Showing 36 of total 36 results (show query)
ropensci
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.
Maintained by John Waller. Last updated 3 days ago.
gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
59.1 match 161 stars 13.26 score 2.1k scripts 20 dependentsropensci
spocc:Interface to Species Occurrence Data Sources
A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.
Maintained by Hannah Owens. Last updated 1 months ago.
specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc
14.5 match 118 stars 10.09 score 552 scripts 5 dependentsropensci
taxize:Taxonomic Information from Around the Web
Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.
Maintained by Zachary Foster. Last updated 11 days ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
7.4 match 274 stars 13.63 score 1.6k scripts 23 dependents
smithsonian
gde:GBIF Dataset Explorer
Functions to explore datasets from the Global Biodiversity Information Facility (GBIF - <https://www.gbif.org/>) using a Shiny interface.
Maintained by Luis J Villanueva. Last updated 2 years ago.
biodiversity-informaticsdata-issuesgbifgbif-dataoccurrenceshinyshiny-r
24.5 match 1 stars 2.70 score
rspatial
dismo:Species Distribution Modeling
Methods for species distribution modeling, that is, predicting the environmental similarity of any site to that of the locations of known occurrences of a species.
Maintained by Robert J. Hijmans. Last updated 4 months ago.
5.6 match 26 stars 11.88 score 2.8k scripts 21 dependentsropensci
CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections
Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Maintained by Alexander Zizka. Last updated 1 years ago.
5.9 match 82 stars 10.93 score 306 scripts 3 dependentsropensci
occCite:Querying and Managing Large Biodiversity Occurrence Datasets
Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.
Maintained by Hannah L. Owens. Last updated 5 months ago.
biodiversity-databiodiversity-informaticsbiodiversity-standardscitationsmuseum-collection-specimensmuseum-collectionsmuseum-metadata
7.0 match 23 stars 7.30 score 43 scripts
luomus
f2g:FinBIF to GBIF
Tools for publishing FinBIF data to GBIF.
Maintained by William K. Morris. Last updated 9 days ago.
14.6 match 1 stars 3.02 score
jbdorey
BeeBDC:Occurrence Data Cleaning
Flags and checks occurrence data that are in Darwin Core format. The package includes generic functions and data as well as some that are specific to bees. This package is meant to build upon and be complimentary to other excellent occurrence cleaning packages, including 'bdc' and 'CoordinateCleaner'. This package uses datasets from several sources and particularly from the Discover Life Website, created by Ascher and Pickering (2020). For further information, please see the original publication and package website. Publication - Dorey et al. (2023) <doi:10.1101/2023.06.30.547152> and package website - Dorey et al. (2023) <https://github.com/jbdorey/BeeBDC>.
Maintained by James B. Dorey. Last updated 4 months ago.
7.7 match 3 stars 5.68 score 7 scripts
b-cubed-eu
b3gbi:General Biodiversity Indicators for Biodiversity Data Cubes
Calculate general biodiversity indicators from GBIF data cubes. Includes many common indicators such as species richness and evenness, which can be calculated over time (trends) or space (maps).
Maintained by Shawn Dove. Last updated 12 days ago.
biodiversity-indicatorsdata-cubes
6.0 match 3 stars 6.26 score 34 scripts 1 dependents
atlasoflivingaustralia
galah:Biodiversity Data from the GBIF Node Network
The Global Biodiversity Information Facility ('GBIF', <https://www.gbif.org>) sources data from an international network of data providers, known as 'nodes'. Several of these nodes - the "living atlases" (<https://living-atlases.gbif.org>) - maintain their own web services using software originally developed by the Atlas of Living Australia ('ALA', <https://www.ala.org.au>). 'galah' enables the R community to directly access data and resources hosted by 'GBIF' and its partner nodes.
Maintained by Martin Westgate. Last updated 1 months ago.
