Package index • mappingAS

Shiny application

The interactive app that ties the whole workflow together — upload points, compute EOO/AOO and habitat conversion, explore and export. The recommended entry point for most users.

run_app(): Launch the mappingAS Shiny application

Occurrence data

Read and prepare occurrence points.

read_occurrences(): Read species occurrence points from XLSX, CSV or vector files
vouchers_from_occ(): Build examined-voucher strings from occurrence attributes

One-call assessment

Run the whole pipeline for one or many species.

assess_species(): Assess one or many species: EOO, AOO, MapBiomas conversion and fire
class_table(): Per-class MapBiomas composition table (every class) for an assessment

Range metrics & Criterion B

Extent of Occurrence, Area of Occupancy and the provisional Criterion B categories.

calc_eoo(): Extent of Occurrence (EOO) via minimum convex polygon
calc_aoo(): Area of Occupancy (AOO) via occupied grid cells
aoo_bounds(): Lower/upper Area of Occupancy bounds and the Criterion B2 category range
iucn_category_B(): Provisional IUCN Red List Criterion B category from range size
iucn_category_B_range(): Criterion B size category range under AOO uncertainty
iucn_criterion_B(): Apply IUCN Red List Criterion B (size thresholds plus sub-criteria)
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)

Habitat conversion (MapBiomas)

Converted vs natural land cover within the range, per-class and over time.

summarise_conversion(): Summarise habitat conversion from MapBiomas class areas
cover_timeseries(): MapBiomas land-cover composition over time for a polygon
timeseries_for_species(): Land-cover time series for one assessed species (EOO or AOO)
mb_class_areas_raster(): Tabulate area per MapBiomas class from a cropped raster
mb_class_areas_gee(): MapBiomas class areas via Google Earth Engine (optional backend)
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_initiatives(): MapBiomas initiatives supported by mappingAS
mb_groups(): Group lookup vectors for MapBiomas conservation groups
mb_legend(): Standardised MapBiomas legend with conservation groupings
mb_palette(): Official MapBiomas colours for a set of class codes
mb_years(): Years available for a MapBiomas initiative/collection

Area of Habitat & elevation

Elevation-refined suitable habitat within the range.

calc_aoh(): Area of Habitat (AOH): suitable land cover within a range and elevation band
map_aoh(): Interactive Area of Habitat (AOH) map for one species
elevation_preferences(): Suggest elevation preferences from the occurrences' elevation

Fragmentation

Subpopulation clustering and severe-fragmentation screening.

assess_fragmentation(): Assess severe fragmentation from occurrences and an isolation distance
fragment_habitat(): Severe fragmentation from suitable-habitat patches and population density

Fire (MapBiomas Fire)

Burned-area metrics and fire time series.

summarise_fire(): Summarise fire pressure inside a range
fire_areas(): Area (km^2) per fire value from a cropped fire raster
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)
fire_raster_local(): Crop a MapBiomas Fire raster to an area of interest (local backend)
fire_palette(): Sequential palette for fire frequency (YlOrRd)
mb_fire_url(): Build a MapBiomas Fire (Fogo) GeoTIFF URL

Protected areas (WDPA)

Overlap of the range with the global World Database on Protected Areas.

protected_areas(): Read Protected areas intersecting an area of interest
summarise_protected(): Overlap between a species' range and federal Protected areas
pa_table(): Per-species table of Protected areas overlapping the range
wdpa_areas(): Read World Database on Protected Areas polygons intersecting an area
wdpa_query_url(): Default WDPA ArcGIS FeatureServer query endpoint

Global land cover (Sentinel-2 / Esri)

Fallback 10 m land cover for ranges outside MapBiomas coverage.

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
esri_legend(): Sentinel-2 / Esri global 10 m land-cover legend

Countries & realm

Countries of occurrence and biogeographical realm.

countries_of_occurrence(): Countries of occurrence and biogeographical realm(s) from a range

Maps & charts

Interactive and publication-ready outputs.

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
plot_conversion(): Habitat composition chart (natural / altered / water / other) for EOO and AOO
plot_conversion_donut(): MapBiomas composition donut charts (EOO and AOO)
plot_timeseries(): Stacked-area chart of land-cover percentage over time
plot_class_trendline(): Regression trendline of one land-cover class through time
plot_fire_timeseries(): Bar/line chart of burned area (%) over time
plot_protection(): Protection chart (inside vs outside Protected areas) for EOO and AOO

Report & export

Written assessment report, factsheet and spatial/raster exports.

assessment_report(): Narrative conservation-assessment report for one species
factsheet_html(): Standalone HTML species factsheet with user metadata and photos
export_ranges(): Export EOO and AOO as spatial files (shapefile or GeoPackage)

Utilities

Projection helpers and the package overview.

laea_crs(): Build a data-centred equal-area CRS (Lambert Azimuthal Equal Area)
mappingAS mappingAS-package: mappingAS: Range Metrics and MapBiomas Habitat Conversion