poppr 2.1.0

IMPROVEMENTS

win.ia and samp.ia gain a significant speedup thanks to Jonah Brooks
implementing the code in C.
The internal code for the genotype_curve has been implemented in C for a 10x
increase in speed.

poppr.msn, bruvo.msn, and plot_poppr_msn gain the ability to take
character vectors for color palettes. See issue #55 for details.
plot_poppr_msn returns the modified graph.
All functions related to Bruvo's distance can now take a named vector of
repeat lengths in any order. See issue #61 for details.
aboot gains the argument strata so that you can automatically convert genind
to genpop.
genotype_curve can now take in loci objects from pegas.
You can now specify the maximum number of loci to analyze in genotype_curve.
filter_stats can now optionally plot a histogram in the background.
bruvo.dist can now optionally return distance matrices by locus. This is
addresed in issue #60
aboot can now handle matrices as previously specified in the documentation.
aboot can now take custom functions to calculate distance for genlight
objects.
poppr.amova can now perform amova using the pegas implementation.

rrmlg will calculate round-robin multilocus genotypes for each locus.
rraf will calculate round-robin allele frequencies for each locus.
pgen will calculate the probabilities of observed genotypes.
psex will calculate the probability that an observed genotype will be
observed more than once by chance.

Documentation for genclone and snpclone classes are more coherent.
Accessors added for internal MLG objects (for developers).
The genotype accumulation curve displays the iteration and locus number
instead of a progress bar.
The genotype accumulation plot is now scaled from 0 to the number of observed
mlgs.
Documentation for poppr.amova no longer references the "hierarchy" slot.

Single locus data sets can now be read in with read.genalex. This was
brought up in issue #58
(Thanks to Nick Wong for spotting it).
A bug in informloci where the MAF argument wasn't being applied to P/A data
has been fixed.
Printing of genclone objects with mixed ploidies previously reported
erroneously due to a sorting error. This has been fixed.
Edge case where a missing cell in the genalex matrix was interpreted as a
literal "NA" was fixed.
msn functions now return nodes that are correctly named. See Issue #66
for details.