`, etc.) that has more than one element. Defaults to 1 (for ``).
+ getTopLevel: function($scope) {
+ for (var i = 1; i <= 6; i++) {
+ var $headings = this.findOrFilter($scope, 'h' + i);
+ if ($headings.length > 1) {
+ return i;
+ }
+ }
+
+ return 1;
+ },
+
+ // returns the elements for the top level, and the next below it
+ getHeadings: function($scope, topLevel) {
+ var topSelector = 'h' + topLevel;
+
+ var secondaryLevel = topLevel + 1;
+ var secondarySelector = 'h' + secondaryLevel;
+
+ return this.findOrFilter($scope, topSelector + ',' + secondarySelector);
+ },
+
+ getNavLevel: function(el) {
+ return parseInt(el.tagName.charAt(1), 10);
+ },
+
+ populateNav: function($topContext, topLevel, $headings) {
+ var $context = $topContext;
+ var $prevNav;
+
+ var helpers = this;
+ $headings.each(function(i, el) {
+ var $newNav = helpers.generateNavItem(el);
+ var navLevel = helpers.getNavLevel(el);
+
+ // determine the proper $context
+ if (navLevel === topLevel) {
+ // use top level
+ $context = $topContext;
+ } else if ($prevNav && $context === $topContext) {
+ // create a new level of the tree and switch to it
+ $context = helpers.createChildNavList($prevNav);
+ } // else use the current $context
+
+ $context.append($newNav);
+
+ $prevNav = $newNav;
+ });
+ },
+
+ parseOps: function(arg) {
+ var opts;
+ if (arg.jquery) {
+ opts = {
+ $nav: arg
+ };
+ } else {
+ opts = arg;
+ }
+ opts.$scope = opts.$scope || $(document.body);
+ return opts;
+ }
+ },
+
+ // accepts a jQuery object, or an options object
+ init: function(opts) {
+ opts = this.helpers.parseOps(opts);
+
+ // ensure that the data attribute is in place for styling
+ opts.$nav.attr('data-toggle', 'toc');
+
+ var $topContext = this.helpers.createChildNavList(opts.$nav);
+ var topLevel = this.helpers.getTopLevel(opts.$scope);
+ var $headings = this.helpers.getHeadings(opts.$scope, topLevel);
+ this.helpers.populateNav($topContext, topLevel, $headings);
+ }
+ };
+
+ $(function() {
+ $('nav[data-toggle="toc"]').each(function(i, el) {
+ var $nav = $(el);
+ Toc.init($nav);
+ });
+ });
+})();
diff --git a/docs/docsearch.css b/docs/docsearch.css
new file mode 100644
index 0000000..e5f1fe1
--- /dev/null
+++ b/docs/docsearch.css
@@ -0,0 +1,148 @@
+/* Docsearch -------------------------------------------------------------- */
+/*
+ Source: https://github.com/algolia/docsearch/
+ License: MIT
+*/
+
+.algolia-autocomplete {
+ display: block;
+ -webkit-box-flex: 1;
+ -ms-flex: 1;
+ flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+ width: 100%;
+ min-width: none;
+ max-width: none;
+ padding: .75rem 0;
+ background-color: #fff;
+ background-clip: padding-box;
+ border: 1px solid rgba(0, 0, 0, .1);
+ box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+ .algolia-autocomplete .ds-dropdown-menu {
+ width: 175%
+ }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+ display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+ padding: 0;
+ background-color: rgb(255,255,255);
+ border: 0;
+ max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+ margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+ padding: 0;
+ overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+ padding: .125rem 1rem;
+ margin-top: 0;
+ font-size: 1.3em;
+ font-weight: 500;
+ color: #00008B;
+ border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+ float: none;
+ padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+ float: none;
+ width: auto;
+ padding: 0;
+ text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+ float: none;
+ width: auto;
+ padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+ display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+ padding-top: .75rem;
+ margin-top: .75rem;
+ border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+ display: block;
+ padding: .1rem 1rem;
+ margin-bottom: 0.1;
+ font-size: 1.0em;
+ font-weight: 400
+ /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+ display: block;
+ padding: .25rem 1rem;
+ margin-bottom: 0;
+ font-size: 0.9em;
+ font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+ padding: 0 1rem .5rem;
+ margin-top: -.25rem;
+ font-size: 0.8em;
+ font-weight: 400;
+ line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+ width: 110px;
+ height: 20px;
+ z-index: 3;
+ margin-top: 10.66667px;
+ float: right;
+ font-size: 0;
+ line-height: 0;
+}
+
+.algolia-autocomplete .algolia-docsearch-footer--logo {
+ background-image: url("data:image/svg+xml;utf8,");
+ background-repeat: no-repeat;
+ background-position: 50%;
+ background-size: 100%;
+ overflow: hidden;
+ text-indent: -9000px;
+ width: 100%;
+ height: 100%;
+ display: block;
+ transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+ color: #FF8C00;
+ background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+ box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+ background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docs/docsearch.js b/docs/docsearch.js
new file mode 100644
index 0000000..b35504c
--- /dev/null
+++ b/docs/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+ // register a handler to move the focus to the search bar
+ // upon pressing shift + "/" (i.e. "?")
