First running version of the IA R package associated quarto document,…

… where document is set up as GitHub Page - First version represents a 'How to Use' document for the IA R package - Added public downloading link for the IA R package directly from the GitHub repository - Added Table of contents - Final document displays all indicators in a three-panel layout - Configured Quarto project to render as a GitHub webpage - Added `docs/` folder to host rendered Quarto files for GitHub Pages - Rendered the `.qmd` files and included the output in the `docs/` directory for publication
IPBES-Data · Sep 20, 2024 · 845029d · 845029d
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diff --git a/.Rprofile b/.Rprofile
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+source("renv/activate.R")
+.libPaths("/home/data3/R/x86_64-pc-linux-gnu-library/4.4")
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
diff --git a/.gitignore b/.gitignore
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+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+
+/.quarto/
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 project:
   title: "IA_quarto"
-
+  type: website
+  output-dir: docs
+output:
+  html:
+    self-contained: true
 editor: visual
 
+
+
+
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+<html xmlns="http://www.w3.org/1999/xhtml">    
+  <head>      
+    <title>Redirect to ia_quarto.html</title>      
+    <meta http-equiv="refresh" content="0;URL='ia_quarto.html'" />    
+  </head>    
+  <body> 
+  </body>  
+</html>     
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@@ -0,0 +1,65 @@
+[
+  {
+    "objectID": "ia_quarto.html",
+    "href": "ia_quarto.html",
+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "",
+    "text": "This Quarto project demonstrates the usage of the IA (Indicator Analysis) R-package, which is designed to systematically display and standardize global indicators of the status and the trends in nature.\nThe IA R-package provides an open-access framework that enables users to access annually and globally aggregated indicators as described and standardized in the IPBES Global Assessment Chapter 2.2 – Supplementary Material: Indicators of Status & Trends in Nature. Furthermore, the AI package offers R users a consistent and replicable way to analyze, plot and compare those indicators.\nPlease note that while the IA R-package is developed with reference to the IPBES report, IPBES does not assume any accountability for the contents or outputs of the package."
+  },
+  {
+    "objectID": "ia_quarto.html#indicators-of-ecosystem-structure",
+    "href": "ia_quarto.html#indicators-of-ecosystem-structure",
+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.1 Indicators of ecosystem structure",
+    "text": "4.1 Indicators of ecosystem structure\n\n4.1.1 Aboveground biomass\n\nplot_indicatorStatusAndTrend(\"Aboveground biomass (PgC)\")\n\n\n\n\n\n\n\n\n\n\n4.1.2 Biodiversity Habitat Index (overall habitat integrity)\n\nplot_indicatorStatusAndTrend(\"All-taxa habitat (BILBI)\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"All-taxa habitat (BILBI) - hotspots\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Invertebrate habitat (BILBI)\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Plant habitat (BILBI)\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Vertebrate habitat (BILBI)\")\n\n\n\n\n\n\n\n\n\n\n4.1.3 Coastal protection habitats\n\nplot_indicatorStatusAndTrend(\"Extent and condition of coastal protection habitats\")\n\n\n\n\n\n\n\n\nSubset: Coastal carbon-rich habitat\n\nplot_indicatorStatusAndTrend(\"Extent and condition of natural coastal carbon sinks\")\n\n\n\n\n\n\n\n\n\n\n4.1.4 Extent of forests\n\nplot_indicatorStatusAndTrend(\"Forest area as a percentage of total land area\")\n\n\n\n\n\n\n\n\n\n\n4.1.5 Extent of intact forest landscapes\n\nplot_indicatorStatusAndTrend(\"Intact Forest Landscape extent\")\n\n\n\n\n\n\n\n\n\n\n4.1.6 Extent of marine wilderness\n\nplot_indicatorStatusAndTrend(\"Marine wilderness %\")\n\n\n\n\n\n\n\n\n\n\n4.1.7 Extent of terrestrial