R Packages contributed

  • 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'). '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, and getting counts of occurrence records.

  • spocc: Interface to Species Occurrence Data Sources

    A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), '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.

  • rvertnet: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records

    Retrieve, map and summarize data from the 'VertNet.org' archives. 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.

  • rinat: Access iNaturalist data through APIs

    A programmatic interface to the API provided by the iNaturalist website.

  • bdvis: Biodiversity Data Visualizations

    Biodiversity data visualizations using R would be helpful to understand completeness of biodiversity inventory, extent of geographical, taxonomic and temporal coverage, gaps and biases in data.

  • bdDwC: : Darwinizer

    The 'shiny' application 'bdDwC' makes biodiversity data field names Darwin Core compatible.

  • bdchecks: Biodiversity Data Checks

    Supplies a Shiny app and a set of functions to perform and managing data checks for biodiversity data.

  • bdclean: A User-Friendly Biodiversity Data Cleaning App for the Inexperienced R User

    Provides features to manage the complete workflow for biodiversity data cleaning. Uploading data, gathering input from users (in order to adjust cleaning procedures), cleaning data and finally, generating various reports and several versions of the data. Facilitates user-level data cleaning, designed for the inexperienced R user. T Gueta et al (2018) . T Gueta et al (2017) .

  • 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..

  • taxotools: Tools to Handle Taxonomic Lists

    Tools include matching and merging taxonomic lists, casting and melting scientific names, managing taxonomic lists from GBIF and ITIS, harvesting names from wikipedia and fuzzy matching.

  • rsqliteadmin: A GUI to Manage SQLite Databases

    A comprehensive tool written in R Shiny to explore, manage and update SQLite Databases.

  • rangemap: Simple Tools for Defining Species Ranges

    A collection of tools to create species range maps based on occurrence data, statistics, and spatial objects. Other tools in this collection can be used to analyze the environmental characteristics of the species ranges. Plotting options to represent results in various manners are also available. Results obtained using these tools can be used to explore the distribution of species and define areas of occupancy and extent of occurrence of species. Other packages help to explore species distributions using distinct methods, but options presented in this set of tools (e.g., using trend surface analysis and concave hull polygons) are exclusive. Description of methods, approaches, and comments for some of the tools implemented here can be found in: IUCN (2001) , Peterson et al. (2011), and Graham and Hijmans (2006).

  • biosurvey: Tools for Biological Survey Planning

    A collection of tools that allows users to plan systems of sampling sites, increasing the efficiency of biodiversity monitoring by considering the relationship between environmental and geographic conditions in a region. The options for selecting sampling sites included here differ from other implementations in that they consider the environmental and geographic conditions of a region to suggest sampling sites that could increase the efficiency of efforts dedicated to monitoring biodiversity. The methods proposed here are new in the sense that they combine various criteria and points previously made in related literature; some of the theoretical and methodological bases considered are described in: Arita et al. (2011) , Soberón and Cavner (2015) , and Soberón et al. (2021).

  • R Packages in making

  • bdsns: Biodiversity data from Social Networking Websites in R

    Harvesting Biodiversity Records from Social Networking Sites Barve, V. (2014). Discovering and developing primary biodiversity data from social networking sites: A novel approach. Ecological Informatics, 24, 194-199. doi:10.1016/j.ecoinf.2014.08.008

  • ENMGadgets: Gadgets for Ecological Niche Modelling

    Frequently required functions to prepare data for Ecological Niche Modelling (ENM) software and post processing the results into meaningful outputs.

  • NicheToolbox: from getting biodiversity data to evaluating species distribution models in a friendly GUI environment.

    R package in making with a friendly Graphical User Interface (GUI) using shiny framework, aims to facilitate the process of building niche models and estimate the species distributions. Functions to curate species occurrence data (clean duplicated records), build models to estimate species niches (Bioclim, MaxEnt, Ellipsoid model) and distributions, evaluate model performance (Partial Roc, Confusion matrices), download a workflow (in html, pdf and .doc) to reproduce the analysis.