Merge pull request #8 from ropensci/joelnitta/issue7

Joelnitta/issue7

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: canaper
 Title: Categorical Analysis of Neo- And Paleo-Endemism
-Version: 0.0.2
+Version: 0.0.3
 Authors@R: 
     c(
     person(given = "Joel H.",
@@ -29,9 +29,9 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE, roclets = c ("collate", "namespace", "rd", "roxyglobals::global_roclet", "srr::srr_stats_roclet"))
 RoxygenNote: 7.2.1
-URL: https://github.com/joelnitta/canaper,
-    https://joelnitta.github.io/canaper/
-BugReports: https://github.com/joelnitta/canaper/issues
+URL: https://github.com/ropensci/canaper,
+    https://docs.ropensci.org/canaper/
+BugReports: https://github.com/ropensci/canaper/issues
 Imports: 
     ape,
     assertr,

NEWS.md

@@ -1,32 +1,60 @@
+canaper  0.0.3
+===============
+
+Includes improvements in response to review on ropensci (https://github.com/ropensci/software-review/issues/475)
+### DOCUMENTATION
+
+* Update README with comparisons to other packages (d8aaf8de5193166d52ab890d8267090ea2f8ef6a)
+
+* Add link to CONTRIBUTING.md to README (d8aaf8de5193166d52ab890d8267090ea2f8ef6a)
+
+* Change Depends: R (>= 3.5.0) to Depends: R (>= 4.1.0) in DESCRIPTION (0f334965fb5a3fe5034eb1bc682b5051548eddb1)
+
+* Add @KlausVigo as reviewer to DESCRIPTION (6e9b3d55202e2294a6436280ca6b01db13d92974)
+
+### BUG FIXES
+
+* Delete redundant checks in internal functions (bccd0278dd3de5853680d9979ca26c1aa38a7fb3)
+
+### TESTS
+
+* 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 (12bbe36bf5516a2a63c1235c76234708c4c5432d, f3af4671d679020aeaa97b1a038b3b5a96633f42)
+
+### OTHER
+
+* Import functions from phyloregion instead of copying (7e8b24950912bfa2a5e10cf4dd9cfa8910d74e76)
+
 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
+* [Fix bug](https://github.com/ropensci/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](https://github.com/joelnitta/canaper/commit/2f3318c1d62f401d7c99bdcc16c64194359c3fbe) for generating a random community
+* [Add `cpr_rand_comm()` function](https://github.com/ropensci/canaper/commit/2f3318c1d62f401d7c99bdcc16c64194359c3fbe) for generating a random community
 
 * Implement user-provided community matrix randomization functions
 
 ### BREAKING CHANGES
 
-* [Use `vegan`](https://github.com/joelnitta/canaper/commit/b0a2d47130398eb62e28eba4783057f781763645) for community matrix randomizations instead of `picante`
+* [Use `vegan`](https://github.com/ropensci/canaper/commit/b0a2d47130398eb62e28eba4783057f781763645) for community matrix randomizations instead of `picante`
 
 
 ### BUG FIXES
 
-* [Fix error](https://github.com/joelnitta/canaper/commit/2f3318c1d62f401d7c99bdcc16c64194359c3fbe) in classification of endemism types with `cpr_classify_endem()`,
+* [Fix error](https://github.com/ropensci/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
 
-* [Fix calculation](https://github.com/joelnitta/canaper/commit/50ed6e975d14adba334f06a984d521ff69ed961c) of RPD, RPE where alternative tree had all branch lengths
+* [Fix calculation](https://github.com/ropensci/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
 

README.Rmd

@@ -19,28 +19,32 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![DOI](https://zenodo.org/badge/359280907.svg)](https://zenodo.org/badge/latestdoi/359280907)
-[![R-CMD-check](https://github.com/joelnitta/canaper/workflows/R-CMD-check/badge.svg)](https://github.com/joelnitta/canaper/actions)
+[![R-CMD-check](https://github.com/ropensci/canaper/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/canaper/actions)
 [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
-[![Codecov test coverage](https://codecov.io/gh/joelnitta/canaper/branch/main/graph/badge.svg)](https://codecov.io/gh/joelnitta/canaper?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/ropensci/canaper/branch/main/graph/badge.svg)](https://codecov.io/gh/ropensci/canaper?branch=main)
 <!-- badges: end -->
 
 ```{r srr-tags-intro, eval = FALSE, echo = FALSE}
 #' @srrstats {G1.1} documents novelty
 ```
 
-The goal of canaper is to enable [categorical analysis of neo- and paleo-endemism (CANAPE)](https://doi.org/10.1038/ncomms5473) in **R**. This is the first implementation in **R** of CANAPE, which was previously only available in [Biodiverse](http://shawnlaffan.github.io/biodiverse/).
+The goal of `canaper` is to enable [categorical analysis of neo- and paleo-endemism (CANAPE)](https://doi.org/10.1038/ncomms5473) in **R**. This is the first implementation in **R** of CANAPE, which was previously only available in [Biodiverse](http://shawnlaffan.github.io/biodiverse/).
 
