Client package
The implemented functions allow the query, download, and import of remotely-stored and version-controlled data items. The inherent meta-database maps data files and import code to programming classes and allows access to these items via files deposited in public repositories. The purpose of the project is to increase reproducibility and establish version tracking of results from (paleo)environmental/ecological research.
Important!
Please note that the primary entities were renamed as part of the update to v0.6. The changes are:
-
database ⮕ source (dat ⮕ src)
-
variable ⮕ series (var ⮕ ser)
-
‘data’ ⮕ product
These changes were necessary so formal variables can be introduced, which will allow the connection of data products that come from different sources. These are not intended to be changed in the future.
Example
Distribution data
library(chronosphere)
# see available datasets
available <- datasets()
# download some data
# NaturalEarth land polygons
ne <- chronosphere::fetch("NaturalEarth", ser="land", ver="4.1.0")
# The entire Paleobiology Database
pbdb <- chronosphere::fetch("pbdb", ver="20230814")
# collections
colls <- unique(pbdb[, c("collection_no","lng", "lat")])
# plot records
plot(ne$geometry, col="gray", border=NA)
points(colls$lng, colls$lat, cex=0.3, pch=16, col="#54121212")
Notes
Planned updates
The following updates are currently scheduled:
- Access to variables: grouping entites that link data series together.
- Access to datafiles via a secondary URL.
- Using datafiles for the offline structuring of the downloaded files.
- Webpages for individual data series.
History
The original chronosphere was a true monolith that included lots of additional functionality to manipulate paleoenvironmental data. For better compliance with UNIX philosophy and more efficient distribution/development, the original package has been split to multiple R packages:
-
chronosphere: version-controlled data distribution. -
rgplates: functions related to tectonic reconstructions. -
via: Virtual Arrays for efficient organisation of high-dimensional data.
This is a beta version, and like R, comes with absolutely no warranty.