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

Query living atlases from R
https://github.com/AtlasOfLivingAustralia/galah-R

r

Last synced: 3 months ago
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Query living atlases from R

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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)

```