+ $(document).on('keydown', function(e) {
+ if (e.shiftKey && e.keyCode == 191) {
+ e.preventDefault();
+ $("#search-input").focus();
+ }
+ });
+
+ $(document).ready(function() {
+ // do keyword highlighting
+ /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+ var mark = function() {
+
+ var referrer = document.URL ;
+ var paramKey = "q" ;
+
+ if (referrer.indexOf("?") !== -1) {
+ var qs = referrer.substr(referrer.indexOf('?') + 1);
+ var qs_noanchor = qs.split('#')[0];
+ var qsa = qs_noanchor.split('&');
+ var keyword = "";
+
+ for (var i = 0; i < qsa.length; i++) {
+ var currentParam = qsa[i].split('=');
+
+ if (currentParam.length !== 2) {
+ continue;
+ }
+
+ if (currentParam[0] == paramKey) {
+ keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+ }
+ }
+
+ if (keyword !== "") {
+ $(".contents").unmark({
+ done: function() {
+ $(".contents").mark(keyword);
+ }
+ });
+ }
+ }
+ };
+
+ mark();
+ });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+ var words = [];
+
+ var hierarchy = hit._highlightResult.hierarchy;
+ // loop to fetch from lvl0, lvl1, etc.
+ for (var idx in hierarchy) {
+ words = words.concat(hierarchy[idx].matchedWords);
+ }
+
+ var content = hit._highlightResult.content;
+ if (content) {
+ words = words.concat(content.matchedWords);
+ }
+
+ // return unique words
+ var words_uniq = [...new Set(words)];
+ return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+ var words = matchedWords(hit);
+ var url = "";
+
+ if (hit.anchor) {
+ url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+ } else {
+ url = hit.url + '?q=' + escape(words.join(" "));
+ }
+
+ return url;
+}
diff --git a/docs/favicon-16x16.png b/docs/favicon-16x16.png
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diff --git a/docs/favicon.ico b/docs/favicon.ico
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diff --git a/docs/index.html b/docs/index.html
new file mode 100644
index 0000000..a0fbf8b
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,357 @@
+
+
+
+
+
+
+
+Access to the List of Mammals Species of Colombia • mammalcol
+
+
+
+
+
+
+
+
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+
+
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+
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+
+
+
+The goal of mammalcol is to allow easy access to the List of Mammal Species of Colombia.
+
+Installation
+
+You can install the development version of mammalcol from GitHub with:
+
+# install.packages("devtools")
+devtools::install_github("dlizcano/mammalcol")
+
+
+Example
+
+
+Search database
+
+This is a basic example which shows you how to search mammal names in Colombia using a vector of mammal names.
+
+# define a vector with species to search for
+splist <- c("Tapirus bairdii", "Tapirus pinchaque", "Tapirus terrestris",
+ "Tapirus terrestris", "Pudu mephistophiles", "Tapirus bairdii")
+
+# search in database
+search_mammalcol(splist)
+#> The following names are repeated in the 'splist': Tapirus bairdii, Tapirus terrestris
+#> name_submitted kingdom phylum class order family
+#> 1 Tapirus bairdii Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 2 Tapirus pinchaque Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 3 Tapirus terrestris Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 4 Pudu mephistophiles Animalia Chordata Mammalia Artiodactyla Cervidae
+#> genus specificEpithet taxonRank scientificNameAuthorship
+#> 1 Tapirus bairdii Especie (Gill, 1865)
+#> 2 Tapirus pinchaque Especie (Roulin, 1829)
+#> 3 Tapirus terrestris Especie (Linnaeus, 1758)
+#> 4 Pudu mephistophiles Especie (de Winton, 1896)
+#> taxonRemarks
+#> 1 Elevación (m): 0-1000
+#> 2 Elevación (m): 1400-4000
+#> 3 Elevación (m): 0-2400
+#> 4 Elevación (m): 3000-3500
+#> bibliographicCitation
+#> 1 HERSHKOVITZ P. 1954. Mammals of northern Colombia. Preliminary report No. 7: Tapirs (genus Tapirus), with a systematic review of American species. Proceedings of the United States National Museum 103:465-496.
+#> 2 ARIAS-ALZATE A, CC DOWNER, C DELGADO-V y J SÁNCHEZ-LONDOÑO. 2010. Un registro de tapir de montaña (Tapirus pinchaque) en el norte de la Cordillera Occidental de Colombia. Mastozoología Neotropical 17:111-116.
+#> 3 ARIAS-ALZATE A, JA PALACIO VIEIRA y J MUÑOZ-DURAN. 2009. Nuevos registros de distribución y oferta de hábitat de la danta colombiana (Tapirus terrestris colombianus) en las tierras bajas del norte de la Cordillera Central (Colombia). Mastozoología Neotropical 16:19-25.
