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updated for 2019-2
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oharac committed Aug 31, 2019
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6 changes: 3 additions & 3 deletions 1a_biodiversity_maps_comp_assessed.Rmd
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# Data sources

* IUCN species API: IUCN. (2018). The IUCN Red List of Threatened Species. Version 2018-1.
* IUCN species shapefiles: IUCN. (2018). The IUCN Red List of Threatened Species. Version 2018-1. Retrieved July 11, 2018, from http://www.iucnredlist.org
* IUCN species API: IUCN. (2019). The IUCN Red List of Threatened Species. Version 2019-2.
* IUCN species shapefiles: IUCN. (2019). The IUCN Red List of Threatened Species. Version 2019-2. Retrieved August 2019, from http://www.iucnredlist.org
* BirdLife International shapefiles: BirdLife International and Handbook of the Birds of the World. (2018). Bird species distribution maps of the world. Version 7.0. Available at http://datazone.birdlife.org/species/requestdis
* Marine Ecoregions of the World: Spalding, M. D., Fox, H. E., Allen, G. R., Davidson, N., Ferdaña, Z. A., Finlayson, M. A. X., … others. (2007). Marine ecoregions of the world: A bioregionalization of coastal and shelf areas. BioScience, 57(7), 573–583.

Expand Down Expand Up @@ -98,7 +98,7 @@ cell_summary_file <- file.path(dir_o_anx, 'cell_summary_unweighted_comp.csv')
reload <- TRUE
if(!file.exists(cell_summary_file) | reload == TRUE) {
dir_taxa_summaries <- file.path(dir_o_anx, 'taxa_summaries')
dir_taxa_summaries <- file.path(dir_o_anx, 'taxa_summaries_2019')
comp_files <- list.files(dir_taxa_summaries,
pattern = sprintf('cell_sum_comp_%s.csv', api_version),
full.names = TRUE)
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10 changes: 5 additions & 5 deletions 1a_biodiversity_maps_comp_assessed.html
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<meta name="generator" content="pandoc" />


<meta name="author" content="Compiled on Sat Jun 22 05:52:46 2019 by ohara" />
<meta name="author" content="Compiled on Sat Aug 31 07:31:00 2019 by ohara" />


<title>Biodiversity risk maps</title>
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<h1 class="title toc-ignore">Biodiversity risk maps</h1>
<h4 class="author"><em>Compiled on Sat Jun 22 05:52:46 2019 by ohara</em></h4>
<h4 class="author"><em>Compiled on Sat Aug 31 07:31:00 2019 by ohara</em></h4>

