diff --git a/.Rbuildignore b/.Rbuildignore index 8d19f04..60ac4ee 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,8 +12,6 @@ ^CONDUCT.md ^record* ^\.httr-oauth -^inst/assets/ -^inst/tmp/ ^\.github/ ^\.Renviron ^paper.bib diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index b86a0e2..bf14f56 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -14,11 +14,11 @@ * Fork this repo to your Github account * Clone your version on your account down to your machine from your account, e.g,. `git clone https://github.com//rcites.git` -* Make sure to track progress upstream (i.e., on our version of `rcites` at `ibartomeus/rcites`) by doing `git remote add upstream https://github.com/ibartomeus/rcites.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step +* Make sure to track progress upstream (i.e., on our version of `rcites` at `ropensci/rcites`) by doing `git remote add upstream https://github.com/ropensci/rcites.git`. Before making changes make sure to pull changes in from upstream by doing either `git fetch upstream` then merge later or `git pull upstream` to fetch and merge in one step * Make your changes (bonus points for making changes on a new feature branch) * Please do write a test(s) for your changes if they affect code and not just docs (see Tests below) * Push up to your account -* Submit a pull request to home base at `ibartomeus/rcites` +* Submit a pull request to home base at `ropensci/rcites` ### Tests diff --git a/.github/issue_template.md b/.github/issue_template.md index ec4d9da..dcb9656 100644 --- a/.github/issue_template.md +++ b/.github/issue_template.md @@ -1,4 +1,8 @@ - +
Session Info diff --git a/.travis.yml b/.travis.yml index b0574c8..41ea28c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -12,6 +12,9 @@ matrix: - os: linux r: release env: NOT_CRAN=true + - os: osx + r: release + env: NOT_CRAN=true - os: linux r: devel env: NOT_CRAN=false diff --git a/DESCRIPTION b/DESCRIPTION index dae40e2..eb1c630 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: rcites Type: Package Title: R Interface to the Species+ Database -Version: 0.1.0.9000 +Version: 0.1.0 Authors@R: c(person("Jonas", "Geschke", role = c("aut"), email = "jonas.e.geschke@gmail.com", comment = c(ORCID = "0000-0002-5654-9313")), person("Kevin", "Cazelles", role = c("aut", "cre"), email = "kevin.cazelles@gmail.com", comment = c(ORCID = "0000-0001-6619-9874")), person("Ignasi", "Bartomeus", role = c("aut"), comment = c(ORCID = "0000-0001-7893-4389")), @@ -11,8 +11,8 @@ Authors@R: c(person("Jonas", "Geschke", role = c("aut"), email = "jonas.e.geschk person("Noam", "Ross", role = c("rev")), person("Margaret", "Siple", role = c("rev"))) Description: A programmatic interface to the Species+ database via the Species+/CITES Checklist API . -URL: https://ibartomeus.github.io/rcites/, https://github.com/ibartomeus/rcites -BugReports: https://github.com/ibartomeus/rcites/issues +URL: https://ropensci.github.io/rcites/, https://github.com/ropensci/rcites +BugReports: https://github.com/ropensci/rcites/issues License: MIT + file LICENSE Depends: R (>= 3.1.0) diff --git a/NEWS.md b/NEWS.md index c30391a..94dc0dc 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,11 +1,13 @@ -# rcites 0.1.1.9000 +# rcites 1.0.0.9000 + +# rcites 1.0.0 - new features: - `spp_taxonconcept()` now includes an auto-pagination that allows to retrieve all entries for queries that have more than 500 results; - `spp_taxonconcept()`, `spp_eu_legislation()`, `spp_cites_legislation()` and `spp_references()` now supports vectors as `taxon_id` argument which allows - bulk analysis. + bulk analysis. - Functions `spp_*` now returns S3 objects: - `spp_taxonconcept()` returns an object of class `spp_taxon`; - `spp_cites_legislation()` returns an object of class `spp_cites_leg` or `spp_cites_leg_multi`; diff --git a/README.md b/README.md index e7c2c35..ad57e86 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,8 @@ ### Current Status [![Build status](https://travis-ci.org/ropensci/rcites.svg?branch=master)](https://travis-ci.org/ropensci/rcites) -[![Build status](https://ci.appveyor.com/api/projects/status/bsd3c7mv12xv959j/branch/master?svg=true)](https://ci.appveyor.com/project/KevCaz/rcites/branch/master) +[![Build