Project repository for the analysis of abiotic niches of Ungulates. Contains source code (R) and data files. The overall layout is as follows:
- script - reusable scripts in Perl and R
- data - data, including occurrences, GIS layers and shape files
- results - analysis output (e.g. maxent output)
- doc - (executable) documentation files, including RMarkdown
The source code that is being developed is intended to be portable such that analysis workflows can be prototyped on laptops, while longer running analyses can be executed in a cloud environment. In addition to the occurrences, other input data include GIS layers for bioclimatic variables, soil, topographic heterogeneity, and vegetation types. However, these are quite large files obtained from 3rd parties, and so we consider these immutable for this project. Hence, we may store some of these separately in a DropBox folder structure. From the combined input data types, we model niches (e.g. using maxent), the results of which we write to the results folder. These are then, subsequently, used for the following:
- to calculate niche overlap between pairs of species, such that we can then cluster species by ecological similarity. This is done in a variety of ways, including by computing projected niche overlap (Schoener's D) and by computing climatic 'trait' values (e.g. those from GIS pixels that coincide with raw occurrences, or GIS pixels in projected suitable habitats) and distances in trait space between species (Gower's D).
- to identify the niche dimensions that determine Ungulate distribution, i.e which GIS layers are the most important.
