diff --git a/NEWS.md b/NEWS.md index c2f78b0f..8eafc987 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,17 +1,22 @@ taxize 0.9.99 ============= +### DEFUNCT + +* `tnrs()` and `tnrs_sources()` functions are defunct. The service has been unreliable for years now, and AFAICT is down for good. Associated changes have been made throughout the package, eg. `resolve()` no longer has an option for tnrs, etc. (#841) (#842) + ### MINOR IMPROVEMENTS -* asdadf (#xxx) -* asdadf (#xxx) -* asdadf (#xxx) +* new article/vignette added on issues with taxonomic ranks, e.g., "NCBI is weird", and how rank information is maintained and used within taxize (#852) +* vignettes are no longer on cran - find them at the docs site linked in DESCRIPTION (#855) +* re-instate a `tol_resolve()` test following new version of `rotl` package on cran (#816) +* improve `class2tree()` function documentation regarding how the function works in more detail (#849) (#851) +* improvements for WORMS, applies to functions `worms_downstream()`, `children(..., db="worms")` and `downstream(..., db="worms")`: now paginate automatically for the user to get all results, and allow parameter `marine_only` to be passed through the high level functions `children()`/`downstream()` down to `worrms::wm_children()` where it toggles whether marine only results are returned (#848) thanks @oharac ! ### BUG FIXES -* asdadf (#xxx) -* asdadf (#xxx) -* asdadf (#xxx) +* fix to `ncbi_downstream()` (which cascades up to `downstream(..., db="ncbi")`): an unneeded line of code was removed that was also throwing an error in some cases (#850) +* fixes for WORMS ranks, applies to functions `worms_downstream()`, `children(..., db="worms")` and `downstream(..., db="worms")`: added ranks `epifamily` and `infraphylum`. In addition, when a rank is missing in data returned from WORMS, we'll change the missing rank to "no rank" (#847) taxize 0.9.98 diff --git a/codemeta.json b/codemeta.json index f5e1d8fb..54d63f80 100644 --- a/codemeta.json +++ b/codemeta.json @@ -10,13 +10,13 @@ "codeRepository": "https://github.com/ropensci/taxize", "issueTracker": "https://github.com/ropensci/taxize/issues", "license": "https://spdx.org/licenses/MIT", - "version": "0.9.98", + "version": "0.9.99", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.0.2 Patched (2020-09-01 r79114)", + "runtimePlatform": "R version 4.0.3 (2020-10-10)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -131,30 +131,6 @@ }, "sameAs": "https://CRAN.R-project.org/package=testthat" }, - { - "@type": "SoftwareApplication", - "identifier": "knitr", - "name": "knitr", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=knitr" - }, - { - "@type": "SoftwareApplication", - "identifier": "rmarkdown", - "name": "rmarkdown", - "provider": { - "@id": "https://cran.r-project.org", - "@type": "Organization", - "name": "Comprehensive R Archive Network (CRAN)", - "url": "https://cran.r-project.org" - }, - "sameAs": "https://CRAN.R-project.org/package=rmarkdown" - }, { "@type": "SoftwareApplication", "identifier": "vegan", @@ -323,7 +299,6 @@ "@type": "SoftwareApplication", "identifier": "rredlist", "name": "rredlist", - "version": ">= 0.5.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -477,7 +452,7 @@ } ], "name": "taxize - taxonomic search and retrieval in R", - "url": "https://f1000research.com/articles/2-191/v2/", + "url": "https://f1000research.com/articles/2-191/v2", "isPartOf": { "@type": "PublicationIssue", "datePublished": "2013", diff --git a/cran-comments.md b/cran-comments.md index 0d1b62c0..bc461ac9 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -14,7 +14,7 @@ ------ -This version xxx. +This version makes a few functions defunct for a web service that is no longer up, improves some docs, and fixes a few bugs. In addition, this fixes a failing test due to the latest rredlist on CRAN (an import here). Thanks! Scott Chamberlain