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galah-R

Query living atlases from R

https://github.com/AtlasOfLivingAustralia/galah-R

Science Score: 36.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 24 committers (20.8%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (20.7%) to scientific vocabulary

Keywords

biodiversity biology ecology r rstats

Keywords from Contributors

ala-product-digivol
Last synced: 10 months ago · JSON representation

Repository

Query living atlases from R

Basic Info
Statistics
  • Stars: 46
  • Watchers: 8
  • Forks: 3
  • Open Issues: 25
  • Releases: 17
Topics
biodiversity biology ecology r rstats
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog

README.Rmd 

---
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)
[![R-CMD-check](https://github.com/AtlasOfLivingAustralia/galah-R/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/AtlasOfLivingAustralia/galah-R/actions/workflows/R-CMD-check.yaml)



## 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:support@ala.org.au).


## 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

  • Name: Atlas of Living Australia
  • Login: AtlasOfLivingAustralia
  • Kind: organization
  • Email: support@ala.org.au
  • Location: Australia

Free and open source IT infrastructure for the aggregation and delivery of biodiversity data. Funded by the Australian government via NCRIS and hosted by CSIRO

GitHub Events

Total
  • Create event: 4
  • Release event: 3
  • Issues event: 33
  • Watch event: 2
  • Member event: 1
  • Issue comment event: 23
  • Push event: 73
  • Pull request review event: 2
  • Pull request event: 19
  • Fork event: 1
Last Year
  • Create event: 4
  • Release event: 3
  • Issues event: 33
  • Watch event: 2
  • Member event: 1
  • Issue comment event: 23
  • Push event: 73
  • Pull request review event: 2
  • Pull request event: 19
  • Fork event: 1

Committers

Last synced: 10 months ago

All Time
  • Total Commits: 2,773
  • Total Committers: 24
  • Avg Commits per committer: 115.542
  • Development Distribution Score (DDS): 0.693
Past Year
  • Commits: 58
  • Committers: 3
  • Avg Commits per committer: 19.333
  • Development Distribution Score (DDS): 0.414
Top Committers
Name Email Commits
Ben Raymond b****n@t****g 850
matilda2812 m****2@g****m 782
Martin Westgate m****e@g****m 592
Dax Kellie d****e@c****u 351
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
Dax Kellie 4****e@u****m 6
Shandiya Balasubramaniam s****b@g****m 6
Dimi Brosens d****s@i****e 4
Ben Raymond b****d@a****u 3
Peter Ansell p****l@y****m 3
Tom Saleeba t****a@g****m 3
Dave Martin d****n@u****m 2
Matt Andrews M****s@c****u 2
Shandiya Balasubramaniam s****b@g****m 2
oliviatorresan o****n@c****u 2
Dave Martin d****n@g****m 1
Nick dos Remedios n****s@c****u 1
cjwaite23 c****0@g****m 1
dewmini 5****i@u****m 1
mbohun m****n@g****m 1
rforge rforge r****e@r****t 1
Committer Domains (Top 20 + Academic)
csiro.au: 5 rforge.net: 1 aad.gov.au: 1 inbo.be: 1 theraymonds.org: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 143
  • Total pull requests: 40
  • Average time to close issues: 6 months
  • Average time to close pull requests: about 20 hours
  • Total issue authors: 22
  • Total pull request authors: 5
  • Average comments per issue: 1.29
  • Average comments per pull request: 0.03
  • Merged pull requests: 37
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 22
  • Pull requests: 19
  • Average time to close issues: 12 days
  • Average time to close pull requests: 1 day
  • Issue authors: 6
  • Pull request authors: 3
  • Average comments per issue: 0.41
  • Average comments per pull request: 0.0
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • daxkellie (54)
  • mjwestgate (49)
  • shandiya (11)
  • matildastevenson (5)
  • fontikar (2)
  • stewartmacdonald (2)
  • wcornwell (2)
  • shahmanash (2)
  • cjwaite23 (2)
  • Acanthiza (2)
  • rasanderson (1)
  • zacha46 (1)
  • fernandabiologia (1)
  • T-LeB (1)
  • williamlai2 (1)
Pull Request Authors
  • mjwestgate (19)
  • DimEvil (12)
  • daxkellie (5)
  • shandiya (3)
  • stewartmacdonald (1)
Top Labels
Issue Labels
bug (56) enhancement (37) documentation (8) question (2) discussion (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 38
proxy.golang.org: github.com/AtlasOfLivingAustralia/galah-R
  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
proxy.golang.org: github.com/atlasoflivingaustralia/galah-r
  • Versions: 19
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago

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