-## Important note
+## Installation
 
-**This package is in early development.** There may be major, breaking changes to functionality in the near future. If you use this package, I highly recommend using a package manager like [renv](https://rstudio.github.io/renv/articles/renv.html) so that later updates won't break your code.
+`canaper` is not currently available on CRAN.
 
-## Installation
+You can install `canaper` from [r-universe](https://r-universe.dev) with:
 
-You can install canaper from [GitHub](https://github.com/) with:
+``` r
+install.packages("canaper", repos = "https://ropensci.r-universe.dev")
+```
+
+or, you can install `canaper` from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("remotes")
-remotes::install_github("joelnitta/canaper")
+remotes::install_github("ropensci/canaper")
 ```
 
 ## Example usage
@@ -105,7 +109,7 @@ This data set is very small, so it doesn't include all possible endemism types.
 - `mixed`: mixture of both paleo and neo
 - `super`: mixed and highly significant (*p* < 0.01)
 
-For a more complete example, please [see the vignette](https://joelnitta.github.io/canaper/articles/canape.html)
+For a more complete example, please [see the vignette](https://docs.ropensci.org/canaper/articles/canape.html)
 
 ## Comparsion with other software
 
@@ -128,9 +132,7 @@ Poster at [Botany 2021](https://2021.botanyconference.org/)
 
 If you use this package, please cite it! Here is an example:
 
-```
-Nitta JH, Laffan SW, Mishler BD, Iwasaki W. (2021) canaper: Categorical analysis of neo- and paleo-endemism in R. doi: 10.5281/zenodo.5094032
-```
+- Nitta JH, Laffan SW, Mishler BD, Iwasaki W. (2021) canaper: Categorical analysis of neo- and paleo-endemism in R. doi: 10.5281/zenodo.5094032
 
 The example DOI above is for the overall package. 
 
@@ -156,8 +158,8 @@ Please note that this package is released with a [Contributor Code of Conduct](h
 
 - Code: [MIT](LICENSE.md)
 - Example datasets
-  - `acacia`, `biod_example`: [GNU General Public License v3.0](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-gpl.txt)
-  - `phylocom`: [BSD-3-Clause](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-bsd3.txt)
+  - `acacia`, `biod_example`: [GNU General Public License v3.0](https://github.com/ropensci/canaper/blob/main/data-raw/LICENSE-gpl.txt)
+  - `phylocom`: [BSD-3-Clause](https://github.com/ropensci/canaper/blob/main/data-raw/LICENSE-bsd3.txt)
 
 ## References
 

README.md

@@ -7,35 +7,38 @@
 <!-- badges: start -->
 
 [![DOI](https://zenodo.org/badge/359280907.svg)](https://zenodo.org/badge/latestdoi/359280907)
-[![R-CMD-check](https://github.com/joelnitta/canaper/workflows/R-CMD-check/badge.svg)](https://github.com/joelnitta/canaper/actions)
+[![R-CMD-check](https://github.com/ropensci/canaper/workflows/R-CMD-check/badge.svg)](https://github.com/ropensci/canaper/actions)
 [![Project Status: WIP – Initial development is in progress, but there
 has not yet been a stable, usable release suitable for the
 public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 [![Codecov test
-coverage](https://codecov.io/gh/joelnitta/canaper/branch/main/graph/badge.svg)](https://codecov.io/gh/joelnitta/canaper?branch=main)
+coverage](https://codecov.io/gh/ropensci/canaper/branch/main/graph/badge.svg)](https://codecov.io/gh/ropensci/canaper?branch=main)
 <!-- badges: end -->
 
-The goal of canaper is to enable [categorical analysis of neo- and
+The goal of `canaper` is to enable [categorical analysis of neo- and
 paleo-endemism (CANAPE)](https://doi.org/10.1038/ncomms5473) in **R**.
 This is the first implementation in **R** of CANAPE, which was
 previously only available in
 [Biodiverse](http://shawnlaffan.github.io/biodiverse/).
 
 ## Important note
 
-**This package is in early development.** There may be major, breaking
-changes to functionality in the near future. If you use this package, I
-highly recommend using a package manager like
-[renv](https://rstudio.github.io/renv/articles/renv.html) so that later
-updates won’t break your code.
-
 ## Installation
 
-You can install canaper from [GitHub](https://github.com/) with:
+`canaper` is not currently available on CRAN.
+
+You can install `canaper` from [r-universe](https://r-universe.dev)
+with:
+
+``` r
+install.packages("canaper", repos = "https://ropensci.r-universe.dev")
+```
+
+or, you can install `canaper` from [GitHub](https://github.com/) with:
 