+#> 4 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
+#> inMDD Col_redlist
+#> 1 1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
+#> 2 1 EN A4cd
+#> 3 1 VU A4cd
+#> 4 1 EN A2cd B1ab (i; ii; iii; iv; v) \r\n
+#> distribution
+#> 1 Antioquia | Chocó | Córdoba
+#> 2 Antioquia | Cauca | Cundinamarca | Huila | Meta | Nariño | Quindío | Risaralda | Tolima | Valle del Cauca | Caldas | Caquetá | Putumayo
+#> 3 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainia | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
+#> 4 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
+#> source endemic
+#> 1 Proceedings of the United States National Museum 103:465-496 No
+#> 2 Mastozoología Neotropical 17:111-116 No
+#> 3 Mastozoología Neotropical 16:19-25 No
+#> 4 Biota Colombiana 1:43-75 No
+#> english_name Distance
+#> 1 Central American Tapir 12
+#> 2 Mountain Tapir 14
+#> 3 Lowland Tapir 16
+#> 4 Northern Pudu 17
+mammalcol has the ability to correct minor typos and lower case in the genus.
+
+# vector with species names and intentional typos
+splist <- c("Tapiru terrestre", "pudu mephistophiles", "tapirus bairdii")
+
+# search in database
+search_mammalcol(splist)
+#> name_submitted kingdom phylum class order family
+#> 1 Tapiru terrestre Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 2 Pudu mephistophiles Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 3 Tapirus bairdii Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> genus specificEpithet taxonRank scientificNameAuthorship
+#> 1 Tapirus terrestris Especie (Linnaeus, 1758)
+#> 2 Pudu mephistophiles Especie (de Winton, 1896)
+#> 3 Tapirus bairdii Especie (Gill, 1865)
+#> taxonRemarks
+#> 1 Elevación (m): 0-2400
+#> 2 Elevación (m): 3000-3500
+#> 3 Elevación (m): 0-1000
+#> bibliographicCitation
+#> 1 ARIAS-ALZATE A, JA PALACIO VIEIRA y J MUÑOZ-DURAN. 2009. Nuevos registros de distribución y oferta de hábitat de la danta colombiana (Tapirus terrestris colombianus) en las tierras bajas del norte de la Cordillera Central (Colombia). Mastozoología Neotropical 16:19-25.
+#> 2 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
+#> 3 HERSHKOVITZ P. 1954. Mammals of northern Colombia. Preliminary report No. 7: Tapirs (genus Tapirus), with a systematic review of American species. Proceedings of the United States National Museum 103:465-496.
+#> inMDD Col_redlist
+#> 1 1 VU A4cd
+#> 2 1 EN A2cd B1ab (i; ii; iii; iv; v) \r\n
+#> 3 1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
+#> distribution
+#> 1 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainia | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
+#> 2 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
+#> 3 Antioquia | Chocó | Córdoba
+#> source endemic
+#> 1 Mastozoología Neotropical 16:19-25 No
+#> 2 Biota Colombiana 1:43-75 No
+#> 3 Proceedings of the United States National Museum 103:465-496 No
+#> english_name Distance
+#> 1 Lowland Tapir 15
+#> 2 Northern Pudu 17
+#> 3 Central American Tapir 12
+
+
+Produce a map
+
+The function mammalmap produces basic a map of distribution at the “Departamento” level for a single species.
+
+# write a species name in the function to map it
+mammalmap("Tapirus pinchaque")
+
+
+
+See the full taxon table
+
+
+
+head(taxon)
+#> scientificName kingdom phylum class order family
+#> 1 Passalites murelia Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 2 Mazama rufina Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 3 Passalites sanctaemartae Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 4 Mazama temama Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 5 Mazama zamora Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 6 Mazama zetta Animalia Chordata Mammalia Artiodactyla Cervidae
+#> genus specificEpithet taxonRank scientificNameAuthorship
+#> 1 Passalites murelia Especie J. A. Allen, 1915
+#> 2 Mazama rufina Especie (Pucheran, 1851)
+#> 3 Passalites sanctaemartae Especie (J. A. Allen, 1915)
+#> 4 Mazama temama Especie (Kerr, 1792)
+#> 5 Mazama zamora Especie J. A. Allen, 1915
+#> 6 Mazama zetta Especie Thomas, 1913
+#> taxonRemarks
+#> 1 Elevación (m): 0-900
+#> 2 Elevación (m): 1500-4000
+#> 3 Elevación (m): 0-900
+#> 4 Elevación (m): 0-68
+#> 5 Elevación (m): 600-1200
+#> 6 Elevación (m): 1600-1950
+#> bibliographicCitation
+#> 1 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> 2 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
+#> 3 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> 4 GROVES C y P GRUBB. 1987. Relationships of living deer. Pp. 21-59, en: Biology and management of the Cervidae (CM Wemmer, ed.). Smithsonian Institution Press, Washington, D.C., USA.
