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

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 4 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (10.8%) to scientific vocabulary

Keywords

r r-package rstats

Keywords from Contributors

landscape-ecology genome point-pattern-analysis biodiversity neutral-landscape-model ecology reproducibility drake makefile ropensci

Last synced: 7 months ago · JSON representation

Repository

Automated flagging of common spatial and temporal errors in biological and palaeontological collection data, for the use in conservation, ecology and palaeontology.

Basic Info

Host: GitHub
Owner: ropensci
Language: HTML
Default Branch: master
Homepage: https://docs.ropensci.org/CoordinateCleaner/
Size: 59.1 MB

Statistics

Stars: 84
Watchers: 14
Forks: 23
Open Issues: 30
Releases: 4

Topics

r r-package rstats

Created over 9 years ago · Last pushed 10 months ago

Metadata Files

Readme Changelog Contributing Codemeta

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

r install.packages("CoordinateCleaner") library(CoordinateCleaner)

Developmental from GitHub

r devtools::install_github("ropensci/CoordinateCleaner") library(CoordinateCleaner)

Usage

A simple example:

```r

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), minma = minages, maxma = 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 %>% ccval()%>% cccap()%>% cdddmm()%>% cfrange(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

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

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GitHub Events

Total

Issues event: 3
Watch event: 6
Issue comment event: 2
Push event: 4
Fork event: 1

Last Year

Issues event: 3
Watch event: 6
Issue comment event: 2
Push event: 4
Fork event: 1

Committers

Last synced: 8 months ago

All Time

Total Commits: 730
Total Committers: 17
Avg Commits per committer: 42.941
Development Distribution Score (DDS): 0.46

Past Year

Commits: 5
Committers: 2
Avg Commits per committer: 2.5
Development Distribution Score (DDS): 0.4

Top Committers

Name	Email	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	6
plantarum	t**r@p**a	3
Hugo Gruson	B****o	2
Jeroen Ooms	j**s@g**m	2
mhesselbarth	m**h@g**m	2
AMBarbosa	A****a	1
John Baumgartner	j**s@g**m	1
Michael Sumner	m**r@g**m	1
John Waller	f**2@s**n	1
Shawn Laffan	s**n@g**m	1
Vince Buffalo	v**A@g**m	1

Committer Domains (Top 20 + Academic)

science.domain: 1 plantarum.ca: 1 idiv.de: 1 bioenv.gu.se: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time

Total issues: 93
Total pull requests: 15
Average time to close issues: 4 months
Average time to close pull requests: 5 months
Total issue authors: 58
Total pull request authors: 13
Average comments per issue: 2.14
Average comments per pull request: 0.33
Merged pull requests: 13
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: about 18 hours
Issue authors: 3
Pull request authors: 1
Average comments per issue: 0.5
Average comments per pull request: 1.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

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Top Authors

Issue Authors

jhnwllr (8)
azizka (6)
jivelasquezt (5)
AMBarbosa (4)
jaum20 (3)
HMB3 (3)
maelle (3)
wcornwell (3)
rvosa (2)
rsbivand (2)
damariszurell (2)
jpstevenson2018 (2)
sandro-unibe (2)
CyanBC (2)
pepbioalerts (2)

Pull Request Authors

maelle (2)
jhnwllr (2)
plantarum (1)
shawnlaffan (1)
Pakillo (1)
vsbuffalo (1)
Bisaloo (1)
isteves (1)
joelnitta (1)
mdsumner (1)
johnbaums (1)
mhesselbarth (1)
AMBarbosa (1)

Top Labels

Issue Labels

enhancement (6)

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- cran 1,651 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
License: GPL-3
Latest release: 3.0.1
published over 2 years ago

Versions: 15
Dependent Packages: 5
Dependent Repositories: 7
Downloads: 1,651 Last month

Rankings

Forks count: 3.6%

Stargazers count: 5.3%

Average: 8.6%

Dependent packages count: 10.7%

Dependent repos count: 11.3%

Downloads: 12.2%

Maintainers (1)

zizka.alexander@gmail.com

Last synced: 7 months ago

Dependencies

DESCRIPTION cran

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

.github/workflows/R-CMD-check.yaml actions

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

.github/workflows/pkgdown.yaml actions

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