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galah

An R interface to biodiversity data hosted by the living atlases; a set of organisations that share a common codebase, and act as nodes of the Global Biodiversity Information Facility.
https://github.com/AtlasOfLivingAustralia/galah-R

r

Last synced: about 2 hours ago
JSON representation

Repository metadata

Query living atlases from R

README

        

---
output: github_document
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "vignettes/README-"
)
```

# galah

[![CRAN
status](https://www.r-pkg.org/badges/version/galah)](https://cran.r-project.org/package=galah)
[![Codecov test coverage](https://codecov.io/gh/AtlasOfLivingAustralia/galah-R/branch/main/graph/badge.svg)](https://app.codecov.io/gh/AtlasOfLivingAustralia/galah-R?branch=main)

## Overview

`galah` is an R interface to biodiversity data hosted by the
[Global Biodiversity Information Facility](https://www.gbif.org) (GBIF) and
those members of the GBIF node network that maintain their own APIs (i.e. the
['living atlases'](https://living-atlases.gbif.org)). These organisations
collate and store observations of individual life forms, using the
['Darwin Core'](https://dwc.tdwg.org) data standard. `galah` was built and is
maintained by the [Science & Decision Support Team](https://labs.ala.org.au) at
the [Atlas of Living Australia](https://www.ala.org.au) (ALA).

`galah` enables users to locate and download species occurrence records
(observations, specimens, eDNA records, etc.), taxonomic information, or
associated media such as images or sounds, and to restrict their queries to
particular taxa or locations. Users can specify which columns are returned by a
query, or restrict their results to occurrences that meet particular
data-quality criteria. All functions return a `tibble` as their standard format.

The package is named for the bird of the same name
(*Eolophus roseicapilla*), a widely-distributed endemic Australian species. The
logo was designed by [Ian Brennan](https://www.iangbrennan.org/).

If you have any comments, questions or suggestions, please [contact us](mailto:[email protected]).

## Getting started

- The [quick start guide](https://galah.ala.org.au/R/articles/quick_start_guide.html) provides an introduction to the package functions.
- For an outline of the package structure, and a list of all the available functions, run `?galah` or view the [reference page](https://galah.ala.org.au/R/index.html).

## Installation

Install from CRAN:
```{r eval=FALSE}
install.packages("galah")
```

Install the development version from GitHub:
```{r eval=FALSE}
install.packages("remotes")
remotes::install_github("AtlasOfLivingAustralia/galah-R")
```

`galah` depends on `sf` for location-based searches. To install `galah` you will
need to make sure your system meets the `sf` system requirements, as specified
[here](https://cran.r-project.org/package=sf).

## Cheat sheet

## Citations
To generate a citation for the package version you are using, you can run

```r
citation(package = "galah")
```
If you're using occurrence data downloaded through `galah` in a publication,
please generate a DOI and cite it. To request a DOI for a download of occurrence
record, set `mint_doi = TRUE` in a call to `atlas_occurrences()`. To generate a
citation for the downloaded occurrence records, pass the `tibble` generated to
`atlas_citation()`.

```{r eval = FALSE}
# Download occurrence records with a DOI
occ <- atlas_occurrences(..., mint_doi = TRUE)

# See DOI
attr(occ, "doi")

# Generate citation
atlas_citation(occ)
```


Owner metadata


GitHub Events

Total
Last Year

Committers metadata

Last synced: 24 days ago

Total Commits: 2,638
Total Committers: 20
Avg Commits per committer: 131.9
Development Distribution Score (DDS): 0.677

Commits in past year: 391
Committers in past year: 5
Avg Commits per committer in past year: 78.2
Development Distribution Score (DDS) in past year: 0.345

Name Email Commits
Ben Raymond b****n@t****g 853
matilda2812 m****2@g****m 782
Martin Westgate m****e@g****m 511
Dax Kellie d****e@c****u 307
Jeremy VanDerWal j****l@g****m 64
Tasilee l****n@g****m 49
Dax Kellie D****e@c****u 24
Peggy Newman p****n@g****m 22
Shandiya Balasubramaniam s****b@g****m 6
Dave Martin d****n 3
Peter Ansell p****l@y****m 3
Tom Saleeba t****a@g****m 3
Matt Andrews M****s@c****u 2
Shandiya Balasubramaniam s****b@g****m 2
oliviatorresan o****n@c****u 2
Nick dos Remedios n****s@c****u 1
rforge rforge r****e@r****t 1
mbohun m****n@g****m 1
dewmini 5****i 1
cjwaite23 c****0@g****m 1

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Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 113
Total pull requests: 19
Average time to close issues: 6 months
Average time to close pull requests: about 2 hours
Total issue authors: 16
Total pull request authors: 4
Average comments per issue: 1.33
Average comments per pull request: 0.05
Merged pull request: 17
Bot issues: 0
Bot pull requests: 0

Past year issues: 42
Past year pull requests: 8
Past year average time to close issues: 3 months
Past year average time to close pull requests: 10 minutes
Past year issue authors: 10
Past year pull request authors: 2
Past year average comments per issue: 1.05
Past year average comments per pull request: 0.0
Past year merged pull request: 7
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/AtlasOfLivingAustralia/galah-R

Top Issue Authors

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Top Pull Request Authors

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Dependencies

DESCRIPTION cran
  • R >= 4.1.0 depends
  • assertthat * imports
  • crul * imports
  • data.table * imports
  • data.tree * imports
  • digest * imports
  • glue >= 1.3.2 imports
  • httr * imports
  • jsonlite >= 0.9.8 imports
  • lifecycle >= 1.0.0 imports
  • rlang * imports
  • sf * imports
  • stringr >= 1.0.0 imports
  • tibble * imports
  • tidyselect * imports
  • utils * imports
  • wellknown * imports
  • covr * suggests
  • dplyr * suggests
  • knitr * suggests
  • magrittr * suggests
  • pkgdown * suggests
  • rmarkdown * suggests
  • taxize * suggests
  • testthat * suggests
  • vcr >= 0.6.0 suggests
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/check-standard.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite

Score: 6.984716320118265