Fix installation of dependencies when installing from r-universe repo (https://github.com/ropensci/canaper/commit/774d89f58af8c55dda178fff3d324b2e48b749fd)
Add warning for abundance data, since CANAPE analysis in canaper treats it the same as presence-absence data. Thanks to an anonymous reviewer for the suggestion (https://github.com/ropensci/canaper/commit/143cadee62a9bf3c5256e3d92240c6243bf803e4)
Fix internal functions count_higher() and
count_lower() that did not distinguish between
NA and NA_integer_. Thanks to @hadley (Hadley Wickham)
(https://github.com/ropensci/canaper/commit/ff6012d6b817d3ba8765d8c8b009e2818da2ab9f)
Remove tidyverse from vignettes and Suggests. Thanks to @hadley for pointing this out. (https://github.com/ropensci/canaper/commit/49aa94b418ad9e85f30e6f751651386674a367d8)
Add more palettes and pr_make_pal() to choose palettes (https://github.com/ropensci/canaper/commit/ec624d4c2e85051e4ee5c07143b407de96be7734)
Add cpr_iter_sim() to help determine number of iterations needed for randomization algorithms (https://github.com/ropensci/canaper/commit/80a47782706816b8238c318ad596b9da47bfba76)
Includes improvements in response to review on ropensci (https://github.com/ropensci/software-review/issues/475)
Update README with comparisons to other packages (https://github.com/ropensci/canaper/commit/d8aaf8de5193166d52ab890d8267090ea2f8ef6a)
Add link to CONTRIBUTING.md to README (https://github.com/ropensci/canaper/commit/d8aaf8de5193166d52ab890d8267090ea2f8ef6a)
Change Depends: R (>= 3.5.0) to Depends: R (>= 4.1.0) in DESCRIPTION (https://github.com/ropensci/canaper/commit/0f334965fb5a3fe5034eb1bc682b5051548eddb1)
Add @KlausVigo as reviewer to DESCRIPTION (https://github.com/ropensci/canaper/commit/6e9b3d55202e2294a6436280ca6b01db13d92974)
Make skipping of extended tests default (https://github.com/joelnitta/canaper/blob/76c277490dcecd0f32df351c48c8f8c891674aad/tests/testthat/test-cpr_rand_test.R#L395)
Decrease number of replicates so tests finish faster (https://github.com/ropensci/canaper/commit/12bbe36bf5516a2a63c1235c76234708c4c5432d, https://github.com/ropensci/canaper/commit/f3af4671d679020aeaa97b1a038b3b5a96633f42)
cpr_rand_test() was failing to return
identical results after set.seed() when parallelization is
onAdd
cpr_rand_comm() function for generating a random
community
Implement user-provided community matrix randomization functions
vegan for community matrix randomizations instead of
picanteFix
error in classification of endemism types with
cpr_classify_endem(), where super-endemic cells were
previously being assigned if pe_obs_p_upper
or pe_obs_alt_p_upper were highly
significant (P > 0.99), to requiring both to be
highly significant
Fix calculation of RPD, RPE where alternative tree had all branch lengths converted to same value, to converting only non-zero branch lengths to same value