rgbif - Interface to the Global Biodiversity Information Facility API
A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.
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gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
13.96 score 177 stars 22 dependents 3.1k scripts 12k downloads
b3gbi - General Biodiversity Indicators for Biodiversity Data Cubes
Calculate general biodiversity indicators from GBIF data cubes. Includes many common indicators such as species richness, evenness, and completeness, which can be calculated over time (trends) or space (maps). Now also supports retaining original cell IDs.
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biodiversity-indicatorsdata-cubes
7.08 score 9 stars 1 dependents 75 scripts
trias - Process Data for the Project Tracking Invasive Alien Species (TrIAS)
R package to provide functionality to facilitate the data processing for the project Tracking Invasive Alien Species (TrIAS <https://trias-project.be>).
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invasive-speciesoscibio
6.11 score 4 stars 45 scriptsebvcube - Working with netCDF for Essential Biodiversity Variables
The concept of Essential Biodiversity Variables (EBV, <https://geobon.org/ebvs/what-are-ebvs/>) comes with a data structure based on the Network Common Data Form (netCDF). The 'ebvcube' 'R' package provides functionality to easily create, access and visualise this data. The EBV netCDFs can be downloaded from the EBV Data Portal: Christian Langer/ iDiv (2020) <https://portal.geobon.org/>.
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biodiversity-standardsessential-biodiversity-variablesnetcdf4
5.62 score 10 stars 35 scripts 79 downloads
gcube - Simulating Biodiversity Data Cubes
This R package provides a simulation framework for biodiversity data cubes. This can start from simulating multiple species distributed in a landscape over a temporal scope. In a second phase, the simulation of a variety of observation processes and effort can generate actual occurrence datasets. Based on their (simulated) spatial uncertainty, occurrences can then be designated to a grid to form a data cube.
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biodiversity-informaticsdata-cubessimulations
4.62 score 11 stars 23 scriptsmgrs - Convert 'MGRS' ('Military Grid Reference System') Coordinates From/To Other Coordinate Systems
The 'Military Grid Reference System' ('MGRS') is the geocoordinate standard used by 'NATO' militaries for locating points on the earth. The 'MGRS' is derived from the 'Universal Transverse Mercator' ('UTM') grid system and the universal polar stereographic ('UPS') grid system, but uses a different labeling convention. The 'MGRS' is used for the entire earth. Methods are provided to convert 'MGRS' coordinates to and from other coordinate systems.
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coordinatesgrid-referencesmgrsprojectionutm-codescpp
4.14 score 31 stars 2 dependents 15 scripts
dubicube - Calculation and Interpretation of Data Cube Indicator Uncertainty
This R package provides functions to explore data cubes using simple measures and cross-validation techniques. It can also be used for uncertainty calculation using the bootstrap resampling method, and functionality is provided for efficient interpretation and visualisation of uncertainty related to indicators based on occurrence cubes.
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biodiversity-indicatorsdata-cubesuncertainty-quantificationuncertainty-visualisation
4.12 score 4 stars 1 dependents 22 scripts
impIndicator - Impact Indicators of Alien Taxa
The negative impact of alien species is recognised as a major threat to biodiversity. However, in the absence of evidence-based impact indicators that follow the Findable, Accessible, Interoperable, and Reusable (FAIR) Data Principles with standardised workflows, the impacts of alien species are not systematically estimated over time, a major gap for policy. We develop the impIndicator R package, using an open-source workflow for computing impact indicators of alien species, by combining occurrence data from the Global Biodiversity Information Facility (GBIF) with Environmental Impact Classification for Alien Taxa (EICAT) assessments.
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biodiversity-indicatorsimpactinvasive-species
3.95 score 7 scripts
dissmapr - Workflow for Compositional Dissimilarity and Biodiversity Turnover Analysis
Tools to compute and map biodiversity turnover at the macroscale.
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biodiversitydissimilarityspatiotemporal
3.58 score 2 stars 14 scripts
pdindicatoR - Calculate and visualize a phylogenetic diversity indicators based on species occurrence data cubes
A package to calculate and produce a map of phylogenetic diversity scores for each grid cell in the input species occurrences data cube, and calculate the percentage of high PD cells within currently protected areas. You provide a phylogenetic tree, the datacube for the corresponding species is downloaded from GBIF (or user-uploaded), and the package does the rest.
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biodiversityconservationdatacubeindicatorphylogenetic-diversity
2.78 score 5 scripts