+#> 5 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> 6 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> inMDD Col_redlist
+#> 1 0 <NA>
+#> 2 1 VU A2 cde\r\n
+#> 3 0 <NA>
+#> 4 1 DD
+#> 5 0 DD
+#> 6 0 DD
+#> distribution
+#> 1 Amazonas | Caquetá | Cauca | Meta | Vaupés | Vichada | Nariño | Putumayo | Cundinamarca
+#> 2 Antioquia | Boyacá | Caldas | Cauca | Cesar | Cundinamarca | Huila | Nariño | Norte de Santander | Quindío | Risaralda | Santander | Tolima | Valle del Cauca | Caquetá
+#> 3 Bolívar | Cesar | La Guajira | Magdalena | Atlántico | Córdoba | Cundinamarca
+#> 4 Chocó | Magdalena
+#> 5 Amazonas | Caquetá | Meta | Putumayo | Vichada
+#> 6 Antioquia | Caldas | Cauca | Nariño | Valle del Cauca | Tolima
+#> source
+#> 1 Bulletin of the American Museum of Natural History 35:191-238
+#> 2 Biota Colombiana 1:43-75
+#> 3 Bulletin of the American Museum of Natural History 35:191-238
+#> 4 Pp. 21-59, en: Biology and management of the Cervidae (CM Wemmer, ed.). Smithsonian Institution Press, Washington, D.C., USA
+#> 5 Bulletin of the American Museum of Natural History 35:191-238
+#> 6 Bulletin of the American Museum of Natural History 35:191-238
+#> endemic english_name
+#> 1 No <NA>
+#> 2 No Little Red Brocket
+#> 3 No <NA>
+#> 4 No Mexican Red Brocket
+#> 5 No <NA>
+#> 6 No <NA>
+
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diff --git a/docs/link.svg b/docs/link.svg
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--- /dev/null
+++ b/docs/link.svg
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+
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diff --git a/docs/logo.png b/docs/logo.png
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diff --git a/docs/news/index.html b/docs/news/index.html
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+++ b/docs/news/index.html
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+
+Changelog • mammalcol
+
+
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+
+ Changelog
+ Source: NEWS.md
+
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diff --git a/docs/pkgdown.css b/docs/pkgdown.css
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index 0000000..80ea5b8
--- /dev/null
+++ b/docs/pkgdown.css
@@ -0,0 +1,384 @@
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+ height: 100%;
+}
+
+body {
+ position: relative;
+}
+
+body > .container {
+ display: flex;
+ height: 100%;
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1 0 auto;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+ flex-shrink: 0;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Ensure in-page images don't run outside their container */
+.contents img {
+ max-width: 100%;
+ height: auto;
+}
+
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
+/* Typographic tweaking ---------------------------------*/
+
+.contents .page-header {
+ margin-top: calc(-60px + 1em);
+}
+
+dd {
+ margin-left: 3em;
+}
+
+/* Section anchors ---------------------------------*/
+
+a.anchor {
+ display: none;
+ margin-left: 5px;
+ width: 20px;
+ height: 20px;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+h1:hover .anchor,
+h2:hover .anchor,
+h3:hover .anchor,
+h4:hover .anchor,
+h5:hover .anchor,
+h6:hover .anchor {
+ display: inline-block;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -40px;
+}
+
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+ position: relative;
+}
+
+.dropdown-submenu>.dropdown-menu {
+ top: 0;
+ left: 100%;
+ margin-top: -6px;
+ margin-left: -1px;
+ border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+ display: block;
+}
+
+.dropdown-submenu>a:after {
+ display: block;
+ content: " ";
+ float: right;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+ border-width: 5px 0 5px 5px;
+ border-left-color: #cccccc;
+ margin-top: 5px;
+ margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+ border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+ float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+ left: -100%;
+ margin-left: 10px;
+ border-radius: 6px 0 6px 6px;
+}
+
+/* Sidebar --------------------------*/
+
+#pkgdown-sidebar {
+ margin-top: 30px;
+ position: -webkit-sticky;
+ position: sticky;
+ top: 70px;
+}
+
+#pkgdown-sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#pkgdown-sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#pkgdown-sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+ padding: 4px 20px 4px 6px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+ padding-left: 5px;
+ color: inherit;
+ border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+ padding-left: 5px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+ border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+ display: none; /* Hide by default, but at >768px, show it */
+ padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+ padding-left: 16px;
+ font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+ padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+ padding-left: 15px;
+ font-weight: 500;
+ font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
+.orcid {
+ font-size: 16px;
+ color: #A6CE39;
+ /* margins are required by official ORCID trademark and display guidelines */
+ margin-left:4px;
+ margin-right:4px;
+ vertical-align: middle;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+
+.ref-index td {vertical-align: top; min-width: 100px}
+.ref-index .icon {width: 40px;}
+.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+pre, code, pre code {
