diff --git a/DESCRIPTION b/DESCRIPTION index a099c3a..9e1fbc3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,15 +1,16 @@ Package: traitdataform Type: Package Title: Formatting and Harmonizing Ecological Trait-Data -Version: 0.5.7 -Date: 2020-03-11 +Version: 0.6.0 +Date: 2020-10-18 Authors@R: c(person("Florian D.", "Schneider",, "florian.dirk.schneider@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1494-5684")), person("Caterina", "Penone", role = c("ctb"), comment = c(ORCID = "0000-0002-8170-6659")), person("Andreas", "Ostrowski", role = c("ctb"), comment = c(ORCID = "0000-0002-2033-779X")), person("Dennis", "Heimann", role = c("ctb")), person("Felix","Neff", role = c("ctb")), - person("Markus J.", "Ankenbrand", role = c("ctb"))) + person("Markus J.", "Ankenbrand", role = c("ctb")), + person("Jessica", "Burnett", role = c("ctb"))) Description: Assistance for handling ecological trait data and applying the Ecological Trait-Data Standard terminology (Schneider et al. 2019 ). There are two major use cases: (1) preparation of @@ -21,7 +22,8 @@ LazyData: TRUE Depends: R (>= 2.10) Imports: - data.table, + data.table, + stats, reshape2, taxize, getPass, @@ -29,10 +31,10 @@ Imports: XML, RCurl, plyr -URL: https://EcologicalTraitData.github.io/traitdataform, https://github.com/EcologicalTraitData/traitdataform -BugReports: https://github.com/EcologicalTraitData/traitdataform/issues +URL: https://ecologicaltraitdata.github.io/traitdataform/, https://github.com/ecologicaltraitdata/traitdataform +BugReports: https://github.com/ecologicaltraitdata/traitdataform/issues VignetteBuilder: knitr -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.1 Encoding: UTF-8 Roxygen: list(markdown = TRUE) Suggests: diff --git a/NEWS.md b/NEWS.md index c8f2fe4..cf82455 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,15 @@ +# traitdataform 0.6.0 + +Major changes: + +- update internal terms to v0.10 of the Ecological Trait-data Standard (ETS). + In ETS v0.10 the assignment of user-defined and standardised measurement values and trait and taxon assignments has been updated, to match labelling practice in DwC and provide a more intuitive content for those fields. Accordingly + - the v0.9.1 terms `scientificName`, `traitName`, `traitValue`, and `traitUnit` have been renamed into `verbatimScientificName`, `verbatimTraitName`, `verbatimTraitValue`, and `verbatimTraitUnit` with new identifiers. + - the terms `scientificNameStd`, `traitNameStd`, `traitValueStd`, and `traitUnitStd` have been renamed into `scientificName`, `traitName`, `traitValue`, and `traitUnit` and now form the default suggested content for trait data complying with the ETS. Definitions have been harmonized. The original *Std identifiers now resolve to these new terms. + + This causes the output file to differ from earlier outputs. To maintain compatibility with earlier versions, an option `conformsTo` has been added to `as.traitdata()` to return the data table in terms of version 0.9. By default, output is returned in ETS version 0.10. Data releases created by `traitdataform` should always be labelled with the version of ETS that applies to the data! + + # traitdataform 0.5.7 - Preparing for R 4.0.0 change to read.table() and data.frame(): handling of factor data (trait and taxon names) is now locale-independent diff --git a/README.md b/README.md index ea650f9..a6e0081 100644 --- a/README.md +++ b/README.md @@ -107,7 +107,7 @@ We are aiming to provide the following features in future iterations of the pack ## Cite as -Schneider, F.D. (2020) traitdataform - harmonizing ecological trait data in R, v0.5.7, DOI: [10.5281/zenodo.1489527](http://dx.doi.org/10.5281/zenodo.1489527) http://ecologicaltraitdata.github.io/traitdataform +Schneider, F.D. (2020) traitdataform - harmonizing ecological trait data in R, v0.6.0, DOI: [10.5281/zenodo.1489527](http://dx.doi.org/10.5281/zenodo.1489527) http://ecologicaltraitdata.github.io/traitdataform ## License diff --git a/codemeta.json b/codemeta.json index 6b4f840..8761c86 100644 --- a/codemeta.json +++ b/codemeta.json @@ -7,23 +7,23 @@ "identifier": "traitdataform", "description": "Assistance for handling ecological trait data and applying the \n Ecological Trait-Data Standard terminology (Schneider et al. 2019\n ). There are two major use cases: (1) preparation of\n own trait datasets for upload into public data bases, and (2) harmonizing\n trait datasets from different sources by re-formatting them into a unified\n format. See 'traitdataform' website for full documentation. ", "name": "traitdataform: Formatting and Harmonizing Ecological Trait-Data", - "codeRepository": "https://github.com/EcologicalTraitData/traitdataform", + "codeRepository": "https://github.com/ecologicaltraitdata/traitdataform", "relatedLink": [ "http://fdschneider.github.io/traitdataform", "http://EcologicalTraitData.github.io/traitdataform", "https://EcologicalTraitData.github.io/traitdataform", - "https://CRAN.R-project.org/package=traitdataform" + "https://CRAN.R-project.org/package=traitdataform", + "https://ecologicaltraitdata.github.io/traitdataform/" ], - "issueTracker": "https://github.com/EcologicalTraitData/traitdataform/issues", + "issueTracker": "https://github.com/ecologicaltraitdata/traitdataform/issues", "license": "https://spdx.org/licenses/MIT", - "version": "0.5.7", + "version": "0.6.0", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", - "version": "3.6.3", "url": "https://r-project.org" }, - "runtimePlatform": "R version 3.6.3 (2020-02-29)", + "runtimePlatform": "R version 4.0.3 (2020-10-10)", "author": [ { "@type": "Person", @@ -60,6 +60,11 @@ "@type": "Person", "givenName": "Markus J.", "familyName": "Ankenbrand" + }, + { + "@type": "Person", + "givenName": "Jessica", + "familyName": "Burnett" } ], "maintainer": [ @@ -128,6 +133,11 @@ }, "sameAs": "https://CRAN.R-project.org/package=data.table" }, + { + "@type": "SoftwareApplication", + "identifier": "stats", + "name": "stats" + }, { "@type": "SoftwareApplication", "identifier": "reshape2", @@ -213,7 +223,7 @@ "sameAs": "https://CRAN.R-project.org/package=plyr" } ], - "releaseNotes": "https://github.com/EcologicalTraitData/traitdataform/blob/master/NEWS.md", + "releaseNotes": "https://github.com/ecologicaltraitdata/traitdataform/blob/master/NEWS.md", "readme": "https://github.com/EcologicalTraitData/traitdataform/blob/master/README.md", "contIntegration": "https://travis-ci.com/EcologicalTraitData/traitdataform", "keywords": [ @@ -223,7 +233,7 @@ "r-package", "ecology" ], - "developmentStatus": "https://www.repostatus.org/#wip", + "developmentStatus": ["https://www.tidyverse.org/lifecycle/#stable", "https://www.repostatus.org/#active"], "citation": [ { "@type": "SoftwareSourceCode", @@ -238,7 +248,7 @@ "url": "https://ecologicaltraitdata.github.io/traitdataform/" } ], - "fileSize": "284.578KB", + "fileSize": "2246.709KB", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", diff --git a/cran-comments.md b/cran-comments.md index d2da1e5..9e8d2b3 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,13 +1,14 @@ ## Resubmission -Preparing package for R 4.0.0 by suppressing stringsAsFactor conversion in read.table() and data.frame(). +Updating internal terminology according to a change in the Ecological Trait-data Standard (ETS). ## Test environments -* local Windows 10 install, R version 3.6.3 (2020-04-04) -* Windows R devel (4.0.0) on win-builder.r-project.org, platform: x86_64-w64-mingw32 (64-bit), R version 3.6.3 (2020-04-04) -* Mac OS X 10.13.6 (on travis-ci), R version 3.6.2 (2020-04-04) -* Ubuntu 16.04.6 LTS (on travis-ci), R version 3.6.2 (2020-04-04) and R devel (4.0.0) (2020-04-04) +* local Windows 10 install, R version 4.0.3 (2020-10-21) +* macOS High Sierra 10.13.6 , R version 4.0.2 (2020-10-19) on travis-ci +* Ubuntu 16.04.6 LTS R version 4.0.2 (2020-10-19) and R devel (2020-10-19) on travis-ci +* Windows Server 2008 R2 SP1, R-devel, 32/64 bit (2020-10-21) on R-hub +* Debian Linux, R-devel (2020-10-17 r79346), clang, ISO-8859-15 locale on R-hub (2020-10-21) ## R CMD check results