'"hespdiv": an R package for spatially constrained, hierarchical, and contiguous regionalization in palaeobiogeography' paper

by Liudas Daumantas and Andrej Spiridonov

https://doi.org/10.5061/dryad.fttdz090q

This repository contains metadata and dataset files, a reference list of contributors to the main dataset, an R script used to process datasets, and R objects that contain the obtained results described in the paper. All results were obtained using the "hespdiv" R package (https://doi.org/10.5281/zenodo.10461941.

Description of the data and file structure

Dataset files:
MIOCENE.txt – contains the dataset originally downloaded from the Paleobiology Database.
MIOCENE_META.txt – contains the metadata of the dataset contained in the MIOCENE.txt
mio_mams.rda – contains the processed MIOCENE.txt dataset that was used in the case study presented in the paper.
us.xlsx - contains the coordinates of the contiguous US polygon (used only for visualisation).

Data contributors list:
occ_references_6.xlsx – contains the references of the contributors to the dataset used in the case study of the paper.

Data processing script:
data_prep.R - contains the script that was used to process the MIOCENE.txt dataset and to obtain the “mio_mams” data frame.

Results:
main_result.RDS – contains the output of the hespdiv() function call defined in the paper.
nn.RDS - contains the output of nulltest() function obtained by applying it to the main_result.
sa.RDS – contains the output of alternative subdivisions obtained with the hsa_detailed() function.
hsa_quant.RDS – contains the output of hsa_quant() function obtained by applying it to the sa.RDS object.

It should be possible to reobtain 'main_result' by applying hespdiv() call defined in the paper to occurrence data extracted from 'mio_mams' data frame.

Sharing/Access information

Links to other publicly accessible locations of the data:

• "Miocene.txt" and 'mio_mams' datasets can be accessed directly in R via hespdiv data package "HDData": https://github.com/Liudas-Dau/hespdiv\\\\\\\\_data . The package can be installed using "devtools" package: devtools::install_github("Liudas-Dau/hespdiv_data")

Data was derived from the following sources:

• Miocene.txt was downloaded from the Palaeobiology Database (https://paleobiodb.org/#/)
• Contiguous US polygon (us.xlsx) was obtained from the “spData” (Bivand et al., 2022) R package (‘world’ dataset)