+ background-color: #f8f8f8;
+ color: #333;
+}
+pre, pre code {
+ white-space: pre-wrap;
+ word-break: break-all;
+ overflow-wrap: break-word;
+}
+
+pre {
+ border: 1px solid #eee;
+}
+
+pre .img, pre .r-plt {
+ margin: 5px 0;
+}
+
+pre .img img, pre .r-plt img {
+ background-color: #fff;
+}
+
+code a, pre a {
+ color: #375f84;
+}
+
+a.sourceLine:hover {
+ text-decoration: none;
+}
+
+.fl {color: #1514b5;}
+.fu {color: #000000;} /* function */
+.ch,.st {color: #036a07;} /* string */
+.kw {color: #264D66;} /* keyword */
+.co {color: #888888;} /* comment */
+
+.error {font-weight: bolder;}
+.warning {font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+/* headroom.js ------------------------ */
+
+.headroom {
+ will-change: transform;
+ transition: transform 200ms linear;
+}
+.headroom--pinned {
+ transform: translateY(0%);
+}
+.headroom--unpinned {
+ transform: translateY(-100%);
+}
+
+/* mark.js ----------------------------*/
+
+mark {
+ background-color: rgba(255, 255, 51, 0.5);
+ border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+ padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+ margin-bottom: 10px;
+}
+
+/* fontawesome ------------------------ */
+
+.fab {
+ font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+ code a:link:after, code a:visited:after {
+ content: "";
+ }
+}
+
+/* Section anchors ---------------------------------
+ Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
+*/
+
+div.csl-bib-body { }
+div.csl-entry {
+ clear: both;
+}
+.hanging-indent div.csl-entry {
+ margin-left:2em;
+ text-indent:-2em;
+}
+div.csl-left-margin {
+ min-width:2em;
+ float:left;
+}
+div.csl-right-inline {
+ margin-left:2em;
+ padding-left:1em;
+}
+div.csl-indent {
+ margin-left: 2em;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
new file mode 100644
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--- /dev/null
+++ b/docs/pkgdown.js
@@ -0,0 +1,108 @@
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+ $(function() {
+
+ $('.navbar-fixed-top').headroom();
+
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ $(window).resize(function(){
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ });
+
+ $('[data-toggle="tooltip"]').tooltip();
+
+ var cur_path = paths(location.pathname);
+ var links = $("#navbar ul li a");
+ var max_length = -1;
+ var pos = -1;
+ for (var i = 0; i < links.length; i++) {
+ if (links[i].getAttribute("href") === "#")
+ continue;
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
+
+ var length = prefix_length(nav_path, cur_path);
+ if (length > max_length) {
+ max_length = length;
+ pos = i;
+ }
+ }
+
+ // Add class to parent
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/link.svg b/docs/link.svg
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+++ b/docs/link.svg
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+
+
+
diff --git a/docs/logo.png b/docs/logo.png
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diff --git a/docs/news/index.html b/docs/news/index.html
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+++ b/docs/news/index.html
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+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 
The goal of mammalcol is to allow easy access to the List of Mammal Species of Colombia.
+
+
+
+Installation +
+You can install the development version of mammalcol from GitHub with:
+
+# install.packages("devtools")
+devtools::install_github("dlizcano/mammalcol")
+
+Example +
+
+
+
+
+Search database +
+This is a basic example which shows you how to search mammal names in Colombia using a vector of mammal names.
+
+# define a vector with species to search for
+splist <- c("Tapirus bairdii", "Tapirus pinchaque", "Tapirus terrestris",
+ "Tapirus terrestris", "Pudu mephistophiles", "Tapirus bairdii")
+
+# search in database
+search_mammalcol(splist)
+#> The following names are repeated in the 'splist': Tapirus bairdii, Tapirus terrestris
+#> name_submitted kingdom phylum class order family
+#> 1 Tapirus bairdii Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 2 Tapirus pinchaque Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 3 Tapirus terrestris Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 4 Pudu mephistophiles Animalia Chordata Mammalia Artiodactyla Cervidae
+#> genus specificEpithet taxonRank scientificNameAuthorship
+#> 1 Tapirus bairdii Especie (Gill, 1865)
+#> 2 Tapirus pinchaque Especie (Roulin, 1829)
+#> 3 Tapirus terrestris Especie (Linnaeus, 1758)
+#> 4 Pudu mephistophiles Especie (de Winton, 1896)
+#> taxonRemarks
+#> 1 Elevación (m): 0-1000
+#> 2 Elevación (m): 1400-4000
+#> 3 Elevación (m): 0-2400
+#> 4 Elevación (m): 3000-3500
+#> bibliographicCitation
+#> 1 HERSHKOVITZ P. 1954. Mammals of northern Colombia. Preliminary report No. 7: Tapirs (genus Tapirus), with a systematic review of American species. Proceedings of the United States National Museum 103:465-496.
+#> 2 ARIAS-ALZATE A, CC DOWNER, C DELGADO-V y J SÁNCHEZ-LONDOÑO. 2010. Un registro de tapir de montaña (Tapirus pinchaque) en el norte de la Cordillera Occidental de Colombia. Mastozoología Neotropical 17:111-116.
+#> 3 ARIAS-ALZATE A, JA PALACIO VIEIRA y J MUÑOZ-DURAN. 2009. Nuevos registros de distribución y oferta de hábitat de la danta colombiana (Tapirus terrestris colombianus) en las tierras bajas del norte de la Cordillera Central (Colombia). Mastozoología Neotropical 16:19-25.