 ``` r
 # install.packages("remotes")
-remotes::install_github("joelnitta/canaper")
+remotes::install_github("ropensci/canaper")
 ```
 
 ## Example usage
@@ -162,7 +165,7 @@ types. In total, they include:
 -   `super`: mixed and highly significant (*p* \< 0.01)
 
 For a more complete example, please [see the
-vignette](https://joelnitta.github.io/canaper/articles/canape.html)
+vignette](https://docs.ropensci.org/canaper/articles/canape.html)
 
 ## Comparsion with other software
 
@@ -186,12 +189,12 @@ comprehensive description of each package.
     `frequency`, `richness`, `independentswap`, and `trialswap`.
 -   [vegan](https://github.com/vegandevs/vegan): Performs a large range
     of mostly non-phylogenetic diversity analyses. Includes the largest
-    selection of null models (\> 20), according to data type (binary
+    selection of null models (> 20), according to data type (binary
     vs. quantitative). `canaper` uses `vegan` to randomize community
     matrices.
 -   [biodiverse](http://shawnlaffan.github.io/biodiverse/): Not an R
     package, but software written in perl with a GUI. Performs all of
-    the calculations needed for CANAPE, and many other metrics (\> 300).
+    the calculations needed for CANAPE, and many other metrics (> 300).
     Includes `rand_structured` null model as well as spatially
     structured null models. None of these null models are currently
     available in any R packages AFAIK, except for `independentswap`.
@@ -207,7 +210,9 @@ Poster at [Botany 2021](https://2021.botanyconference.org/)
 
 If you use this package, please cite it! Here is an example:
 
-    Nitta JH, Laffan SW, Mishler BD, Iwasaki W. (2021) canaper: Categorical analysis of neo- and paleo-endemism in R. doi: 10.5281/zenodo.5094032
+-   Nitta JH, Laffan SW, Mishler BD, Iwasaki W. (2021) canaper:
+    Categorical analysis of neo- and paleo-endemism in R. doi:
+    10.5281/zenodo.5094032
 
 The example DOI above is for the overall package.
 
@@ -247,9 +252,9 @@ project, you agree to abide by its terms.
 -   Code: [MIT](LICENSE.md)
 -   Example datasets
     -   `acacia`, `biod_example`: [GNU General Public License
-        v3.0](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-gpl.txt)
+        v3.0](https://github.com/ropensci/canaper/blob/main/data-raw/LICENSE-gpl.txt)
     -   `phylocom`:
-        [BSD-3-Clause](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-bsd3.txt)
+        [BSD-3-Clause](https://github.com/ropensci/canaper/blob/main/data-raw/LICENSE-bsd3.txt)
 
 ## References
 

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://joelnitta.github.io/canaper/
+url: https://docs.ropensci.org/canaper/
 home:
   title: Categorical Analysis of Neo- and Paleo-endemism in R
   description: |

codemeta.json

@@ -4,11 +4,11 @@
   "identifier": "canaper",
   "description": "Provides functions to conduct categorical analysis of neo- and paleo-endemism (CANAPE).",
   "name": "canaper: Categorical Analysis of Neo- And Paleo-Endemism",
-  "relatedLink": "https://joelnitta.github.io/canaper/",
-  "codeRepository": "https://github.com/joelnitta/canaper",
-  "issueTracker": "https://github.com/joelnitta/canaper/issues",
+  "relatedLink": "https://docs.ropensci.org/canaper/",
+  "codeRepository": "https://github.com/ropensci/canaper",
+  "issueTracker": "https://github.com/ropensci/canaper/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.0.2",
+  "version": "0.0.3",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -385,7 +385,7 @@
     },
     "SystemRequirements": null
   },
-  "fileSize": "9237.93KB",
+  "fileSize": "280.144KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -404,14 +404,12 @@
       ],
       "name": "canaper: Categorical analysis of neo- and paleo-endemism in {R}",
       "identifier": "10.5281/zenodo.5094032",
-      "url": "https://github.com/joelnitta/canaper",
+      "url": "https://github.com/ropensci/canaper",
       "@id": "https://doi.org/10.5281/zenodo.5094032",
       "sameAs": "https://doi.org/10.5281/zenodo.5094032"
     }
   ],
-  "releaseNotes": "https://github.com/joelnitta/canaper/blob/master/NEWS.md",
-  "readme": "https://github.com/joelnitta/canaper/blob/main/README.md",
-  "contIntegration": ["https://github.com/joelnitta/canaper/actions", "https://codecov.io/gh/joelnitta/canaper?branch=main"],
-  "developmentStatus": "https://www.repostatus.org/#wip",
-  "keywords": ["biodiversity", "canape"]
