Fix installation of dependencies when installing from r-universe repo (https:/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:/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:/ropensci/canaper/commit/ff6012d6b817d3ba8765d8c8b009e2818da2ab9f)
Remove tidyverse from vignettes and Suggests. Thanks to @hadley for pointing this out. (https:/ropensci/canaper/commit/49aa94b418ad9e85f30e6f751651386674a367d8)
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Add more palettes and pr_make_pal() to choose palettes (https:/ropensci/canaper/commit/ec624d4c2e85051e4ee5c07143b407de96be7734)
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Add cpr_iter_sim() to help determine number of iterations needed for randomization algorithms (https:/ropensci/canaper/commit/80a47782706816b8238c318ad596b9da47bfba76)
Includes improvements in response to review on ropensci (ropensci/software-review#475)
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Update README with comparisons to other packages (https:/ropensci/canaper/commit/d8aaf8de5193166d52ab890d8267090ea2f8ef6a)
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Add link to CONTRIBUTING.md to README (https:/ropensci/canaper/commit/d8aaf8de5193166d52ab890d8267090ea2f8ef6a)
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Change Depends: R (>= 3.5.0) to Depends: R (>= 4.1.0) in DESCRIPTION (https:/ropensci/canaper/commit/0f334965fb5a3fe5034eb1bc682b5051548eddb1)
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Add @KlausVigo as reviewer to DESCRIPTION (https:/ropensci/canaper/commit/6e9b3d55202e2294a6436280ca6b01db13d92974)
- Delete redundant checks in internal functions (https:/ropensci/canaper/commit/bccd0278dd3de5853680d9979ca26c1aa38a7fb3)
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Make skipping of extended tests default (https:/joelnitta/canaper/blob/76c277490dcecd0f32df351c48c8f8c891674aad/tests/testthat/test-cpr_rand_test.R#L395)
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Decrease number of replicates so tests finish faster (https:/ropensci/canaper/commit/12bbe36bf5516a2a63c1235c76234708c4c5432d, https:/ropensci/canaper/commit/f3af4671d679020aeaa97b1a038b3b5a96633f42)
- Import functions from phyloregion instead of copying (https:/ropensci/canaper/commit/7e8b24950912bfa2a5e10cf4dd9cfa8910d74e76)
- Fix bug where
cpr_rand_test()was failing to return identical results afterset.seed()when parallelization is on
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Add
cpr_rand_comm()function for generating a random community -
Implement user-provided community matrix randomization functions
- Use
veganfor community matrix randomizations instead ofpicante
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Fix error in classification of endemism types with
cpr_classify_endem(), where super-endemic cells were previously being assigned ifpe_obs_p_upperorpe_obs_alt_p_upperwere 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
- Initial release on github