4.0 match 43 stars 9.17 score 275 scripts 1 dependentsb-cubed-eu
impIndicator:Impact Indicators of Alien Taxa
Compute impact indicators of alien taxa using GBIF occurrence cube and EICAT assessment of alien species. Aggregates species impact of various scores due to mecahnism. Aggregates site impact of various scores due to species.
Maintained by Mukhtar Muhammed Yahaya. Last updated 15 hours ago.
biodiversity-indicatorsimpactinvasive-species
8.2 match 4.38 score 4 scripts
avrodrigues
naturaList:Classify Occurrences by Confidence Levels in the Species ID
Classify occurrence records based on confidence levels of species identification. In addition, implement tools to filter occurrences inside grid cells and to manually check for possibles errors with an interactive shiny application.
Maintained by Arthur Vinicius Rodrigues. Last updated 1 years ago.
6.6 match 4.66 score 23 scripts
inbo
inborutils:Collection of Useful R Utilities
While working on research projects, typical small functionalities are useful across these projects. Instead of copy-pasting these functions in all individual project repositories/folders, this package collects these functions for reuse by ourself and - if useful - others as well.
Maintained by Hans Van Calster. Last updated 1 years ago.
4.8 match 10 stars 6.26 score 102 scripts
traitecoevo
APCalign:Resolving Plant Taxon Names Using the Australian Plant Census
The process of resolving taxon names is necessary when working with biodiversity data. 'APCalign' uses the Australian Plant Census (APC) and the Australian Plant Name Index (APNI) to align and update plant taxon names to current, accepted standards. 'APCalign' also supplies information about the established status of plant taxa across different states/territories.
Maintained by Daniel Falster. Last updated 1 months ago.
3.8 match 4 stars 7.30 score 23 scripts 1 dependents
nataliepatten
gatoRs:Geographic and Taxonomic Occurrence R-Based Scrubbing
Streamlines downloading and cleaning biodiversity data from Integrated Digitized Biocollections (iDigBio) and the Global Biodiversity Information Facility (GBIF).
Maintained by Natalie N. Patten. Last updated 10 months ago.
4.1 match 11 stars 6.16 score 66 scripts
adamlilith
enmSdmX:Species Distribution Modeling and Ecological Niche Modeling
Implements species distribution modeling and ecological niche modeling, including: bias correction, spatial cross-validation, model evaluation, raster interpolation, biotic "velocity" (speed and direction of movement of a "mass" represented by a raster), interpolating across a time series of rasters, and use of spatially imprecise records. The heart of the package is a set of "training" functions which automatically optimize model complexity based number of available occurrences. These algorithms include MaxEnt, MaxNet, boosted regression trees/gradient boosting machines, generalized additive models, generalized linear models, natural splines, and random forests. To enhance interoperability with other modeling packages, no new classes are created. The package works with 'PROJ6' geodetic objects and coordinate reference systems.
Maintained by Adam B. Smith. Last updated 24 days ago.
bias-correctionbiogeographyecological-niche-modelingecological-niche-modellingniche-modelingniche-modellingspecies-distribution-modelingopenjdk
4.0 match 25 stars 5.62 score 37 scriptstraitecoevo
infinitylists:A Shiny-Based Application for Generating Place-Based Species Lists
This shiny-based application allows users to extract species occurrence records from the Atlas of Living Australia or GBIF and generate a species list for a defined area. All records associated with either a physical voucher (stored in herbaria or museums) or a photographic or audio voucher (stored in iNaturalist) are extracted. For each species within the defined area, the application will return voucher type, number of vouchers, date of the most recent voucher, spatial coordinates, voucher location, and the voucher collector. Records are displayed both in a table and on a map, and are downloadable as a CSV.
Maintained by Thomas Mesaglio. Last updated 5 days ago.
4.1 match 3 stars 4.82 score 7 scriptsrspatial
geodata:Download Geographic Data
Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.
Maintained by Robert J. Hijmans. Last updated 1 months ago.