status](https://ci.appveyor.com/api/projects/status/kgimo4v7rvtpkp5e?svg=true)](https://ci.appveyor.com/project/KevCaz/rcites-mo3vb) [![codecov](https://codecov.io/gh/ropensci/rcites/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/rcites) -[![Coverage Status](https://coveralls.io/repos/github/ropensci/rcites/badge.svg?branch=master)](https://coveralls.io/github/ropensci/rcites?branch=master) [![ROpenSci status](https://badges.ropensci.org/244_status.svg)](https://github.com/ropensci/onboarding/issues/244) [![CRAN status](https://www.r-pkg.org/badges/version/rcites)](https://www.r-pkg.org/badges/version/rcites) [![CRAN downloads](https://cranlogs.r-pkg.org/badges/grand-total/rcites)](https://cran.r-project.org/package=rcites) @@ -13,7 +12,7 @@ # rcites -An R package to access information from the [Speciesplus](https://speciesplus.net/) database via the [Species+/CITES Checklist API](https://api.speciesplus.net/documentation/v1.html). The package is available for download from [CRAN](https://cran.r-project.org/package=rcites) (stable version) and [Github](https://github.com/ibartomeus/rcites) (development version). +An R package to access information from the [Speciesplus](https://speciesplus.net/) database via the [Species+/CITES Checklist API](https://api.speciesplus.net/documentation/v1.html). The package is available for download from [CRAN](https://cran.r-project.org/package=rcites) (stable version) and [Github](https://github.com/ropensci/rcites) (development version). Please see the [release paper](link to come) for background information about the Convention on International Trade in Endangered Species of Wild Fauna and Flora ([CITES](https://cites.org)), the Species+ database and basic information about the aim of the package. @@ -30,7 +29,7 @@ library("rcites") The development version can be installed via the `devtools` package: ```R -devtools::install_github("ibartomeus/rcites") +devtools::install_github("ropensci/rcites") library("rcites") ``` @@ -39,12 +38,12 @@ library("rcites") To set up a connection to the CITES Species+ database, a personal authentication token is required. Please see the vignette for details how to get a token and -how to set the token for package use: [Get started with rcites](https://ibartomeus.github.io/rcites/articles/get_started.html) +how to set the token for package use: [Get started with rcites](https://ropensci.github.io/rcites/articles/get_started.html) Additional information about specific use examples are provided for the -[African bush elephant (*Loxodonta africana*)](https://ibartomeus.github.io/rcites/articles/elephant.html). +[African bush elephant (*Loxodonta africana*)](https://ropensci.github.io/rcites/articles/elephant.html). The package usage for querying multiple species is described in another -vignette entitled ['Bulk analysis with rcites'](https://ibartomeus.github.io/rcites/articles/bulk_analysis.html). +vignette entitled ['Bulk analysis with rcites'](https://ropensci.github.io/rcites/articles/bulk_analysis.html). ### Key features @@ -69,13 +68,13 @@ The package functions have three different prefixes: ### Citation information -When citing, please refer to both the [package citation](https://ibartomeus.github.io/rcites/authors.html). +When citing, please refer to both the [package citation](https://ropensci.github.io/rcites/authors.html). ## Contributors -- [Main contributors](https://github.com/ibartomeus/rcites/graphs/contributors) +- [Main contributors](https://github.com/ropensci/rcites/graphs/contributors) - Reviewers of the package: - [Noam Ross](https://github.com/noamross) diff --git a/_pkgdown.yml b/_pkgdown.yml index 496999b..89cef01 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -7,3 +7,5 @@ authors: href: https://kevcaz.github.io/ Ignasi Bartomeus: href: https://bartomeuslab.com/ + Jonas Geschke: + href: https://www.linkedin.com/in/jonasgeschke/?originalSubdomain=de diff --git a/docs/CONDUCT.html b/docs/CONDUCT.html index 34a2242..47ff200 100644 --- a/docs/CONDUCT.html +++ b/docs/CONDUCT.html @@ -58,7 +58,7 @@ rcites - 0.1.0.9000 + 0.1.0 @@ -98,7 +98,7 @@
  • - + @@ -135,7 +135,7 @@

    Contributor Code of Conduct