diff --git a/DESCRIPTION b/DESCRIPTION index ddeedd3..e999f02 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: canaper Title: Categorical Analysis of Neo- And Paleo-Endemism -Version: 0.0.1 +Version: 0.0.2 Authors@R: c( person(given = "Joel H.", diff --git a/NEWS.md b/NEWS.md index 365de13..87d753a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,28 +1,34 @@ +canaper 0.0.2 +=============== + +### BUG FIXES + +* [Fix bug](https://github.com/joelnitta/canaper/commit/acb40172c2d5ffb04e13519c6cad7c6d00fa451a) where `cpr_rand_test()` was failing to return identical results after `set.seed()` when parallelization is on + canaper 0.0.1 =============== ### NEW FEATURES -* Add `cpr_rand_comm()` function for generating a random community -2f3318c1d62f401d7c99bdcc16c64194359c3fbe +* [Add `cpr_rand_comm()` function](https://github.com/joelnitta/canaper/commit/2f3318c1d62f401d7c99bdcc16c64194359c3fbe) for generating a random community * Implement user-provided community matrix randomization functions ### BREAKING CHANGES -* Use `vegan` for community matrix randomizations instead of `picante` -b0a2d47130398eb62e28eba4783057f781763645 +* [Use `vegan`](https://github.com/joelnitta/canaper/commit/b0a2d47130398eb62e28eba4783057f781763645) for community matrix randomizations instead of `picante` + ### BUG FIXES -* Fix error in classification of endemism types with `cpr_classify_endem()`, +* [Fix error](https://github.com/joelnitta/canaper/commit/2f3318c1d62f401d7c99bdcc16c64194359c3fbe) 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 2f3318c1d62f401d7c99bdcc16c64194359c3fbe +**both** to be highly significant -* Fix calculation of RPD, RPE where alternative tree had all branch lengths +* [Fix calculation](https://github.com/joelnitta/canaper/commit/50ed6e975d14adba334f06a984d521ff69ed961c) of RPD, RPE where alternative tree had all branch lengths converted to same value, to converting only non-zero branch lengths to same -value 50ed6e975d14adba334f06a984d521ff69ed961c +value canaper 0.0.0.9000 =============== diff --git a/codemeta.json b/codemeta.json index 0066251..3713a1c 100644 --- a/codemeta.json +++ b/codemeta.json @@ -10,13 +10,13 @@ "codeRepository": "https://github.com/joelnitta/canaper", "issueTracker": "https://github.com/joelnitta/canaper/issues", "license": "https://spdx.org/licenses/MIT", - "version": "0.0.1", + "version": "0.0.2", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.1.1 (2021-08-10)", + "runtimePlatform": "R version 4.1.2 (2021-11-01)", "author": [ { "@type": "Person", @@ -370,7 +370,7 @@ } ], "releaseNotes": "https://github.com/joelnitta/canaper/blob/master/NEWS.md", - "fileSize": "7891.857KB", + "fileSize": "8154.89KB", "contIntegration": ["https://github.com/joelnitta/canaper/actions", "https://codecov.io/gh/joelnitta/canaper?branch=main"], "developmentStatus": "https://www.repostatus.org/#wip", "keywords": [ diff --git a/inst/WORDLIST b/inst/WORDLIST index 9fe1e8a..dd284e5 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,25 +1,52 @@ -Affero AGPL +Affero +Biodiverse +BugReports +CMD +Codecov +Commun +ComputerLanguage +Config +DOI +DOIs +Endemism +González +Iwasaki +Knerr +Laffan +LazyData +MERCHANTABILITY +Mishler +Nitta +ORCID +Orozco +Paleo +Phylocom +README +RPD +RPE +Roxygen +RoxygenNote +SoftwareApplication +SoftwareSourceCode +Sublicensing +VignetteBuilder +WIP +WIPO +Wataru al anthonynorth assertr assertthat aut -Biodiverse bioRxiv -BugReports canaper -CMD +codeRepository codecov -Codecov codemeta -codeRepository -Commun -ComputerLanguage -Config contIntegration -copyrightable copyrightHolder +copyrightable covr cran cre @@ -27,12 +54,9 @@ ctb datePublished developmentStatus doi -DOI -DOIs dplyr dtc endemism -Endemism et familyName fileSize @@ -42,42 +66,30 @@ gh github givenName gmail -González http https io issueTracker -Iwasaki joelnitta -Knerr knitr -Laffan -LazyData lgpl licensors magrittr md -MERCHANTABILITY -Mishler ncomms neo neoendemic -Nitta noncommercially orcid -ORCID -Orozco paleo -Paleo paleoendemic +parallelization phangorn -Phylocom phyloregion programmingLanguage progressr purrr readme -README releaseNotes relicensing renv @@ -85,28 +97,19 @@ repostatus rmarkdown roclet roclets -Roxygen -RoxygenNote roxyglobals runtimePlatform sameAs -SoftwareApplication softwareRequirements -SoftwareSourceCode softwareSuggestions spdx srr stringr sublicenses -Sublicensing testthat tibble tictoc tidyverse -VignetteBuilder -Wataru wip -WIP -WIPO www zenodo