wilderness\n\nplot_indicatorStatusAndTrend(\"Global wilderness extent (km2)\")\n\n\n\n\n\n\n\n\n\n\n4.1.8 Fraction of ocean not fished per year\n\nplot_indicatorStatusAndTrend(\"Ocean not fished in given year\")\n\n\n\n\n\n\n\n\n\n\n4.1.9 Land not cultivated or urban\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban (overall)\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - hotspot\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - indigenous land\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - tundra & mountains\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - deserts & drylands\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - temperate forests\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - Mediterranean forests\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - tropical grassland\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - tropical forests\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Land not cropland or urban - temperate grassland\")\n\n\n\n\n\n\n\n\n\n\n4.1.10 Leaf Area Index\n\nplot_indicatorStatusAndTrend(\"Leaf Area Index\")\n\n\n\n\n\n\n\n\n\n\n4.1.11 Mangrove forest area\n\nplot_indicatorStatusAndTrend(\"Area of mangrove forest cover (km2)\")\n\n\n\n\n\n\n\n\n\n\n4.1.12 Natural habitat extent\n\nplot_indicatorStatusAndTrend(\"Percentage natural habitat extent\")\n\n\n\n\n\n\n\n\n\n\n4.1.13 Percentage of live coral cover\n\nplot_indicatorStatusAndTrend(\"Percentage live coral cover\")\n\n\n\n\n\n\n\n\n\n\n4.1.14 Permanent surface water extent\n\nplot_indicatorStatusAndTrend(\"Permanent surface water extent\")\n\n\n\n\n\n\n\n\n\n\n4.1.15 Remaining primary vegetation\n\nplot_indicatorStatusAndTrend(\"Percentage primary LUH2\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Primary vegetation (Hotspots)\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Primary vegetation (Indigenous lands)\")\n\n\n\n\n\n\n\n\n\n\n4.1.16 Seagrass meadow area\n\nplot_indicatorStatusAndTrend(\"Seagrass meadow extent\")\n\n\n\n\n\n\n\n\n\n\n4.1.17 Soil organic carbon (correlative model)\n\nplot_indicatorStatusAndTrend(\"Soil organic carbon\")\n\n\n\n\n\n\n\n\n\n\n4.1.18 Soil organic carbon (mechanistic models)\n\nplot_indicatorStatusAndTrend(\"cSoil (PgC)\")\n\n\n\n\n\n\n\n\n\n\n4.1.19 Tree cover\n\nplot_indicatorStatusAndTrend(\"Tree cover change (Song)\")\n\n\n\n\n\n\n\n\n\n\n4.1.20 Vegetation biomass (mechanistic model)\n\nplot_indicatorStatusAndTrend(\"cVeg (PgC)\")\n\n\n\n\n\n\n\n\n\n\n4.1.21 Wetland Extent Trends index\n\nplot_indicatorStatusAndTrend(\"Wetland Extent Trends Index\")"
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+    "href": "ia_quarto.html#indicators-of-ecosystem-function",
+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.2 Indicators of ecosystem function",
+    "text": "4.2 Indicators of ecosystem function\n\n4.2.1 Biological pump efficiency\n\nplot_indicatorStatusAndTrend(\"Biological pump efficiency\")\n\n\n\n\n\n\n\n\n\n\n4.2.2 Biomass turnover rate\n\nplot_indicatorStatusAndTrend(\"Biomass turnover rate\")\n\n\n\n\n\n\n\n\n\n\n4.2.3 Evapotranspiration (model ensemble)\n\nplot_indicatorStatusAndTrend(\"Evapotranspiration (1000km3/year)\")\n\n\n\n\n\n\n\n\n\n\n4.2.4 Marine net primary productivity (remote-sensing)\n\nplot_indicatorStatusAndTrend(\"Ocean Net Primary Productivity (PgC)\")\n\n\n\n\n\n\n\n\n\n\n4.2.5 NPP remaining in terrestrial ecosystems\n\nplot_indicatorStatusAndTrend(\"NPP_eco (Pg C)\")\n\n\n\n\n\n\n\n\n\n\n4.2.6 Oceanic carbon sequestration\n\nplot_indicatorStatusAndTrend(\"Ocean carbon sink PgC\")   \n\n\n\n\n\n\n\n\n\n\n4.2.7 Terrestrial carbon sequestration (model ensemble)\n\nplot_indicatorStatusAndTrend(\"NBP (PgC/yr)\")    \n\n\n\n\n\n\n\n\n\n\n4.2.8 Terrestrial NPP (model ensemble)\n\nplot_indicatorStatusAndTrend(\"NPP (PgC/yr)\")    \n\n\n\n\n\n\n\n\n\n#plot_indicatorStatusAndTrend(\"GPP (PgC/yr)\") ERROR: no dataset yet\n\n\n\n4.2.9 Terrestrial NPP (remote-sensing)\n\nplot_indicatorStatusAndTrend(\"Terrestrial Net Primary Productivity (PgC)\")"
+  },
+  {
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+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.3 Indicators of community composition – local scale",