+#> 4 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
+#> inMDD Col_redlist
+#> 1 1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
+#> 2 1 EN A4cd
+#> 3 1 VU A4cd
+#> 4 1 EN A2cd B1ab (i; ii; iii; iv; v) \r\n
+#> distribution
+#> 1 Antioquia | Chocó | Córdoba
+#> 2 Antioquia | Cauca | Cundinamarca | Huila | Meta | Nariño | Quindío | Risaralda | Tolima | Valle del Cauca | Caldas | Caquetá | Putumayo
+#> 3 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainia | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
+#> 4 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
+#> source endemic
+#> 1 Proceedings of the United States National Museum 103:465-496 No
+#> 2 Mastozoología Neotropical 17:111-116 No
+#> 3 Mastozoología Neotropical 16:19-25 No
+#> 4 Biota Colombiana 1:43-75 No
+#> english_name Distance
+#> 1 Central American Tapir 12
+#> 2 Mountain Tapir 14
+#> 3 Lowland Tapir 16
+#> 4 Northern Pudu 17mammalcol has the ability to correct minor typos and lower case in the genus.
+# vector with species names and intentional typos
+splist <- c("Tapiru terrestre", "pudu mephistophiles", "tapirus bairdii")
+
+# search in database
+search_mammalcol(splist)
+#> name_submitted kingdom phylum class order family
+#> 1 Tapiru terrestre Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> 2 Pudu mephistophiles Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 3 Tapirus bairdii Animalia Chordata Mammalia Perissodactyla Tapiridae
+#> genus specificEpithet taxonRank scientificNameAuthorship
+#> 1 Tapirus terrestris Especie (Linnaeus, 1758)
+#> 2 Pudu mephistophiles Especie (de Winton, 1896)
+#> 3 Tapirus bairdii Especie (Gill, 1865)
+#> taxonRemarks
+#> 1 Elevación (m): 0-2400
+#> 2 Elevación (m): 3000-3500
+#> 3 Elevación (m): 0-1000
+#> bibliographicCitation
+#> 1 ARIAS-ALZATE A, JA PALACIO VIEIRA y J MUÑOZ-DURAN. 2009. Nuevos registros de distribución y oferta de hábitat de la danta colombiana (Tapirus terrestris colombianus) en las tierras bajas del norte de la Cordillera Central (Colombia). Mastozoología Neotropical 16:19-25.
+#> 2 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
+#> 3 HERSHKOVITZ P. 1954. Mammals of northern Colombia. Preliminary report No. 7: Tapirs (genus Tapirus), with a systematic review of American species. Proceedings of the United States National Museum 103:465-496.
+#> inMDD Col_redlist
+#> 1 1 VU A4cd
+#> 2 1 EN A2cd B1ab (i; ii; iii; iv; v) \r\n
+#> 3 1 EN A2cd+ B1ab (i,ii,iii)+ B2ab (i, ii, iii)
+#> distribution
+#> 1 Antioquia | Amazonas | Arauca | Caquetá | Cauca | Cesar | Córdoba | Guainia | La Guajira | Meta | Magdalena | Vaupés | Vichada | Guaviare | Casanare | Norte de Santander | Putumayo
+#> 2 Cauca | Huila | Nariño | Risaralda | Quindío | Tolima | Valle del Cauca
+#> 3 Antioquia | Chocó | Córdoba
+#> source endemic
+#> 1 Mastozoología Neotropical 16:19-25 No
+#> 2 Biota Colombiana 1:43-75 No
+#> 3 Proceedings of the United States National Museum 103:465-496 No
+#> english_name Distance
+#> 1 Lowland Tapir 15
+#> 2 Northern Pudu 17
+#> 3 Central American Tapir 12
+
+
+Produce a map +
+The function mammalmap produces basic a map of distribution at the “Departamento” level for a single species.
+
+# write a species name in the function to map it
+mammalmap("Tapirus pinchaque")
+
+
+See the full taxon table +
+
+
+head(taxon)
+#> scientificName kingdom phylum class order family
+#> 1 Passalites murelia Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 2 Mazama rufina Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 3 Passalites sanctaemartae Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 4 Mazama temama Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 5 Mazama zamora Animalia Chordata Mammalia Artiodactyla Cervidae
+#> 6 Mazama zetta Animalia Chordata Mammalia Artiodactyla Cervidae
+#> genus specificEpithet taxonRank scientificNameAuthorship
+#> 1 Passalites murelia Especie J. A. Allen, 1915
+#> 2 Mazama rufina Especie (Pucheran, 1851)
+#> 3 Passalites sanctaemartae Especie (J. A. Allen, 1915)
+#> 4 Mazama temama Especie (Kerr, 1792)
+#> 5 Mazama zamora Especie J. A. Allen, 1915
+#> 6 Mazama zetta Especie Thomas, 1913
+#> taxonRemarks
+#> 1 Elevación (m): 0-900
+#> 2 Elevación (m): 1500-4000
+#> 3 Elevación (m): 0-900
+#> 4 Elevación (m): 0-68
+#> 5 Elevación (m): 600-1200
+#> 6 Elevación (m): 1600-1950
+#> bibliographicCitation
+#> 1 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> 2 ALBERICO M, A CADENA, JI HERNÁNDEZ-CAMACHO y Y MUÑOZ-SABA. 2000b. Mamíferos (Synapsida: Theria) de Colombia. Biota Colombiana 1:43-75.