1.8 match 162 stars 10.75 score 1.5k scripts 7 dependents
philipmostert
PointedSDMs:Fit Models Derived from Point Processes to Species Distributions using 'inlabru'
Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models. Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking. We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them. There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions. An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Maintained by Philip Mostert. Last updated 2 months ago.
1.7 match 25 stars 8.57 score 50 scripts 1 dependents
danlwarren
ENMTools:Analysis of Niche Evolution using Niche and Distribution Models
Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Maintained by Dan Warren. Last updated 2 months ago.
1.8 match 105 stars 6.91 score 126 scriptsphilipmostert
intSDM:Reproducible Integrated Species Distribution Models Across Norway using 'INLA'
Integration of disparate datasets is needed in order to make efficient use of all available data and thereby address the issues currently threatening biodiversity. Data integration is a powerful modeling framework which allows us to combine these datasets together into a single model, yet retain the strengths of each individual dataset. We therefore introduce the package, 'intSDM': an R package designed to help ecologists develop a reproducible workflow of integrated species distribution models, using data both provided from the user as well as data obtained freely online. An introduction to data integration methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Maintained by Philip Mostert. Last updated 2 months ago.
1.8 match 5 stars 6.26 score 12 scripts
r-a-dobson
dynamicSDM:Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution
A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Maintained by Rachel Dobson. Last updated 26 days ago.
dynamicsdmgoogle-earth-enginegoogledrivesdmspatiotemporalspatiotemporal-data-analysisspatiotemporal-forecastingspecies-distribution-modellingspecies-distributions
1.8 match 6 stars 6.16 score 20 scripts
macroecology
letsR:Data Handling and Analysis in Macroecology
Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.
Maintained by Bruno Vilela. Last updated 2 months ago.
1.2 match 29 stars 8.87 score 104 scriptsinbo
movepub:Prepare Movebank Data for Publication
Prepare animal tracking data from 'Movebank' (<https://movebank.org>) for publication in a research repository. With 'movepub' you can document data with metadata following the Data Package standard and transform these to Darwin Core and Ecological Metadata Language ('EML') for publication to the Global Biodiversity Information Facility ('GBIF') and the Ocean Biodiversity Information System ('OBIS').
Maintained by Peter Desmet. Last updated 3 days ago.
2.0 match 3 stars 4.65 score 5 scripts
vascobranco
red:IUCN Redlisting Tools
Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <https://www.iucn.org/> for more information) red list criteria.
Maintained by Vasco V. Branco. Last updated 3 months ago.
1.9 match 1 stars 4.54 score 29 scripts 1 dependents
lleisong
itsdm:Isolation Forest-Based Presence-Only Species Distribution Modeling
Collection of R functions to do purely presence-only species distribution modeling with isolation forest (iForest) and its variations such as Extended isolation forest and SCiForest. See the details of these methods in references: Liu, F.T., Ting, K.M. and Zhou, Z.H. (2008) <doi:10.1109/ICDM.2008.17>, Hariri, S., Kind, M.C. and Brunner, R.J. (2019) <doi:10.1109/TKDE.2019.2947676>, Liu, F.T., Ting, K.M. and Zhou, Z.H. (2010) <doi:10.1007/978-3-642-15883-4_18>, Guha, S., Mishra, N., Roy, G. and Schrijvers, O. (2016) <https://proceedings.mlr.press/v48/guha16.html>, Cortes, D. (2021) <arXiv:2110.13402>. Additionally, Shapley values are used to explain model inputs and outputs. See details in references: Shapley, L.S. (1953) <doi:10.1515/9781400881970-018>, Lundberg, S.M. and Lee, S.I. (2017) <https://dl.acm.org/doi/abs/10.5555/3295222.3295230>, Molnar, C. (2020) <ISBN:978-0-244-76852-2>, Štrumbelj, E. and Kononenko, I. (2014) <doi:10.1007/s10115-013-0679-x>. itsdm also provides functions to diagnose variable response, analyze variable importance, draw spatial dependence of variables and examine variable contribution. As utilities, the package includes a few functions to download bioclimatic variables including 'WorldClim' version 2.0 (see Fick, S.E. and Hijmans, R.J. (2017) <doi:10.1002/joc.5086>) and 'CMCC-BioClimInd' (see Noce, S., Caporaso, L. and Santini, M. (2020) <doi:10.1038/s41597-020-00726-5>.
