├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── rhub.yaml │ └── test-coverage.yaml ├── .gitignore ├── CONTRIBUTING.md ├── DESCRIPTION ├── LICENSE.md ├── NAMESPACE ├── NEWS.md ├── R ├── GBIFLogin.R ├── GBIFLoginManager.R ├── GBIFtableCleanup.R ├── data.R ├── gbifRetriever.R ├── getBIENpoints.R ├── getGBIFpoints.R ├── occCitation.R ├── occCiteCitation.R ├── occCiteData.R ├── occCitePrint.R ├── occCite_plotting.R ├── occQuery.R ├── occSum.R ├── prevGBIFdownload.R ├── studyTaxonList.R ├── tabGBIF.R └── taxonRectification.R ├── README.md ├── _config.yml ├── _pkgdown.yml ├── codecov.yaml ├── codemeta.json ├── cran-comments.md ├── data └── myOccCiteObject.rda ├── docs ├── 404.html ├── CONTRIBUTING.html ├── LICENSE.html ├── apple-touch-icon-120x120.png ├── apple-touch-icon-152x152.png ├── apple-touch-icon-180x180.png ├── apple-touch-icon-60x60.png ├── apple-touch-icon-76x76.png ├── apple-touch-icon.png ├── articles │ ├── a_Simple.html │ ├── a_Simple_files │ │ └── figure-html │ │ │ ├── plotting a simple search-1.png │ │ │ ├── plotting a simple search-2.png │ │ │ └── plotting a simple search-3.png │ ├── b_Advanced.html │ ├── b_Advanced_files │ │ └── figure-html │ │ │ ├── plotting all species-1.png │ │ │ ├── plotting all species-2.png │ │ │ ├── plotting all species-3.png │ │ │ ├── plotting phylogenetic search by species-1.png │ │ │ ├── plotting phylogenetic search by species-2.png │ │ │ ├── plotting phylogenetic search by species-3.png │ │ │ ├── plotting phylogenetic search by species-4.png │ │ │ ├── plotting phylogenetic search by species-5.png │ │ │ └── plotting phylogenetic search by species-6.png │ └── index.html ├── authors.html ├── deps │ ├── bootstrap-5.3.1 │ │ ├── bootstrap.bundle.min.js │ │ ├── bootstrap.bundle.min.js.map │ │ └── bootstrap.min.css │ ├── bootstrap-toc-1.0.1 │ │ └── bootstrap-toc.min.js │ ├── clipboard.js-2.0.11 │ │ └── clipboard.min.js │ ├── data-deps.txt │ ├── font-awesome-6.5.2 │ │ ├── css │ │ │ ├── all.css │ │ │ ├── all.min.css │ │ │ ├── v4-shims.css │ │ │ └── v4-shims.min.css │ │ └── webfonts │ │ │ ├── fa-brands-400.ttf │ │ │ ├── fa-brands-400.woff2 │ │ │ ├── fa-regular-400.ttf │ │ │ ├── fa-regular-400.woff2 │ │ │ ├── fa-solid-900.ttf │ │ │ ├── fa-solid-900.woff2 │ │ │ ├── fa-v4compatibility.ttf │ │ │ └── fa-v4compatibility.woff2 │ ├── headroom-0.11.0 │ │ ├── headroom.min.js │ │ └── jQuery.headroom.min.js │ ├── jquery-3.6.0 │ │ ├── jquery-3.6.0.js │ │ ├── jquery-3.6.0.min.js │ │ └── jquery-3.6.0.min.map │ └── search-1.0.0 │ │ ├── autocomplete.jquery.min.js │ │ ├── fuse.min.js │ │ └── mark.min.js ├── favicon-16x16.png ├── favicon-32x32.png ├── favicon.ico ├── index.html ├── katex-auto.js ├── lightswitch.js ├── link.svg ├── logo.png ├── news │ └── index.html ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── GBIFLogin-class.html │ ├── GBIFLogin.html │ ├── GBIFLoginManager.html │ ├── figures │ │ ├── logo.png │ │ ├── occHex.ai │ │ ├── occHex.png │ │ └── occTag.png │ ├── getBIENpoints.html │ ├── getGBIFpoints.html │ ├── index.html │ ├── myOccCiteObject.html │ ├── occCitation.html │ ├── occCiteCitation-class.html │ ├── occCiteCitation.html │ ├── occCiteData-class.html │ ├── occCiteData.html │ ├── occCiteMap.html │ ├── occQuery.html │ ├── plot.occCiteData-1.png │ ├── plot.occCiteData-2.png │ ├── plot.occCiteData-3.png │ ├── plot.occCiteData.html │ ├── prevGBIFdownload.html │ ├── print.occCiteCitation.html │ ├── studyTaxonList.html │ ├── summary.occCiteData.html │ └── taxonRectification.html ├── search.json └── sitemap.xml ├── inst ├── CITATION └── extdata │ ├── 0169441-210914110416597.zip │ ├── Fish_12Tax_time_calibrated.tre │ ├── Protea_cynaroides │ └── 0169441-210914110416597.zip │ ├── Tetrapturus_angustirostris │ └── 0006577-190621201848488.zip │ ├── Tetrapturus_belone │ └── 0006578-190621201848488.zip │ └── Tetrapturus_pfluegeri │ └── 0006585-190621201848488.zip ├── man ├── GBIFLogin-class.Rd ├── GBIFLoginManager.Rd ├── figures │ ├── logo.png │ ├── occHex.ai │ ├── occHex.png │ └── occTag.png ├── getBIENpoints.Rd ├── getGBIFpoints.Rd ├── myOccCiteObject.Rd ├── occCitation.Rd ├── occCiteCitation-class.Rd ├── occCiteData-class.Rd ├── occCiteMap.Rd ├── occQuery.Rd ├── plot.occCiteData.Rd ├── prevGBIFdownload.Rd ├── print.occCiteCitation.Rd ├── studyTaxonList.Rd ├── summary.occCiteData.Rd └── taxonRectification.Rd ├── occCite.Rproj ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── apple-touch-icon.png │ ├── favicon-16x16.png │ ├── favicon-32x32.png │ └── favicon.ico ├── tests ├── testthat.R └── testthat │ ├── test-GBIFLoginManager.R │ ├── test-GBIFtableCleanup.R │ ├── test-gbifRetriever.R │ ├── test-getBIENpoints.R │ ├── test-getGBIFpoints.R │ ├── test-map.R │ ├── test-occCitation.R │ ├── test-occCitePrint.R │ ├── test-occSum.R │ ├── test-prevGBIFdownload.R │ ├── test-studyTaxonList.R │ 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