Showing 21 of total 21 results (show query)
ropensci
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 25 days ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperbiodiversitydarwincoredatataxize
274 stars 13.63 score 1.6k scripts 23 dependentsropensci
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 17 days ago.
gbifspecimensapiweb-servicesoccurrencesspeciestaxonomybiodiversitydatalifewatchoscibiospocc
161 stars 13.26 score 2.1k scripts 20 dependentsropensci
rredlist:'IUCN' Red List Client
'IUCN' Red List (<https://api.iucnredlist.org/>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.
Maintained by William Gearty. Last updated 2 months ago.
iucnbiodiversityapiweb-servicestraitshabitatspeciesconservationapi-wrapperiucn-red-listtaxize
53 stars 11.49 score 195 scripts 24 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 2 months ago.
specimensapiweb-servicesoccurrencesspeciestaxonomygbifinatvertnetebirdidigbioobisalaantwebbisondataecoengineinaturalistoccurrencespecies-occurrencespocc
118 stars 10.09 score 552 scripts 5 dependentsropensci
worrms:World Register of Marine Species (WoRMS) Client
Client for World Register of Marine Species (<https://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.
Maintained by Bart Vanhoorne.. Last updated 1 years ago.
biologysciencemarineapiwebapi-clientwormsspeciesapi-wrapperbiological-datafishjerico-relevantmarine-biologymarine-speciestaxizetaxonomy
27 stars 10.04 score 372 scripts 27 dependents
usa-npn
rnpn:Interface to the National 'Phenology' Network 'API'
Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.
Maintained by Jeff Switzer. Last updated 4 days ago.
datanational-phenology-networkphenologyspeciesweb-api
21 stars 8.91 score 109 scripts
mobiodiv
mobr:Measurement of Biodiversity
Functions for calculating metrics for the measurement biodiversity and its changes across scales, treatments, and gradients. The methods implemented in this package are described in: Chase, J.M., et al. (2018) <doi:10.1111/ele.13151>, McGlinn, D.J., et al. (2019) <doi:10.1111/2041-210X.13102>, McGlinn, D.J., et al. (2020) <doi:10.1101/851717>, and McGlinn, D.J., et al. (2023) <doi:10.1101/2023.09.19.558467>.
Maintained by Daniel McGlinn. Last updated 9 days ago.
biodiversityconservationecologyrarefactionspeciesstatistics
23 stars 8.65 score 93 scriptsropensci
traits:Species Trait Data from Around the Web
Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.
Maintained by David LeBauer. Last updated 2 months ago.
traitsapiweb-servicesspeciestaxonomyapi-client
41 stars 8.65 score 82 scripts 11 dependentsropensci
rvertnet:Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Retrieve, map and summarize data from the 'VertNet.org' archives (<https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.
Maintained by Dave Slager. Last updated 5 months ago.
speciesoccurrencesbiodiversitymapsvertnetmammalsmammaliaspecimensapi-wrapperspecimenspocc
7 stars 8.43 score 35 scripts 6 dependents
luomus
finbif:Interface for the 'Finnish Biodiversity Information Facility' API
A programmatic interface to the 'Finnish Biodiversity Information Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates Finnish biodiversity data from multiple sources in a single open access portal for researchers, citizen scientists, industry and government. 'FinBIF' allows users of biodiversity information to find, access, combine and visualise data on Finnish plants, animals and microorganisms. The 'finbif' package makes the publicly available data in 'FinBIF' easily accessible to programmers. Biodiversity information is available on taxonomy and taxon occurrence. Occurrence data can be filtered by taxon, time, location and other variables. The data accessed are conveniently preformatted for subsequent analyses.
Maintained by William K. Morris. Last updated 10 days ago.
apibiodiversitybiodiversity-informaticsbiodiversity-informationfinbiffinbif-accessoccurrencesr-programmingspeciesspecimenstaxontaxonomyweb-services
5 stars 8.07 score 42 scripts 3 dependentsropensci
wikitaxa:Taxonomic Information from 'Wikipedia'
'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
Maintained by Zachary Foster. Last updated 6 months ago.
taxonomyspeciesapiweb-serviceswikipediavernacularwikispecieswikicommonstaxizewikipedia-api
21 stars 8.05 score 11 scripts 24 dependents
oganm
homologene:Quick Access to Homologene and Gene Annotation Updates
A wrapper for the homologene database by the National Center for Biotechnology Information ('NCBI'). It allows searching for gene homologs across species. Data in this package can be found at <ftp://ftp.ncbi.nih.gov/pub/HomoloGene/build68/>. The package also includes an updated version of the homologene database where gene identifiers and symbols are replaced with their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.
