Spatial Metrics and Habitat Conversion for Extinction Risk Assessment

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Documentation for package ‘mappingAS’ version 1.13.2

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assessment_report Narrative conservation-assessment report for one species
assess_species Assess one or many species: EOO, AOO, MapBiomas conversion and fire
calc_aoo Area of Occupancy (AOO) via occupied grid cells
calc_eoo Extent of Occurrence (EOO) via minimum convex polygon
calc_locations Estimate of number of locations (occupied-grid-cell method, optionally protected-area aware)
calc_subpop Estimate of number of subpopulations (circular-buffer method)
class_table Per-class MapBiomas composition table (every class) for an assessment
cover_timeseries MapBiomas land-cover composition over time for a polygon
esri_legend Sentinel-2 / Esri global 10 m land-cover legend
export_ranges Export EOO and AOO as spatial files (shapefile or GeoPackage)
factsheet_html Standalone HTML species factsheet with user metadata and photos
fire_areas Area (km^2) per fire value from a cropped fire raster
fire_palette Sequential palette for fire frequency (YlOrRd)
fire_raster_local Crop a MapBiomas Fire raster to an area of interest (local backend)
fire_timeseries Burned-area time series for a polygon (% of range x year)
fire_timeseries_for_species Burned-area time series for one assessed species (EOO or AOO)
iucn_category_B Provisional IUCN Red List Criterion B category from range size
iucn_criterion_B Apply IUCN Red List Criterion B (size thresholds plus sub-criteria)
map_species Interactive map of a species' points, EOO and AOO (MapBiomas + fire)
map_static Publication-ready static map of a species (MapBiomas + EOO + AOO + points)
mas_plotly Turn a mappingAS chart into an interactive plotly widget
mb_class_areas_gee MapBiomas class areas via Google Earth Engine (optional backend)
mb_class_areas_raster Tabulate area per MapBiomas class from a cropped raster
mb_fire_url Build a MapBiomas Fire (Fogo) GeoTIFF URL
mb_groups Group lookup vectors for MapBiomas conservation groups
mb_initiatives MapBiomas initiatives supported by mappingAS
mb_legend Standardised MapBiomas legend with conservation groupings
mb_palette Official MapBiomas colours for a set of class codes
mb_raster_local Crop a MapBiomas LULC raster to an area of interest (local backend)
mb_source_url Build the MapBiomas land-use GeoTIFF URL for a given year and initiative
mb_years Years available for a MapBiomas initiative/collection
pa_table Per-species table of Protected areas overlapping the range
plot_class_trendline Regression trendline of one land-cover class through time
plot_conversion Habitat composition chart (natural / altered / water / other) for EOO and AOO
plot_conversion_donut MapBiomas composition donut charts (EOO and AOO)
plot_fire_timeseries Bar/line chart of burned area (%) over time
plot_protection Protection chart (inside vs outside Protected areas) for EOO and AOO
plot_timeseries Stacked-area chart of land-cover percentage over time
protected_areas Read Protected areas intersecting an area of interest
read_occurrences Read species occurrence points from XLSX, CSV or vector files
run_app Launch the mappingAS Shiny application
s2_raster_local Crop a Sentinel-2 / Esri LULC mosaic to an area of interest
s2_source_url Build the Sentinel-2 / Esri land-cover GeoTIFF URL for a tile and year
s2_years Years available for the global Sentinel-2 / Esri land-cover series
summarise_conversion Summarise habitat conversion from MapBiomas class areas
summarise_fire Summarise fire pressure inside a range
summarise_protected Overlap between a species' range and federal Protected areas
timeseries_for_species Land-cover time series for one assessed species (EOO or AOO)
vouchers_from_occ Build examined-voucher strings from occurrence attributes
wdpa_areas Read World Database on Protected Areas polygons intersecting an area
wdpa_query_url Default WDPA ArcGIS FeatureServer query endpoint