v.2.9.6

This prevents the random seed from accidentally being modified when poppr is loaded.

Thanks to @TimTaylor for opening the issue. See #259

Full Changelog: v.2.9.5...v.2.9.6

poppr version 2.9.5

This is a maintenance release for CRAN that has no user-facing changes

poppr version 2.9.4

What's Changed

Fix cran bug #256 by @zkamvar in #257

Full Changelog: v.2.9.3...v.2.9.4

poppr 2.9.3

This is purely a maintenance release to address failures on clang13 (see #245 for details) and will not have any user-visible changes.

poppr 2.9.2

This is a CRAN maintenance release that has no user-visible changes.

poppr 2.9.0

poppr version 2.9.0

minor note: This release has all the same functionality as the one on CRAN, but I was being an absolute walnut and tagged it on the current main branch instead of the commit that was actually sent to CRAN (1a0aa1b), which contains minor fixes to valid URLs and, perhaps most importantly, the version properly recorded.

Thanks to @davefol, this release has a new function called bruvo.between(), which will use Bruvo's distance to compare a subset of data against a larger database. In addition the argument to drop populations from the analysis has been renamed to exclude.

Some important bug fixes include a fix for people who have SNP data that they wish to export to the GenAlEx format and a fix for Windows users who want to use bitwise.ia() for a large sample size.

NEW FEATURES

• bruvo.between() will calculate bruvo's distances between a query dataset
  and a reference dataset (@davefol, #223)

DEPRECATION

• The argument blacklist has been deprecated in favor of exclude for the
  following functions: bruvo.msn(), poppr.msn(), clonecorrect(), poppr(),
  mlg.table(), mlg.crosspop(), and popsub(). It will be removed in the
  poppr version 2.10 (@zkamvar, #218)

GITHUB

• The default branch for the repository is now "main" (@zkamvar, #218)

BUG FIX

• genind2genalex() no longer converts diploid sequence data to zeros on export
  This fixes #231 (@zkamvar, #233).
• bitwise.ia() will no longer have integer overflows early on Windows
  (@zkamvar, #235)

poppr 2.8.7

This is a minor fix for CRAN that fixes URL formatting for their never ending picking of nits.

Poppr version 2.8.6

poppr 2.8.6

BUG FIX

• read.genalex() now can import columns with entirely "T" alleles as "T"
  instead of "TRUE". (See #214 for details, thanks to @planteering for pointing it out).

NEW IMPORTS

• Progress bars are now implemented via the {progressr} package,
  which gives the user control over what should be displayed (or not). For
  example, to get auditory updates instead of a progress bar, you can use the
  "beepr" package and set progressr::handlers("beepr"). This will play an alert
  for each step (~50) and a final sound. To suppress all progress bars entirely,
  you can use progressr::handlers("void"). These progress bars have replaced
  the utils::txtProgressBar() and dplyr::progress_estimated() bars.

Here's a fun demonstration of how you can customize poppr's progress bars, which you can read more about in the {progressr} documentation

if (!require("progress")) install.packages("progress")
library("poppr")
data(Pinf)

library("progressr")
handlers( 
  handler_progress( 
    format = ":spin :current/:total [:bar] :percent in :elapsed ETA: :eta", 
    complete   = "^", 
    incomplete = "_", 
    current    = "😻", 
    clear = FALSE 
  ) 
) 
ia(Pinf, sample = 399, plot = FALSE) 

Poppr version 2.8.5

This version of poppr will change the behavior of the poppr() function slightly. It will return the "Pop" and "File" columns as characters, not factors (discussed in #212). If you have been relying on this output to be a factor, it is possible to retain the old method by using:

res <- poppr(data, ...)
res$Pop <- factor(res$Pop)
res$File <- factor(res$File)

Poppr version 2.8.4

This is a CRAN maintenance release to update documentation (see #211)