DOI: 10.5281/zenodo.15641857
title: Data files and scripts for the manuscript entitled "Biogeographic regions within Indomalaya: an integrated approach using bird distributions"

description: NOTE: This repository is currently anonymized for peer review and will include author and paper details if accepted.

This repository contains R scripts and data files associated with analyses presented in the manuscript entitled "Biogeographic regions within Indomalaya: an integrated approach using bird distributions." 

 

The presence-absence matrices can be used to replicate all three biogeographic region delimitation analyses presented in the manuscript using the code and instructions provided in the R scripts. Specific input files for each analysis are also provided. Users who wish to begin the process with raw unfiltered distribution maps should request the spatial data from BirdLife International (https://datazone.birdlife.org/).

 

Description of the files (listed alphabetically):



01_IndomalayaBioregions_Dataset.R: This is the R script used for setting up and filtering the raw range distribution data into the final 1544-species dataset. This script also includes information about work done externally on ArcGIS and QGIS.

02_IndomalayaBioregions_NDM.R: This is the R script used for setting up the NDM input files (from the presence-absence matrix csv files), extracting information from output files from the NDM/VNDM software, and plotting the resulting AOEs as presented in the manuscript. This script also includes information about work done externally on NDM/VNDM.

03_IndomalayaBioregions_Ecostructure.R: This is the R script used for Ecostructure Grade of Membership model fitting, visualization of results as rasters, calculation of motif overlap, and construction of network graph tracking motif stability, as presented in the manuscript.

04_IndomalayaBioregions_hclust.R: This is the R script for the hierarchical clustering analysis, which includes procedures for selecting the best clustering algorithm and most optimal number(s) of clusters, as well as code for visualizing clustering results both on a dendrogram and on a map, as presented in the manuscript.

any_indomalaya.csv: This is the list of all 2827 species with any native and resident occurrence in Indomalaya. This list is the starting point for the area percentage filtering process in described in the script 01_IndomalayaBioregions_Dataset.R.

Asia_Tropic_Map_2023: Four files (.dbf, .prj, .shp, and .shx) associated with the shapefile for a rectangular map of tropical Asia that can be used as a basemap for plotting spatial data. 

gom_fit_KX.rds (X in the filename is an integer from 2 to 20): All 19 Ecostructure model fit results from K = 2 to K = 20 in RDS format.

IM60_1deg.dat: Input file to be imported into the NDM/VNDM for NDM analysis at 1° resolution, as presented in the manuscript.

IM60_1deg_2percent_DATA.out: Output file exported from NDM/VNDM software containing information about the 2% consensus areas (and the endemic species that support their delineation) found at 1° spatial resolution.

IM60_2deg.dat: Input file to be imported into the NDM/VNDM for NDM analysis at 2° resolution, as presented in the manuscript. 

IM60_2deg_2percent_DATA.out: Output file exported from NDM/VNDM software containing information about the 2% consensus areas (and the endemic species that support their delineation) found at 2° spatial resolution.

IM60_5deg.dat: Input file to be imported into the NDM/VNDM for NDM analysis at 5° resolution, as presented in the manuscript.

IM60_1deg_5percent_DATA.out: Output file exported from NDM/VNDM software containing information about the 2% consensus areas (and the endemic species that support their delineation) found at 5° spatial resolution.

IM60_halfdeg.dat: Input file to be imported into the NDM/VNDM for NDM analysis at 0.5° resolution, as presented in the manuscript.

IM60_halfdeg_2percent_DATA.out: Output file exported from NDM/VNDM software containing information about the 2% consensus areas (and the endemic species that support their delineation) found at 0.5° spatial resolution.

IM60_Presab_1deg.csv: Presence-absence data at 1° spatial resolution for the final 1544-species dataset (IM60 means Indomalaya 60%).

IM60_Presab_2deg.csv: Presence-absence data at 2° spatial resolution for the final 1544-species dataset (IM60 means Indomalaya 60%).

IM60_Presab_5deg.csv: Presence-absence data at 5° spatial resolution for the final 1544-species dataset (IM60 means Indomalaya 60%).

IM60_Presab_halfdeg.csv: Presence-absence data at 0.5° spatial resolution for the final 1544-species dataset (IM60 means Indomalaya 60%).

indomalaya_map_2023: Four files (.dbf, .prj, .shp, and .shx) associated with the shapefile for the Indomalayan Realm (as defined by the WWF) that is used as a reference for filtering range data and interpretations out all downstream output. 

matrix_1.csv: This is a modified 1° presence-absence matrix that serves as the input file for ecostructure model fitting, as well as a starting point for generating a beta-similarity distance matrix for hierarchical clustering. 04_IndomalayaBioregions_hclust.R also contains code to remove cells with <5 species from this dataset before computing beta-similarity distances.

motif_names_v4.csv: A list of all motif names (plus three-letter abbreviations) for the Ecostructure results, plus a column containing a series of graph index for use in plotting the network graph as presented in the manuscript.

NDMconsensus.xlsx: This is a spreadsheet with four separate tabs (corresponding to four spatial resolutions) that summarizes the NDM results contained in the four .out files into one document.