This file provides an overview of the scripts used to generate the data used in pastclim. All R scripts assume that you are in the root directory of the package.
dataset_list_included.R
is a script to update the internal dataframe which stores the link between variable names and file names and locations. It is based on ./data_files/dataset_list_included.csv
.
mis_boundaries.R
create internal dataset of mis boundaries.
region_extent.R
create internal dataset of regional extents.
region_outlines.R
create outlines for regions.
internal_seas
combines the .shp of the internal seas into an RDS object.verify_completeness_of_variables.R
this script is used to check that all
variables have the same extent (same number of missing values).
verify_files_by_dataset_R
script to check files paths for a given dataset.
check_returns_in_documentation.R
script to check that all .Rd files are have a /value returned.
NOTE: these scripts were used with terra <1.6-41, which changed the way time is coded. Make sure that you check the scripts before running, as they might not function as expected. Scripts yet to be updated/checked have been moved to "to_update".
create_internal_seas_raster.R
generates a mask for internal seas (Caspian and Black sea) which are not removed in some reconstructions. We use a fix outline over time, as there are no good reconstructions through time of their depth levels. Based on shapefiles_internal_seas.zip
This is used when editing the beyer2020
dataset.
repackage_beyer2020.sh
script to repackage the Beyer2020
data for use in pastclim
(it needs the internal sea file created by 1.). This script calls
repackage_beyer2020_split_annual_monthly.R
, which splits the annual and monthly
variables into two separate files.
create_example_dataset.sh
script to create an example dataset by subsetting Beyer2020
(it needs the file created by 2.).
extract_topography_for_beyer2020_part1.R
and extract_topography_for_beyer2020_part2.sh
create the topography variables for beyer2020
. The R
script generates a rugosity and altitude file, and the bash
file combines them and formats them nicely.
repackage_krapp2021.sh
script to repackage the Krapp2021
data for use in pastclim
.
extract_topography_for_krapp2021_part1.R
and extract_topography_for_krapp2021_part2.sh
create the topography variables for Krapp2021
. Due to a bug in terra
which does not clean temp files fully, extract_topography_for_krapp2021_part1.R
has to be run repeatedly until all time steps have been processed. The system might have to be restarted after a while to avoid running out of space on the hdd.
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