Life on the edge: A new toolbox for population-level climate change vulnerability assessments

Global change is impacting biodiversity across all habitats on earth. New selection pressures from changing climatic conditions and other anthropogenic activities are creating heterogeneous ecological and evolutionary responses across many species’ geographic ranges. Yet we currently lack standardised and reproducible tools to effectively predict the resulting patterns in species vulnerability to declines or range changes.
We developed an informatic toolbox that integrates ecological, environmental and genomic data and analyses (environmental dissimilarity, species distribution models, landscape connectivity, neutral and adaptive genetic diversity, genotype-environment associations and genomic offset) to estimate population vulnerability. In our toolbox, functions and data structures are coded in a standardised way so that it is applicable to any species or geographic region where appropriate data are available, for example individual or population sampling and genomic datasets (e.g. RA..., Raw sequence data is available at the European Nucleotide Archive (ENA): Myotis escalerai and M. crypticus (PRJEB29086), and the NCBI Short Read Archive (SRA): Afrixalus fornasini – (SRP150605). Input data (processed genomic data and spatial-environmental data prior to running the toolbox) available as part of this repository.
Methods: see methods text of manuscript and tutorials: Setup and running the LotE toolbox - https://cd-barratt.github.io/Life_on_the_edge.github.io/Vignette, Full tutorials for setup and running the LotE toolbox - https://cd-barratt.github.io/Life_on_the_edge.github.io/Vignette
This software is intended for HPC use. Please make sure the software below is installed and functional in your HPC environment before proceeding:

Life on the edge data and scripts (also available here: https://github.com/cd-barratt/Life_on_the_edge)

Singularity (3.5) and bioconductor container with correct R version: https://cloud.sylabs.io/library/sinwood/bioconductor/bioconductor_3.14

R (4.1.3). Dependencies for toolbox installed within R version in singularity container upon setup (you specify your R libraries in the script where annotated)
Julia (1.7.2)

Additionally you need to download the following and place in the correct directories to be sure the toolbox will function properly:
* Environmental predictor data - please download and place environmental layers used for SDMs, GEAs etc in separate folders for current and future environmental conditions. These f..., # Life on the edge: a new toolbox for population-level climate change vulnerability assessments

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Dataset contains input files needed to run Life on the edge for an example dataset (Afrixalus fornasini)
You may run data for your focal species following the structure and content of the example files provided

First you need to download the following and place in the correct directories to be sure the toolbox will function properly:

* Environmental predictor data (e.g. Worldclim2/CHELSA, land cover, see below)
* A working plink and maxent version (see below)
* Country border data (e.g. Natural Earth data, see below)

## Tutorials for initial setup and running the toolbox

Full setup and how to run the LotE toolbox - [https://cd-barratt.github.io/Life_on_the_edge.github.io/Vignette](https://cd-barratt.github.io/Life_on_the_edge.github.io/Vignette)

## Description of the data and file structure

* Params.tsv is a tab separated file that contains all parameters for running each species ...