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updated refs in the R markdown scripts
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oharac committed Jun 22, 2019
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9 changes: 5 additions & 4 deletions 1a_biodiversity_maps_comp_assessed.Rmd
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* Range-rarity-weighted mean and variance of risk
* Range rarity-weighted species richness

# Data Sources
# Data sources

IUCN Red List spatial data download
IUCN Red List API
Gina Ralph (IUCN)
* 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
* 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.

# Methods

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13 changes: 9 additions & 4 deletions 1a_biodiversity_maps_comp_assessed.html
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<meta name="generator" content="pandoc" />


<meta name="author" content="Compiled on Mon Apr 8 13:08:09 2019 by ohara" />
<meta name="author" content="Compiled on Sat Jun 22 05:52:46 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 Mon Apr 8 13:08:09 2019 by ohara</em></h4>
<h4 class="author"><em>Compiled on Sat Jun 22 05:52:46 2019 by ohara</em></h4>

</div>

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</ul>
</div>
<div id="data-sources" class="section level1">
<h1><span class="header-section-number">2</span> Data Sources</h1>
<p>IUCN Red List spatial data download IUCN Red List API Gina Ralph (IUCN)</p>
<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>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>
</div>
<div id="methods" class="section level1">
<h1><span class="header-section-number">3</span> Methods</h1>
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13 changes: 7 additions & 6 deletions 1b_biodiversity_maps_rr_comp_assessed.Rmd
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Expand Up @@ -48,11 +48,12 @@ Create a set of maps of the distribution of biodiversity intactness - all specie

A selection of these maps will be generated for taxonomic groups and range sizes in a separate Rmd.

# Data Sources
# Data sources

IUCN Red List spatial data download
IUCN Red List API
Gina Ralph (IUCN)
* 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
* 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.

# Methods

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cell_summary_file <- file.path(dir_o_anx, 'cell_summary_rr_weighted_comp.csv')
### unlink(cell_summary_file)
reload <- TRUE
reload <- FALSE
if(!file.exists(cell_summary_file) | reload == TRUE) {
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``` {r mean_risk_raster}
reload <- TRUE
reload <- FALSE
rast_base <- raster(file.path(dir_spatial, 'cell_id_rast.tif'))
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