+    "text": "4.3 Indicators of community composition – local scale\n\n4.3.1 Biodiversity Intactness Index (overall)\n\nplot_indicatorStatusAndTrend(\"Biodiversity Intactness Index (global)\")  \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"BII (Hotspots)\")  \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"BII (Indigenous Lands)\")  \n\n\n\n\n\n\n\n\nSubset: Tropical Forest BII\n\nplot_indicatorStatusAndTrend(\"Biodiversity Intactness Index (tropical forest only)\")        \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"BII tropical forest (Hotspots)\")      \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"BII tropical forest (Indigenous Lands)\")      \n\n\n\n\n\n\n\n\n\n\n4.3.2 Local species richness (BioTime)\n\nplot_indicatorStatusAndTrend(\"BioTime Local Species Richness\")  \n\n\n\n\n\n\n\n\n\n\n4.3.3 Local species richness (PREDICTS)\n\nplot_indicatorStatusAndTrend(\"PREDICTS SR-weighted mean local species richness (global)\")\n\n\n\n\n\n\n\n\n\n\n4.3.4 Mean Species Abundance index\n\nplot_indicatorStatusAndTrend(\"Mean Species Abundance LU\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Mean Species Abundance CC\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"MSA (hotspots)\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"MSA (IL)\")"
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+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.4 Indicators of community composition – regional scale",
+    "text": "4.4 Indicators of community composition – regional scale\n\n4.4.1 Bird species per grid cell (cSAR)\n#plot_indicatorStatusAndTrend(“sar_iDiv_Allbirds_Localtoglobal.csv”)\n\nplot_indicatorStatusAndTrend(\"cSAR Local results aggregated to Global all birds\")\n\n\n\n\n\n\n\n\nSubset: Forest-specialist bird species per grid cell (cSAR)\n\nplot_indicatorStatusAndTrend(\"cSAR Local results aggregated to Global forest specialists\")\n\n\n\n\n\n\n\n\n\n\n4.4.2 Cumulative number of alien species\n\nplot_indicatorStatusAndTrend(\"Cumulative number of alien species\")\n\n\n\n\n\n\n\n\n\n\n4.4.3 Cumulative introduced invasive aliens\n\nplot_indicatorStatusAndTrend(\"Number of invasive alien species introductions\")\n\n\n\n\n\n\n\n\n\n\n4.4.4 Functional intactness (Madingley)\n\n plot_indicatorStatusAndTrend(\"Madingley functional richness (50%quantile)\")  \n\n\n\n\n\n\n\n\n\n\n4.4.5 Species richness per grid cell (AIM)\n\nplot_indicatorStatusAndTrend(\"Change in grid-cell species richness (all taxa) - AIM\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Change in grid-cell species richness (amphibians) - AIM\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Change in grid-cell species richness (birds) - AIM\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Change in grid-cell species richness (mammals) - AIM\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Change in grid-cell species richness (plants - AIM\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Change in grid-cell species richness (reptiles) - AIM\")"
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+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.5 Indicators of species population – species persistence",
+    "text": "4.5 Indicators of species population – species persistence\n\n4.5.1 Biodiversity Habitat Index (species persistence)\n\nplot_indicatorStatusAndTrend(\"All-taxa richness (BILBI)\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"All-taxa richness (BILBI) - hotspots\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Invertebrate habitat (BILBI)\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Plant richness (BILBI)\") \n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Vertebrate habitat (BILBI)\") \n\n\n\n\n\n\n\n\n\n\n4.5.2 Global bird species richness change (cSAR)\n\nplot_indicatorStatusAndTrend(\"cSAR Global calculation all birds\")\n\n\n\n\n\n\n\n\nSubset: Global forest-specialist bird richness (cSAR)\n\nplot_indicatorStatusAndTrend(\"cSAR Global calculation forest specialists\")\n\n\n\n\n\n\n\n\n\n\n4.5.3 Global mammal and bird