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*
Automated 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
- General coordinate validity
- Country and province centroids
- Capital coordinates
- Coordinates of biodiversity institutions
- Spatial outliers
- Temporal outliers
- Coordinate-country discordance
- Duplicated coordinates per species
- Assignment to the location of the GBIF headquarters
- Urban areas
- Plain zeros
- Equal longitude and latitude
- Rounded coordinates
- DDMM to DD.DD coordinate conversion errors
- Large temporal uncertainty (fossils)
- Equal minimum and maximum ages (fossils)
- Spatio-temporal outliers (fossils)
CoordinateCleaner can be particularly useful to improve data quality when using data from GBIF (e.g. obtained with rgbif) or the Paleobiology database (e.g. obtained with paleobioDB) for historical biogeography (e.g. with BioGeoBEARS or phytools), automated conservation assessment (e.g. with speciesgeocodeR or conR) or species distribution modelling (e.g. with dismo or sdm). See scrubr and taxize for complementary taxonomic cleaning or biogeo for correcting spatial coordinate errors.
See News for update information.
A simple example:
# Simulate example data minages <- runif(250, 0, 65) exmpl <- data.frame(species = sample(letters, size = 250, replace = TRUE), decimalLongitude = runif(250, min = 42, max = 51), decimalLatitude = runif(250, min = -26, max = -11), min_ma = minages, max_ma = minages + runif(250, 0.1, 65), dataset = "clean") # Run record-level tests rl <- clean_coordinates(x = exmpl) summary(rl) plot(rl) # Dataset level dsl <- clean_dataset(exmpl) # For fossils fl <- clean_fossils(x = exmpl, taxon = "species", lon = "decimalLongitude", lat = "decimalLatitude") summary(fl) # Alternative example using the pipe library(tidyverse) cl <- exmpl %>% cc_val()%>% cc_cap()%>% cd_ddmm()%>% cf_range(lon = "decimalLongitude", lat = "decimalLatitude", taxon ="species")
Pipelines for cleaning data from the Global Biodiversity Information Facility (GBIF) and the Paleobiology Database (PaleobioDB) are available in here.
See the CONTRIBUTING document.
Zizka 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 & Antonelli A (2019) CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution, 10(5):744-751, doi:10.1111/2041-210X.13152, https://github.com/ropensci/CoordinateCleaner