Maintained by Ogan Mancarci. Last updated 1 years ago.
bioinformaticshomologenemancarci-2017ncbi-taxonomyogan-biospecieswrapper
43 stars 7.88 score 164 scripts 4 dependentsmobiodiv
mobsim:Spatial Simulation and Scale-Dependent Analysis of Biodiversity Changes
Simulation, analysis and sampling of spatial biodiversity data (May, Gerstner, McGlinn, Xiao & Chase 2017) <doi:10.1111/2041-210x.12986>. In the simulation tools user define the numbers of species and individuals, the species abundance distribution and species aggregation. Functions for analysis include species rarefaction and accumulation curves, species-area relationships and the distance decay of similarity.
Maintained by Felix May. Last updated 4 months ago.
biodiversitymacroecologypoint-pattern-analysisrarefactionsimulationspeciesspecies-abundance-distributionscpp
20 stars 7.84 score 76 scripts
ericmarcon
entropart:Entropy Partitioning to Measure Diversity
Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.
Maintained by Eric Marcon. Last updated 2 months ago.
biodiversitydiversityentropy-partitioningestimatormeasurespecies
9 stars 7.81 score 115 scripts 1 dependentsropensci
ritis:Integrated Taxonomic Information System Client
An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
Maintained by Julia Blum. Last updated 2 months ago.
taxonomybiologynomenclaturejsonapiwebapi-clientidentifiersspeciesnamesapi-wrapperitistaxize
16 stars 7.72 score 64 scripts 24 dependentsropensci
rsnps:Get 'SNP' ('Single-Nucleotide' 'Polymorphism') Data on the Web
A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database (<https://www.ncbi.nlm.nih.gov/projects/SNP/>). Functions are included for searching for 'NCBI'. For 'OpenSNP', functions are included for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.
Maintained by Julia Gustavsen. Last updated 2 years ago.
genesnpsequenceapiwebapi-clientspeciesdbsnpopensnpncbigenotypedatasnpsweb-api
53 stars 7.08 score 63 scripts 1 dependentsropensci
natserv:'NatureServe' Interface
Interface to 'NatureServe' (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps.
Maintained by Christopher Tracey. Last updated 2 months ago.
taxonomyspeciesapiweb-servicesnatureservemetadatamapstaxize
11 stars 7.06 score 18 scripts 24 dependentsropensci
phylocomr:Interface to 'Phylocom'
Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.
Maintained by Luna Luisa Sanchez Reyes. Last updated 2 years ago.
phylogenyphylocomphylodiversitycommunity structurecharacter evolutionspeciescommunity-ecologyecologyevolution
15 stars 6.81 score 19 scripts 3 dependents
mpio-be
rangeMapper:A Platform for the Study of Macro-Ecology of Life History Traits
Tools for generation of (life-history) traits and diversity maps on hexagonal or square grids. Valcu et al.(2012) <doi:10.1111/j.1466-8238.2011.00739.x>.
Maintained by Mihai Valcu. Last updated 2 years ago.
assemblage-levelecologygloballife-history-traitsraster-cellspecies
8 stars 5.38 score 30 scripts
fmestre1
MetaLandSim:Landscape and Range Expansion Simulation
Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change). References: Mestre, F., Canovas, F., Pita, R., Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017) <doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja, P. (2020) <doi:10.1186/s12898-019-0273-5>.
Maintained by Frederico Mestre. Last updated 2 years ago.
biogeographyecologymetapopulationspecies
3 stars 5.10 score 28 scripts
psolymos
opticut:Likelihood Based Optimal Partitioning and Indicator Species Analysis
Likelihood based optimal partitioning and indicator species analysis. Finding the best binary partition for each species based on model selection, with the possibility to take into account modifying/confounding variables as described in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>. The package implements binary and multi-level response models, various measures of uncertainty, Lorenz-curve based thresholding, with native support for parallel computations.
Maintained by Peter Solymos. Last updated 10 months ago.
ecologyindicator-species-analysislikelihoodoptimal-partitioningspecies
2 stars 3.91 score 82 scripts