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Data Cleaning and Standardization","monthly_downloads":2024,"total_dependent_repos":7,"total_dependent_packages":5,"readme":"# CoordinateCleaner v3.0\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/CoordinateCleaner)](https://cranlogs.r-pkg.org:443/badges/CoordinateCleaner)\n[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/CoordinateCleaner)](https://cranlogs.r-pkg.org:443/badges/grand-total/CoordinateCleaner)\n[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/CoordinateCleaner)](https://cranlogs.r-pkg.org:443/badges/CoordinateCleaner)\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2539408.svg)](https://doi.org/10.5281/zenodo.2539408)\n[![rOpenSci peer-review](https://badges.ropensci.org/210_status.svg)](https://github.com/ropensci/software-review/issues/210)\n\n**CoordinateCleaner has been updated to version 3.0 on github and on CRAN to adapt to the retirement of sp and raster. The update may not be compatible with analysis-pipelines build with version 2.x***\n\nAutomated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology. Specifically includes tests for\n\n* General coordinate validity\n* Country and province centroids\n* Capital coordinates\n* Coordinates of biodiversity institutions\n* Spatial outliers\n* Temporal outliers\n* Coordinate-country discordance\n* Duplicated coordinates per species\n* Assignment to the location of the GBIF headquarters\n* Urban areas\n* Seas\n* Plain zeros\n* Equal longitude and latitude\n* Rounded coordinates\n* DDMM to DD.DD coordinate conversion errors\n* Large temporal uncertainty (fossils)\n* Equal minimum and maximum ages (fossils)\n* Spatio-temporal outliers (fossils)\n\nCoordinateCleaner can be particularly useful to improve data quality when using data from GBIF (e.g. obtained with [rgbif]( https://github.com/ropensci/rgbif)) or the Paleobiology database (e.g. obtained with [paleobioDB](https://github.com/ropensci/paleobioDB)) for historical biogeography (e.g. with [BioGeoBEARS](https://CRAN.R-project.org/package=BioGeoBEARS) or [phytools](https://CRAN.R-project.org/package=phytools)), automated conservation assessment (e.g. with [speciesgeocodeR](https://github.com/azizka/speciesgeocodeR/wiki) or [conR](https://CRAN.R-project.org/package=ConR)) or species distribution modelling (e.g. with [dismo](https://CRAN.R-project.org/package=dismo) or [sdm](https://CRAN.R-project.org/package=sdm)). See [scrubr](https://github.com/ropensci-archive/scrubr) and [taxize](https://github.com/ropensci/taxize) for complementary taxonomic cleaning or [biogeo](https://github.com/cran/biogeo) for correcting spatial coordinate errors.\n\nSee [News](https://github.com/ropensci/CoordinateCleaner/blob/master/NEWS.md) for update information.\n\n# Installation\n## Stable from CRAN\n\n```r\ninstall.packages(\"CoordinateCleaner\")\nlibrary(CoordinateCleaner)\n```\n\n## Developmental from GitHub\n```r\ndevtools::install_github(\"ropensci/CoordinateCleaner\")\nlibrary(CoordinateCleaner)\n```\n\n# Usage\nA simple example:\n\n```r\n# Simulate example data\nminages \u003c- runif(250, 0, 65)\nexmpl \u003c- data.frame(species = sample(letters, size = 250, replace = TRUE),\n                    decimalLongitude = runif(250, min = 42, max = 51),\n                    decimalLatitude = runif(250, min = -26, max = -11),\n                    min_ma = minages,\n                    max_ma = minages + runif(250, 0.1, 65),\n                    dataset = \"clean\")\n\n# Run record-level tests\nrl \u003c- clean_coordinates(x = exmpl)\nsummary(rl)\nplot(rl)\n\n# Dataset level \ndsl \u003c- clean_dataset(exmpl)\n\n# For fossils\nfl \u003c- clean_fossils(x = exmpl,\n                          taxon = \"species\",\n                          lon = \"decimalLongitude\", \n                          lat = \"decimalLatitude\")\nsummary(fl)\n\n# Alternative example using the pipe\nlibrary(tidyverse)\n\ncl \u003c- exmpl %\u003e%\n  cc_val()%\u003e%\n  cc_cap()%\u003e%\n  cd_ddmm()%\u003e%\n  cf_range(lon = \"decimalLongitude\", \n           lat = \"decimalLatitude\", \n           taxon  =\"species\")\n```\n\n# Documentation\nPipelines for cleaning data from the Global Biodiversity Information Facility (GBIF) and the Paleobiology Database (PaleobioDB) are available in [here](https://ropensci.github.io/CoordinateCleaner/articles/).\n\n\n# Contributing\nSee the [CONTRIBUTING](https://github.com/ropensci/CoordinateCleaner/blob/master/CONTRIBUTING.md) document.\n\n# Citation\nZizka A, Silvestro D, Andermann T, Azevedo J, Duarte Ritter C, Edler D, Farooq H, Herdean A, Ariza M, Scharn R, Svanteson S, Wengtrom N, Zizka V \u0026 Antonelli A (2019) CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. 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