species remaining\n\nplot_indicatorStatusAndTrend(\"Numbers of extant mammal and bird species\") \n\n\n\n\n\n\n\n\n\n\n4.5.4 Red List Index (overall)\n\nplot_indicatorStatusAndTrend(\"Red List Index\") \n\n\n\n\n\n\n\n\nSubset: Red List Index (species used in food and medicine)\n\n# plot_indicatorStatusAndTrend(\"Red List Index (species used for food and medicine) \") ERROR: does ont find name\n\nSubset: Red List Index (forest specialists)\n\nplot_indicatorStatusAndTrend(\"Red List index (forest specialists)\") \n\n\n\n\n\n\n\n\nSubset: Red List Index (pollinators)\n\n#plot_indicatorStatusAndTrend(\"Red List Index (pollinator species)\") ERROR name not found\n\nSubset: Red List Index (internationally traded species)\n\nplot_indicatorStatusAndTrend(\"Red List Index (internationally traded species)\")\n\n\n\n\n\n\n\n\nSubset: Red List Index (wild relatives)\n\n#plot_indicatorStatusAndTrend(\"Red List Index (wild relatives of farmed and domesticated species) \") ERROR does not find name\n\n\n\n4.5.5 Driver-specific Red List Indices\nSubset: Red List Index (impacts of invasive alien species)\n\nplot_indicatorStatusAndTrend(\"Red List Index (impacts of invasive alien species)\")\n\n\n\n\n\n\n\n\nRed List Index (impacts of utilisation)\n\nplot_indicatorStatusAndTrend(\"Red List Index (impacts of utilisation)\")\n\n\n\n\n\n\n\n\nRed List Index (Impacts of pollution)\n\nplot_indicatorStatusAndTrend(\"Red List Index (impacts of pollution)\")\n\n\n\n\n\n\n\n\nRed List Index (Impacts of fisheries)\n\nplot_indicatorStatusAndTrend(\"Red List Index (impacts of fisheries)\")"
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+    "section": "4.6 Indicators of species population – geographic distribution",
+    "text": "4.6 Indicators of species population – geographic distribution\n\n4.6.1 Extent of suitable habitat (mammals)\n\nplot_indicatorStatusAndTrend(\"Extent of Suitable Habitat\")\n\n\n\n\n\n\n\n\n\n\n4.6.2 Mammalian range size\n\nplot_indicatorStatusAndTrend(\"Terrestrial mammal grid cells\")\n\n\n\n\n\n\n\n\nSubset: Megafaunal range size\n\nplot_indicatorStatusAndTrend(\"Terrestrial megafaunal grid cells\")\n\n\n\n\n\n\n\n\n\n\n4.6.3 Species Habitat Index\n\nplot_indicatorStatusAndTrend(\"Species Habitat Index\")"
+  },
+  {
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+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.7 Indicators of species population – population size",
+    "text": "4.7 Indicators of species population – population size\n\n4.7.1 Fish stocks biologically sustainable\n\nplot_indicatorStatusAndTrend(\"Proportion of fish stocks within biologically sustainable levels\")\n\n\n\n\n\n\n\n\n\n\n4.7.2 Living Planet Index\n\n#plot_indicatorStatusAndTrend(\"Living Planet Index (overall) \") # name\nplot_indicatorStatusAndTrend(\"Freshwater LPI\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Marine LPI\")\n\n\n\n\n\n\n\nplot_indicatorStatusAndTrend(\"Terrestrial LPI\")\n\n\n\n\n\n\n\n\n\n\n4.7.3 Predatory fish biomass\n\nplot_indicatorStatusAndTrend(\"Predatory sea fish biomass\")\n\n\n\n\n\n\n\n\n\n\n4.7.4 Prey fish biomass\n\nplot_indicatorStatusAndTrend(\"Prey sea fish biomass\")\n\n\n\n\n\n\n\n\n\n\n4.7.5 Wild Bird Index (habitat specialists)\n\nplot_indicatorStatusAndTrend(\"Wild Bird Index (habitat specialists)\")\n\n\n\n\n\n\n\n\n\n\n4.7.6 Wild mammal biomass\n\nplot_indicatorStatusAndTrend(\"Wild mammal biomass\")"
+  },
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+    "title": "Indicator Analyses with the IA R-Package",
+    "section": "4.8 Indicators of species traits",
+    "text": "4.8 Indicators of species traits\n\n4.8.1 Functional richness (Madingley)\n\nplot_indicatorStatusAndTrend(\"Madingley functional richness (50%quantile)\")\n\n\n\n\n\n\n\n\n\n\n4.8.2 Mammalian body mass\n\nplot_indicatorStatusAndTrend(\"Median mammalian body mass\")\n\n\n\n\n\n\n\n\n\n\n4.8.3 Region-based Marine Trophic Index\n\nplot_indicatorStatusAndTrend(\"Marine Trophic Index\")"
+  }
+]
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		source("renv/activate.R")
		.libPaths("/home/data3/R/x86_64-pc-linux-gnu-library/4.4")