</div>

Expand Down Expand Up @@ -1735,8 +1735,8 @@ <h1><span class="header-section-number">1</span> Summary</h1>
<div id="data-sources" class="section level1">
<h1><span class="header-section-number">2</span> Data sources</h1>
<ul>
<li>IUCN species API: IUCN. (2018). The IUCN Red List of Threatened Species. Version 2018-1.</li>
<li>IUCN species shapefiles: IUCN. (2018). The IUCN Red List of Threatened Species. Version 2018-1. Retrieved July 11, 2018, from <a href="http://www.iucnredlist.org" class="uri">http://www.iucnredlist.org</a></li>
<li>IUCN species API: IUCN. (2019). The IUCN Red List of Threatened Species. Version 2019-2.</li>
<li>IUCN species shapefiles: IUCN. (2019). The IUCN Red List of Threatened Species. Version 2019-2. Retrieved August 2019, from <a href="http://www.iucnredlist.org" class="uri">http://www.iucnredlist.org</a></li>
<li>BirdLife International shapefiles: BirdLife International and Handbook of the Birds of the World. (2018). Bird species distribution maps of the world. Version 7.0. Available at <a href="http://datazone.birdlife.org/species/requestdis" class="uri">http://datazone.birdlife.org/species/requestdis</a></li>
<li>Marine Ecoregions of the World: Spalding, M. D., Fox, H. E., Allen, G. R., Davidson, N., Ferdaña, Z. A., Finlayson, M. A. X., … others. (2007). Marine ecoregions of the world: A bioregionalization of coastal and shelf areas. BioScience, 57(7), 573–583.</li>
</ul>
Expand Down Expand Up @@ -1771,7 +1771,7 @@ <h3><span class="header-section-number">3.1.1</span> Aggregate mean risk and var
<a class="sourceLine" id="cb2-3" title="3">reload &lt;-<span class="st"> </span><span class="ot">TRUE</span></a>
<a class="sourceLine" id="cb2-4" title="4"></a>
<a class="sourceLine" id="cb2-5" title="5"><span class="cf">if</span>(<span class="op">!</span><span class="kw">file.exists</span>(cell_summary_file) <span class="op">|</span><span class="st"> </span>reload <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>) {</a>
<a class="sourceLine" id="cb2-6" title="6"> dir_taxa_summaries &lt;-<span class="st"> </span><span class="kw">file.path</span>(dir_o_anx, <span class="st">&#39;taxa_summaries&#39;</span>)</a>
<a class="sourceLine" id="cb2-6" title="6"> dir_taxa_summaries &lt;-<span class="st"> </span><span class="kw">file.path</span>(dir_o_anx, <span class="st">&#39;taxa_summaries_2019&#39;</span>)</a>
<a class="sourceLine" id="cb2-7" title="7"> comp_files &lt;-<span class="st"> </span><span class="kw">list.files</span>(dir_taxa_summaries,</a>
<a class="sourceLine" id="cb2-8" title="8"> <span class="dt">pattern =</span> <span class="kw">sprintf</span>(<span class="st">&#39;cell_sum_comp_%s.csv&#39;</span>, api_version),</a>
<a class="sourceLine" id="cb2-9" title="9"> <span class="dt">full.names =</span> <span class="ot">TRUE</span>)</a>
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10 changes: 5 additions & 5 deletions 1b_biodiversity_maps_rr_comp_assessed.Rmd
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Expand Up @@ -50,8 +50,8 @@ A selection of these maps will be generated for taxonomic groups and range sizes

# Data sources

* IUCN species API: IUCN. (2018). The IUCN Red List of Threatened Species. Version 2018-1.
* IUCN species shapefiles: IUCN. (2018). The IUCN Red List of Threatened Species. Version 2018-1. Retrieved July 11, 2018, from http://www.iucnredlist.org
* IUCN species API: IUCN. (2019). The IUCN Red List of Threatened Species. Version 2019-2.
* IUCN species shapefiles: IUCN. (2019). The IUCN Red List of Threatened Species. Version 2019-2. Retrieved August 2019, from http://www.iucnredlist.org
* BirdLife International shapefiles: BirdLife International and Handbook of the Birds of the World. (2018). Bird species distribution maps of the world. Version 7.0. Available at http://datazone.birdlife.org/species/requestdis
* Marine Ecoregions of the World: Spalding, M. D., Fox, H. E., Allen, G. R., Davidson, N., Ferdaña, Z. A., Finlayson, M. A. X., … others. (2007). Marine ecoregions of the world: A bioregionalization of coastal and shelf areas. BioScience, 57(7), 573–583.

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cell_summary_file <- file.path(dir_o_anx, 'cell_summary_rr_weighted_comp.csv')
### unlink(cell_summary_file)
reload <- FALSE
reload <- TRUE
if(!file.exists(cell_summary_file) | reload == TRUE) {
dir_taxa_summaries <- file.path(dir_o_anx, 'taxa_summaries')
dir_taxa_summaries <- file.path(dir_o_anx, 'taxa_summaries_2019')
comp_files <- list.files(dir_taxa_summaries,
pattern = sprintf('cell_sum_comp_rrweight_%s.csv', api_version),
full.names = TRUE)
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``` {r mean_risk_raster}
reload <- FALSE
reload <- TRUE
rast_base <- raster(file.path(dir_spatial, 'cell_id_rast.tif'))
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