  to subset genclone and snpclone objects. See
  #114 for details.
• A plotting bug for mlg.table() was fixed so that the plots now show the
  maximum value.
• Bugs with subsetting bootgen and bruvomat objects with no loci specified were
  fixed. See #118 for details.