There were some changes to the documentation of CoordinateCleaner with version 2.0-17. You can find three vignettes on cleaning point occurrence records (for instance from www.gbif.org), fossil data and using custom gazetteers with the package now. Additional information on dataset-level cleaning and identifying geographic outliers can be found here.
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
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