CoordinateCleaner
Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.
https://github.com/ropensci/coordinatecleaner
Category: Biosphere
Sub Category: Biodiversity Data Cleaning and Standardization
Keywords
r r-package rstats
Keywords from Contributors
biodiversity gbif spocc ecology spatial-analysis gdal geo openscience hugo genome
Last synced: about 14 hours ago
JSON representation
Repository metadata
Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.
- Host: GitHub
- URL: https://github.com/ropensci/coordinatecleaner
- Owner: ropensci
- Created: 2016-10-25T08:47:23.000Z (over 8 years ago)
- Default Branch: master
- Last Pushed: 2024-03-05T17:43:40.000Z (about 1 year ago)
- Last Synced: 2025-04-17T21:25:18.519Z (9 days ago)
- Topics: r, r-package, rstats
- Language: HTML
- Homepage: https://docs.ropensci.org/CoordinateCleaner/
- Size: 58.8 MB
- Stars: 81
- Watchers: 14
- Forks: 22
- Open Issues: 26
- Releases: 4
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
README.md
CoordinateCleaner v3.0
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
- Seas
- 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.
Installation
Stable from CRAN
install.packages("CoordinateCleaner")
library(CoordinateCleaner)
Developmental from GitHub
devtools::install_github("ropensci/CoordinateCleaner")
library(CoordinateCleaner)
Usage
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")
Documentation
Pipelines for cleaning data from the Global Biodiversity Information Facility (GBIF) and the Paleobiology Database (PaleobioDB) are available in here.
Contributing
See the CONTRIBUTING document.
Citation
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
Owner metadata
- Name: rOpenSci
- Login: ropensci
- Email: [email protected]
- Kind: organization
- Description:
- Website: https://ropensci.org/
- Location: Berkeley, CA
- Twitter: rOpenSci
- Company:
- Icon url: https://avatars.githubusercontent.com/u/1200269?v=4
- Repositories: 307
- Last ynced at: 2023-03-10T20:30:59.242Z
- Profile URL: https://github.com/ropensci
GitHub Events
Total
- Issues event: 1
- Watch event: 3
- Fork event: 1
Last Year
- Issues event: 1
- Watch event: 3
- Fork event: 1
Committers metadata
Last synced: 5 days ago
Total Commits: 725
Total Committers: 16
Avg Commits per committer: 45.313
Development Distribution Score (DDS): 0.457
Commits in past year: 33
Committers in past year: 4
Avg Commits per committer in past year: 8.25
Development Distribution Score (DDS) in past year: 0.121
| Name | Commits | |
|---|---|---|
| azizka | a****a@b****e | 394 |
| azizka | z****r@g****m | 187 |
| Zizka | a****y@i****e | 51 |
| BrunoVilela | b****a@h****m | 29 |
| Pakillo | f****c@g****m | 28 |
| Irene | j****e@e****m | 20 |
| Maëlle Salmon | m****n@y****e | 4 |
| Hugo Gruson | B****o | 2 |
| Jeroen Ooms | j****s@g****m | 2 |
| mhesselbarth | m****h@g****m | 2 |
| John Baumgartner | j****s@g****m | 1 |
| John Waller | f****2@s****n | 1 |
| Shawn Laffan | s****n@g****m | 1 |
| Vince Buffalo | v****A@g****m | 1 |
| AMBarbosa | A****a | 1 |
| Michael Sumner | m****r@g****m | 1 |
Committer domains:
- science.domain: 1
- idiv.de: 1
- bioenv.gu.se: 1
Issue and Pull Request metadata
Last synced: about 14 hours ago
Total issues: 91
Total pull requests: 14
Average time to close issues: 4 months
Average time to close pull requests: 5 months
Total issue authors: 57
Total pull request authors: 12
Average comments per issue: 2.19
Average comments per pull request: 0.29
Merged pull request: 12
Bot issues: 0
Bot pull requests: 0
Past year issues: 5
Past year pull requests: 0
Past year average time to close issues: 7 days
Past year average time to close pull requests: N/A
Past year issue authors: 5
Past year pull request authors: 0
Past year average comments per issue: 0.6
Past year average comments per pull request: 0
Past year merged pull request: 0
Past year bot issues: 0
Past year bot pull requests: 0
Top Issue Authors
- jhnwllr (8)
- azizka (6)
- jivelasquezt (5)
- AMBarbosa (4)
- HMB3 (3)
- jaum20 (3)
- wcornwell (3)
- maelle (3)
- pepbioalerts (2)
- CyanBC (2)
- jpstevenson2018 (2)
- sandro-unibe (2)
- rvosa (2)
- damariszurell (2)
- rsbivand (2)
Top Pull Request Authors
- maelle (2)
- jhnwllr (2)
- joelnitta (1)
- mdsumner (1)
- johnbaums (1)
- shawnlaffan (1)
- mhesselbarth (1)
- Pakillo (1)
- vsbuffalo (1)
- Bisaloo (1)
- isteves (1)
- AMBarbosa (1)
Top Issue Labels
- enhancement (6)
Top Pull Request Labels
Package metadata
- Total packages: 1
-
Total downloads:
- cran: 1,324 last-month
- Total dependent packages: 5
- Total dependent repositories: 7
- Total versions: 15
- Total maintainers: 1
cran.r-project.org: CoordinateCleaner
Automated Cleaning of Occurrence Records from Biological Collections
- Homepage: https://ropensci.github.io/CoordinateCleaner/
- Documentation: http://cran.r-project.org/web/packages/CoordinateCleaner/CoordinateCleaner.pdf
- Licenses: GPL-3
- Latest release: 3.0.1 (published over 1 year ago)
- Last Synced: 2025-04-25T12:08:08.976Z (1 day ago)
- Versions: 15
- Dependent Packages: 5
- Dependent Repositories: 7
- Downloads: 1,324 Last month
-
Rankings:
- Forks count: 3.648%
- Stargazers count: 5.337%
- Average: 8.638%
- Dependent packages count: 10.686%
- Dependent repos count: 11.271%
- Downloads: 12.247%
- Maintainers (1)
Dependencies
- R >= 3.5.0 depends
- dplyr * imports
- geosphere * imports
- ggplot2 * imports
- grDevices * imports
- graphics * imports
- methods * imports
- raster * imports
- rgbif * imports
- rgdal * imports
- rgeos * imports
- rnaturalearth * imports
- sp * imports
- stats * imports
- tidyselect * imports
- utils * imports
- countrycode * suggests
- covr * suggests
- knitr * suggests
- magrittr * suggests
- maps * suggests
- paleobioDB * suggests
- rmarkdown * suggests
- rnaturalearthdata * suggests
- testthat * suggests
- viridis * suggests
- actions/checkout v2 composite
- actions/upload-artifact main composite
- r-lib/actions/check-r-package v1 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
- actions/checkout v2 composite
- r-lib/actions/setup-pandoc v1 composite
- r-lib/actions/setup-r v1 composite
- r-lib/actions/setup-r-dependencies v1 composite
Score: 14.64360113380363