data-raw/readme.md

In EvolEcolGroup/pastclim: Manipulate Time Series of Palaeoclimate Reconstructions

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.

scripts to make data for pastclim (accessible with data())

1. 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.

2. mis_boundaries.R create internal dataset of mis boundaries.

3. region_extent.R create internal dataset of regional extents.

4. region_outlines.R create outlines for regions.

scripts to make extdata for pastclim (stored in inst/extdata)

1. internal_seas combines the .shp of the internal seas into an RDS object.

helpful scripts (this should be turned into tests) - stored under ./helper_functions/

1. verify_completeness_of_variables.R this script is used to check that all variables have the same extent (same number of missing values).

2. verify_files_by_dataset_R script to check files paths for a given dataset.

3. 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".

scripts to package the climate time series into nc files (old, these are being rewritten to clean up)

1. 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.

2. 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.

3. create_example_dataset.sh script to create an example dataset by subsetting Beyer2020 (it needs the file created by 2.).

4. 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.

5. repackage_krapp2021.sh script to repackage the Krapp2021 data for use in pastclim.

6. 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.

EvolEcolGroup/pastclim documentation built on Nov. 6, 2023, 5:11 a.m.