The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.
galaxias
is an R package that helps users describe,
bundle, and share biodiversity information using the ‘Darwin Core’ data standard.
galaxias
provides tools in R to build a Darwin
Core Archive, a zip file containing standardised data and metadata
accepted by global data infrastructures. The package mirrors
functionality in devtools, usethis, and dplyr to manage data, files, and
folders. galaxias
was created by the Science & Decision Support Team
at the Atlas of Living Australia
(ALA).
The package is named for a genus of freshwater fish that is found only in the Southern Hemisphere, and predominantly in Australia and Aotearoa New Zealand. The logo shows a Spotted Galaxias (Galaxias truttaceus) drawn by Ian Brennan.
If you have any comments, questions, or suggestions, please contact us.
You can install the latest version from GitHub with:
install.packages("remotes")
::install_github("atlasoflivingaustralia/galaxias") remotes
Once on CRAN, you can use:
install.packages("galaxias")
To load the package, call:
library(galaxias)
galaxias
contains tools to:
tibbles
containing biodiversity
observations to match the Darwin Core Standard.galaxias
draws on functionality from two underlying
packages that address different challenges of the data publication
workflow: corella
,
which converts tibbles to use standard column names; and delma
which converts
markdown files to EML
format.
Here we have a small example dataset of species observations.
library(tibble)
<- tibble(
df scientificName = c("Callocephalon fimbriatum", "Eolophus roseicapilla"),
latitude = c(-35.310, -35.273),
longitude = c(149.125, 149.133),
eventDate = lubridate::dmy(c("14-01-2023", "15-01-2023")),
status = c("present", "present")
)
df#> # A tibble: 2 × 5
#> scientificName latitude longitude eventDate status
#> <chr> <dbl> <dbl> <date> <chr>
#> 1 Callocephalon fimbriatum -35.3 149. 2023-01-14 present
#> 2 Eolophus roseicapilla -35.3 149. 2023-01-15 present
We can standardise data according to Darwin Core Standard using
set_
functions.
<- df |>
df_dwc set_occurrences(occurrenceID = random_id(),
basisOfRecord = "humanObservation",
occurrenceStatus = status) |>
set_coordinates(decimalLatitude = latitude,
decimalLongitude = longitude)
df_dwc#> # A tibble: 2 × 7
#> scientificName eventDate basisOfRecord occurrenceID occurrenceStatus
#> <chr> <date> <chr> <chr> <chr>
#> 1 Callocephalon fimbriat… 2023-01-14 humanObserva… e16986de-57… present
#> 2 Eolophus roseicapilla 2023-01-15 humanObserva… e16986f2-57… present
#> # ℹ 2 more variables: decimalLatitude <dbl>, decimalLongitude <dbl>
We can then specify that we wish to use these standardised data in a
Darwin Core Archive with use_data()
. This saves
df_dwc
with a valid file name and extension, and in a
standardised location (a new directory called
/data-publish
).
use_data(df_dwc)
Before publishing your data, it is also necessary to create a
metadata statement that describes who owns the data, what the data
shows, and what licence it is released under. galaxias
enables you to write your metadata statement in R Markdown or Quarto
format, and seamlessly convert it to EML for publication.
# 1. Create a boilerplate file
use_metadata_template("metadata.Rmd")
# 2. Edit in your preferred IDE
# 3. Load into /data-publish as an EML file
use_metadata("metadata.Rmd")
The final step in your data publication workflow is to zip your directory into a single file. This file is placed in your parent directory.
build_archive(file = "my_biodiversity_data.zip")
You can share your data via any mechanism you wish, but
galaxias
provides the submit_archive()
function to open a submission window for the Atlas of Living
Australia.
Please see the Quick Start Guide for a more in-depth explanation of building Darwin Core Archives.
To generate a citation for the package version you are using, you can run:
citation(package = "galaxias")
The current recommended citation is:
Westgate MJ, Balasubramaniam S & Kellie D (2025) galaxias: Describe, Package, and Share Biodiversity Data. R Package version 0.1.0.
Developers who have contributed to galaxias
are as
follows (in alphabetical order by surname):
Amanda Buyan (@acbuyan), Fonti Kar (@fontikar), Peggy Newman (@peggynewman) & Andrew Schwenke (@andrew-1234)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.