+#> 3 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> 4 GROVES C y P GRUBB. 1987. Relationships of living deer. Pp. 21-59, en: Biology and management of the Cervidae (CM Wemmer, ed.). Smithsonian Institution Press, Washington, D.C., USA.
+#> 5 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> 6 ALLEN JA. 1916. List of mammals collected in Colombia by the American Museum of Natural History expeditions, 1910-1915. Bulletin of the American Museum of Natural History 35:191-238.
+#> inMDD Col_redlist
+#> 1 0 <NA>
+#> 2 1 VU A2 cde\r\n
+#> 3 0 <NA>
+#> 4 1 DD
+#> 5 0 DD
+#> 6 0 DD
+#> distribution
+#> 1 Amazonas | Caquetá | Cauca | Meta | Vaupés | Vichada | Nariño | Putumayo | Cundinamarca
+#> 2 Antioquia | Boyacá | Caldas | Cauca | Cesar | Cundinamarca | Huila | Nariño | Norte de Santander | Quindío | Risaralda | Santander | Tolima | Valle del Cauca | Caquetá
+#> 3 Bolívar | Cesar | La Guajira | Magdalena | Atlántico | Córdoba | Cundinamarca
+#> 4 Chocó | Magdalena
+#> 5 Amazonas | Caquetá | Meta | Putumayo | Vichada
+#> 6 Antioquia | Caldas | Cauca | Nariño | Valle del Cauca | Tolima
+#> source
+#> 1 Bulletin of the American Museum of Natural History 35:191-238
+#> 2 Biota Colombiana 1:43-75
+#> 3 Bulletin of the American Museum of Natural History 35:191-238
+#> 4 Pp. 21-59, en: Biology and management of the Cervidae (CM Wemmer, ed.). Smithsonian Institution Press, Washington, D.C., USA
+#> 5 Bulletin of the American Museum of Natural History 35:191-238
+#> 6 Bulletin of the American Museum of Natural History 35:191-238
+#> endemic english_name
+#> 1 No <NA>
+#> 2 No Little Red Brocket
+#> 3 No <NA>
+#> 4 No Mexican Red Brocket
+#> 5 No <NA>
+#> 6 No <NA>
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
new file mode 100644
index 0000000..80ea5b8
--- /dev/null
+++ b/docs/pkgdown.css
@@ -0,0 +1,384 @@
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+ height: 100%;
+}
+
+body {
+ position: relative;
+}
+
+body > .container {
+ display: flex;
+ height: 100%;
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1 0 auto;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+ flex-shrink: 0;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Ensure in-page images don't run outside their container */
+.contents img {
+ max-width: 100%;
+ height: auto;
+}
+
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+ display: list-item;
+}
+
+/* Typographic tweaking ---------------------------------*/
+
+.contents .page-header {
+ margin-top: calc(-60px + 1em);
+}
+
+dd {
+ margin-left: 3em;
+}
+
+/* Section anchors ---------------------------------*/
+
+a.anchor {
+ display: none;
+ margin-left: 5px;
+ width: 20px;
+ height: 20px;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+h1:hover .anchor,
+h2:hover .anchor,
+h3:hover .anchor,
+h4:hover .anchor,
+h5:hover .anchor,
+h6:hover .anchor {
+ display: inline-block;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -40px;
+}
+
+/* Navbar submenu --------------------------*/
+
+.dropdown-submenu {
+ position: relative;
+}
+
+.dropdown-submenu>.dropdown-menu {
+ top: 0;
+ left: 100%;
+ margin-top: -6px;
+ margin-left: -1px;
+ border-radius: 0 6px 6px 6px;
+}
+
+.dropdown-submenu:hover>.dropdown-menu {
+ display: block;
+}
+
+.dropdown-submenu>a:after {
+ display: block;
+ content: " ";
+ float: right;
+ width: 0;
+ height: 0;
+ border-color: transparent;
+ border-style: solid;
+ border-width: 5px 0 5px 5px;
+ border-left-color: #cccccc;
+ margin-top: 5px;
+ margin-right: -10px;
+}
+
+.dropdown-submenu:hover>a:after {
+ border-left-color: #ffffff;
+}
+
+.dropdown-submenu.pull-left {
+ float: none;
+}
+
+.dropdown-submenu.pull-left>.dropdown-menu {
+ left: -100%;
+ margin-left: 10px;
+ border-radius: 6px 0 6px 6px;
+}
+
+/* Sidebar --------------------------*/
+
+#pkgdown-sidebar {
+ margin-top: 30px;
+ position: -webkit-sticky;
+ position: sticky;
+ top: 70px;
+}
+
+#pkgdown-sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#pkgdown-sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#pkgdown-sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* bootstrap-toc tweaks ------------------------------------------------------*/
+
+/* All levels of nav */
+
+nav[data-toggle='toc'] .nav > li > a {
+ padding: 4px 20px 4px 6px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+}
+
+nav[data-toggle='toc'] .nav > li > a:hover,
+nav[data-toggle='toc'] .nav > li > a:focus {
+ padding-left: 5px;
+ color: inherit;
