0. Preliminaries

The R project will have the following sections describing each one of the tasks performed during the exploration of the areas of endemism.

1. Producing NDM/VNDM input files
2. Importing NDM/VNDM outputs into R
3. Exploration of the consensus areas
4. Drawing maps

Scripts are organized in separate files as follows:

1. Functions: Source files with the functions designed for different tasks.
2. Workflow (This script): General pipeline of the analysis.
3. Additional scripts detailing the exploration of the consensus areas.

This R project is organized in the following system of directories:

  Working_directory/
  data/           -> Data files
  docs/           -> Working manuscripts and markdown files
  output/         -> Outputs of the analysis
  figs/           -> Figures
  R/              -> R Scripts

The content from ./figs and ./output can completely be reproduced from ./R.

VNDM-NDM outputs nomenclature.

Output files, figures, and Consensus areas in GIS format were saved using the following nomenclature. This nomenclature was designed to trace the NDM outputs to their respective analyses, spatial scale, and their geographical location. In order to reproduce the analysis below the nomenclature must be strictly followed.

Area name code:

It considers the spatial scale of analysis or grid size, the NDM code of the consensus area, relative geographical location, and type of GIS file (i.e grids or points) produced using VNDM-NDM save options.

Example: 1dgD_CA0_AF-grid stands for:

1dg = grid size; 
D = Default analysis; 
CA0 = Consensus area number 0;
AF = A name for the geographical region where the area is located.
grid/point = ndm grid output file type.

General regular expression = "^.*grid.txt"