Maintained by Lei Song. Last updated 2 years ago.
isolation-forestoutlier-detectionpresence-onlymodelshapley-valuespecies-distribution-modelling
1.3 match 4 stars 5.59 score 65 scripts
liviobaetscher
ElevDistr:Calculate the Distance to the Nearest Local Treeline
A method to calculate the distance to the climatic tree line for large data sets of coordinates (World Geodetic System 1984) with geographical uncertainty. The default thresholds and the treeline definition is based on Paulsen and Körner (2014) <doi:10.1007/s00035-014-0124-0>, users are free to decide what climate layers they would like to use.
Maintained by Livio Bätscher. Last updated 5 months ago.
1.3 match 4.40 score 3 scripts
bimanc
PopulationGrowthR:Linear Population Growth Scenarios
Fit linear splines to species time series to detect population growth scenarios based on Hyndman, R J and Mesgaran, M B and Cousens, R D (2015) <doi:10.1007/s10530-015-0962-8>.
Maintained by Biman Chakraborty. Last updated 3 years ago.
4.0 match 1.00 score 2 scripts
cran
spidR:Spider Knowledge Online
Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Maintained by Pedro Cardoso. Last updated 3 years ago.
2.6 match 1.00 scorecran
arakno:ARAchnid KNowledge Online
Allows the user to connect with the World Spider Catalogue (WSC; <https://wsc.nmbe.ch/>) and the World Spider Trait (WST; <https://spidertraits.sci.muni.cz/>) databases. Also performs several basic functions such as checking names validity, retrieving coordinate data from the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/>), and mapping.
Maintained by Pedro Cardoso. Last updated 3 years ago.
2.6 match 1.00 score
eduardoarle
bRacatus:A Method to Estimate the Accuracy and Biogeographical Status of Georeferenced Biological Data
Automated assessment of accuracy and geographical status of georeferenced biological data. The methods rely on reference regions, namely checklists and range maps. Includes functions to obtain data from the Global Biodiversity Information Facility <https://www.gbif.org/> and from the Global Inventory of Floras and Traits <https://gift.uni-goettingen.de/home>. Alternatively, the user can input their own data. Furthermore, provides easy visualisation of the data and the results through the plotting functions. Especially suited for large datasets. The reference for the methodology is: Arlé et al. (under review).
Maintained by Eduardo Arlé. Last updated 11 months ago.
0.5 match 8 stars 4.08 score 4 scripts
cboettig
taxalight:A Lightweight and Lightning-Fast Taxonomic Naming Interface
Creates a local Lightning Memory-Mapped Database ('LMDB') of many commonly used taxonomic authorities and provides functions that can quickly query this data. Supported taxonomic authorities include the Integrated Taxonomic Information System ('ITIS'), National Center for Biotechnology Information ('NCBI'), Global Biodiversity Information Facility ('GBIF'), Catalogue of Life ('COL'), and Open Tree Taxonomy ('OTT'). Name and identifier resolution using 'LMDB' can be hundreds of times faster than either relational databases or internet-based queries. Precise data provenance information for data derived from naming providers is also included.
Maintained by Carl Boettiger. Last updated 4 years ago.
0.5 match 5 stars 3.40 score 4 scriptsb-cubed-eu
pdindicatoR:Calculate and visualize a phylogenetic diversity indicators based on species occurence data cubes
A package to calculate and produce a map of phylogenetic diversity scores for each grid cell in the input species occurences 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.
Maintained by Lissa Breugelmans. Last updated 4 months ago.
biodiversityconservationdatacubeindicatorphylogenetic-diversity
0.5 match 3.22 score 3 scripts