+  "releaseNotes": "https://github.com/ropensci/canaper/blob/master/NEWS.md",
+  "contIntegration": ["https://github.com/ropensci/canaper/actions", "https://codecov.io/gh/ropensci/canaper?branch=main"],
+  "developmentStatus": "https://www.repostatus.org/#wip"
 }

inst/CITATION

@@ -1,4 +1,4 @@
-citHeader("This is how you can cite canaper in publications (please replace the DOI below with the one matching the version in use; for more information, see the README at https://github.com/joelnitta/canaper)")
+citHeader("This is how you can cite canaper in publications (please replace the DOI below with the one matching the version in use; for more information, see the README at https://github.com/ropensci/canaper)")
 
 citEntry(
   entry    = "Manual",
@@ -7,7 +7,7 @@ citEntry(
                      as.person("Wataru Iwasaki")
           ),
   year     = "2021",
-  url      = "https://github.com/joelnitta/canaper",
+  url      = "https://github.com/ropensci/canaper",
   doi = "10.5281/zenodo.5094032",
   textVersion = paste("Nitta JH, Iwasaki W. (2021) canaper: Categorical analysis of neo- and paleo-endemism in R. doi: 10.5281/zenodo.5094032")
 )

inst/WORDLIST

@@ -20,6 +20,8 @@ branchlengths
 BugReports
 canaper
 centroids
+citEntry
+citHeader
 CMD
 cmd
 Codecov
@@ -84,6 +86,7 @@ io
 issueTracker
 Iwasaki
 JamesIves
+JH
 joelnitta
 Kembel
 Knerr
@@ -132,6 +135,7 @@ params
 parellelization
 pc
 perl
+personList
 phangorn
 phylo
 Phylocom
@@ -162,6 +166,7 @@ reprex
 rmarkdown
 roclet
 roclets
+ropensci
 Rosauer
 Roxygen
 roxygen
@@ -194,6 +199,7 @@ Sublicensing
 sudo
 SystemRequirements
 testthat
+textVersion
 tibble
 tictoc
 tidyverse

vignettes/canape.Rmd

@@ -70,10 +70,10 @@ The main purpose of `canaper` is to perform these randomization tests.
 
 `canaper` generates random communities using the [`vegan` package](https://CRAN.R-project.org/package=vegan). There are a large number of pre-defined randomization algorithms available in `vegan`^[`r length(unique(vegan::make.commsim()))` as of `vegan` v`r as.character(packageVersion("vegan"))`, though not all may be applicable.], as well as an option to provide a user-defined algorithm. Selecting the appropriate algorithm is not trivial, and can greatly influence results^[For a good review of randomization algorithms and their implications for analysis results, see @Strona2018]. For details about the pre-defined algorithms, see `vegan::commsim()`.
 
-This example also demonstrates one of the strengths of `canaper`: the ability to run randomizations in parallel^[For more information on how and when to use parallel computing in `canaper`, [see the "Parallel computing" vignette](https://joelnitta.github.io/canaper/articles/parallel.html)]. 
+This example also demonstrates one of the strengths of `canaper`: the ability to run randomizations in parallel^[For more information on how and when to use parallel computing in `canaper`, [see the "Parallel computing" vignette](https://docs.ropensci.org/canaper/articles/parallel.html)]. 
 This is by far the most time-consuming part of CANAPE, since we have to repeat the calculations many (e.g., hundreds or more) times across the randomized communities to obtain reliable results. Here, we set the number of iterations (`n_iterations`; i.e., the number of swaps used to produce each randomized community) fairly high because this community matrix is large and includes many zeros; thorough mixing by swapping many times is required to completely randomize the matrix. 
 
-We will use a low number of random communities (`n_reps`) so things finish relatively quickly; you should consider increasing `n_reps` for a "real" analysis^[For more information on setting the appropriate number of iterations and replicates, [see the "How many randomizations?" vignette](https://joelnitta.github.io/canaper/articles/how-many-rand.html).].
+We will use a low number of random communities (`n_reps`) so things finish relatively quickly; you should consider increasing `n_reps` for a "real" analysis^[For more information on setting the appropriate number of iterations and replicates, [see the "How many randomizations?" vignette](https://docs.ropensci.org/canaper/articles/how-many-rand.html).].
 We will use the `curveball` randomization algorithm, which maintains species richness and abundance patterns while randomizing species identity [@Strona2014]^[`curveball` is similar to `swap` but runs much faster so I chose it for this large dataset.].
 
 ```{r acacia-rand}