{"id":108,"date":"2013-05-22T16:47:24","date_gmt":"2013-05-22T15:47:24","guid":{"rendered":"http:\/\/borisleroy.com\/en\/?p=108"},"modified":"2013-05-22T16:59:04","modified_gmt":"2013-05-22T15:59:04","slug":"rarity-package-for-calculation-of-indices-of-rarity","status":"publish","type":"post","link":"https:\/\/borisleroy.com\/en\/2013\/05\/22\/rarity-package-for-calculation-of-indices-of-rarity\/","title":{"rendered":"Rarity package for calculation of Indices of rarity"},"content":{"rendered":"<p>The package &#8220;Rarity&#8221;, which allows calculating rarity indices for species and assemblages of species, is <a href=\"http:\/\/cran.r-project.org\/web\/packages\/Rarity\/index.html\">now available on the Comprehensive R Archive Network.<\/a><\/p>\n<p>This package allows easy calculation of the new indices integrating rarity cut-offs; this flexibility allows fitting indices to the considered taxon, geographical area and\/or spatial scale, <em>i.e.<\/em>, to the considered database. See <a title=\"Rarity Indices\" href=\"http:\/\/borisleroy.com\/en\/research\/rarity-indices\/\">the rarity indices section for more details and examples.<\/a><\/p>\n<p>This package simply requires occurrence data to calculate species rarity weights, and presence-absence or abundance data per site\/assemblage\/community to calculate rarity indices of sites\/assemblages\/species.<\/p>\n<p>The Rarity package has two major functions:<\/p>\n<ul>\n<li>rWeights &#8211; This function allows for calculating rarity weights for species with respect to the chosen rarity cut-off point. Multiscale rarity weights can also be calculated with this function. Classical weighting methods (<em>e.g.<\/em>, the inverse of occurrence) can also be calculated with this function.<\/li>\n<\/ul>\n<figure id=\"attachment_83\" aria-describedby=\"caption-attachment-83\" style=\"width: 300px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/borisleroy.com\/en\/wp-content\/uploads\/sites\/2\/2013\/02\/Weight-assignation-curve.png\"><img loading=\"lazy\" decoding=\"async\" class=\"size-medium wp-image-83\" alt=\"Weight assignation curve adjusted to an arbitrary rarity cut-off.\" src=\"http:\/\/borisleroy.com\/en\/wp-content\/uploads\/sites\/2\/2013\/02\/Weight-assignation-curve-300x192.png\" width=\"300\" height=\"192\" srcset=\"https:\/\/borisleroy.com\/en\/wp-content\/uploads\/sites\/2\/2013\/02\/Weight-assignation-curve-300x192.png 300w, https:\/\/borisleroy.com\/en\/wp-content\/uploads\/sites\/2\/2013\/02\/Weight-assignation-curve-234x150.png 234w, https:\/\/borisleroy.com\/en\/wp-content\/uploads\/sites\/2\/2013\/02\/Weight-assignation-curve.png 817w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><figcaption id=\"caption-attachment-83\" class=\"wp-caption-text\">Weight assignation curve adjusted to an arbitrary rarity cut-off.<\/figcaption><\/figure>\n<p>&nbsp;<\/p>\n<ul>\n<li>Irr &#8211; This function allows calculating rarity indices for assemblages of species, on the basis of the calculated rarity weights.<\/li>\n<\/ul>\n<p>A PDF presentation of the package with examples is available on this link, although in French: <a href=\"http:\/\/borisleroy.com\/wp-content\/uploads\/2013\/05\/rarity-package.pdf\">rarity-package<\/a><\/p>\n<p><strong>References<\/strong><\/p>\n<p><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/ddi.12040\/abstract\" target=\"_blank\"><b>Leroy B.<\/b>, Canard A. &amp; Ysnel F. <i>In Press.<\/i> Integrating multiple scales in rarity assessments of invertebrate taxa. <i>Diversity and Distributions<\/i><\/a><\/p>\n<p><a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/j.1752-4598.2011.00148.x\/abstract\" target=\"_blank\"><b>Leroy B.<\/b>, P\u00e9tillon J., Gallon R., Canard A. &amp; Ysnel F. <b>2012<i>. <\/i><\/b>Improving occurrence-based rarity metrics in conservation studies by including multiple rarity cut-offs. <i>Insect Conservation and Diversity <\/i><b>5<\/b>:159-168<i>.<\/i><\/a><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The package &#8220;Rarity&#8221;, which allows calculating rarity indices for species and assemblages of species, is now available on the Comprehensive R Archive Network. This package allows easy calculation of the new indices integrating rarity cut-offs; this flexibility allows fitting indices to the considered taxon, geographical area and\/or spatial scale, i.e., to the considered database. See the rarity indices section for more details and examples. This package simply requires occurrence data.. <a href=\"https:\/\/borisleroy.com\/en\/2013\/05\/22\/rarity-package-for-calculation-of-indices-of-rarity\/\">Read More<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[9,18,8,6],"class_list":["post-108","post","type-post","status-publish","format-standard","hentry","category-news","tag-cran","tag-r","tag-r-package","tag-rarity"],"featured_image_src":null,"featured_image_src_square":null,"author_info":{"display_name":"Boris","author_link":"https:\/\/borisleroy.com\/en\/author\/farewell\/"},"_links":{"self":[{"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/posts\/108","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/comments?post=108"}],"version-history":[{"count":6,"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/posts\/108\/revisions"}],"predecessor-version":[{"id":115,"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/posts\/108\/revisions\/115"}],"wp:attachment":[{"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/media?parent=108"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/categories?post=108"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/borisleroy.com\/en\/wp-json\/wp\/v2\/tags?post=108"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}