+ border-left: 1px solid #878787;
+}
+
+nav[data-toggle='toc'] .nav > .active > a,
+nav[data-toggle='toc'] .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav > .active:focus > a {
+ padding-left: 5px;
+ font-size: 1.5rem;
+ font-weight: 400;
+ color: inherit;
+ border-left: 2px solid #878787;
+}
+
+/* Nav: second level (shown on .active) */
+
+nav[data-toggle='toc'] .nav .nav {
+ display: none; /* Hide by default, but at >768px, show it */
+ padding-bottom: 10px;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a {
+ padding-left: 16px;
+ font-size: 1.35rem;
+}
+
+nav[data-toggle='toc'] .nav .nav > li > a:hover,
+nav[data-toggle='toc'] .nav .nav > li > a:focus {
+ padding-left: 15px;
+}
+
+nav[data-toggle='toc'] .nav .nav > .active > a,
+nav[data-toggle='toc'] .nav .nav > .active:hover > a,
+nav[data-toggle='toc'] .nav .nav > .active:focus > a {
+ padding-left: 15px;
+ font-weight: 500;
+ font-size: 1.35rem;
+}
+
+/* orcid ------------------------------------------------------------------- */
+
+.orcid {
+ font-size: 16px;
+ color: #A6CE39;
+ /* margins are required by official ORCID trademark and display guidelines */
+ margin-left:4px;
+ margin-right:4px;
+ vertical-align: middle;
+}
+
+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+
+.ref-index td {vertical-align: top; min-width: 100px}
+.ref-index .icon {width: 40px;}
+.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+pre, code, pre code {
+ background-color: #f8f8f8;
+ color: #333;
+}
+pre, pre code {
+ white-space: pre-wrap;
+ word-break: break-all;
+ overflow-wrap: break-word;
+}
+
+pre {
+ border: 1px solid #eee;
+}
+
+pre .img, pre .r-plt {
+ margin: 5px 0;
+}
+
+pre .img img, pre .r-plt img {
+ background-color: #fff;
+}
+
+code a, pre a {
+ color: #375f84;
+}
+
+a.sourceLine:hover {
+ text-decoration: none;
+}
+
+.fl {color: #1514b5;}
+.fu {color: #000000;} /* function */
+.ch,.st {color: #036a07;} /* string */
+.kw {color: #264D66;} /* keyword */
+.co {color: #888888;} /* comment */
+
+.error {font-weight: bolder;}
+.warning {font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+ position: relative;
+}
+
+.btn-copy-ex {
+ position: absolute;
+ right: 0;
+ top: 0;
+ visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+ visibility: visible;
+}
+
+/* headroom.js ------------------------ */
+
+.headroom {
+ will-change: transform;
+ transition: transform 200ms linear;
+}
+.headroom--pinned {
+ transform: translateY(0%);
+}
+.headroom--unpinned {
+ transform: translateY(-100%);
+}
+
+/* mark.js ----------------------------*/
+
+mark {
+ background-color: rgba(255, 255, 51, 0.5);
+ border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+ padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+ margin-bottom: 10px;
+}
+
+/* fontawesome ------------------------ */
+
+.fab {
+ font-family: "Font Awesome 5 Brands" !important;
+}
+
+/* don't display links in code chunks when printing */
+/* source: https://stackoverflow.com/a/10781533 */
+@media print {
+ code a:link:after, code a:visited:after {
+ content: "";
+ }
+}
+
+/* Section anchors ---------------------------------
+ Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71
+*/
+
+div.csl-bib-body { }
+div.csl-entry {
+ clear: both;
+}
+.hanging-indent div.csl-entry {
+ margin-left:2em;
+ text-indent:-2em;
+}
+div.csl-left-margin {
+ min-width:2em;
+ float:left;
+}
+div.csl-right-inline {
+ margin-left:2em;
+ padding-left:1em;
+}
+div.csl-indent {
+ margin-left: 2em;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
new file mode 100644
index 0000000..6f0eee4
--- /dev/null
+++ b/docs/pkgdown.js
@@ -0,0 +1,108 @@
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+ $(function() {
+
+ $('.navbar-fixed-top').headroom();
+
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ $(window).resize(function(){
+ $('body').css('padding-top', $('.navbar').height() + 10);
+ });
+
+ $('[data-toggle="tooltip"]').tooltip();
+
+ var cur_path = paths(location.pathname);
+ var links = $("#navbar ul li a");
+ var max_length = -1;
+ var pos = -1;
+ for (var i = 0; i < links.length; i++) {
+ if (links[i].getAttribute("href") === "#")
+ continue;
+ // Ignore external links
+ if (links[i].host !== location.host)
+ continue;
+
+ var nav_path = paths(links[i].pathname);
+
+ var length = prefix_length(nav_path, cur_path);
+ if (length > max_length) {
+ max_length = length;
+ pos = i;
+ }
+ }
+
+ // Add class to parent
+
+
+
+
+
+
+
+
+
+
+
+
+ Changelog
+ Source:NEWS.md
+