Resources - Software and data

Our work is highly interdisciplinary, and we often have to manipulate and analyse large datasets from various sources. For these big-data problems, we have developed a number of software packages (mostly in ) and curated datasets to make those tasks simpler. Follow the links below, or explore our GitHub repositories.

Software

`pastclim`

R

SDM

climate

palaeoclimate

An R library designed to provide an easy way to extract and manipulate palaeoclimate reconstructions for ecological and anthropological analyses. It is also able to handle time series of current and future reconstructions.

`tidysdm`

R

SDM

tidysdm implements Species Distribution Models using the tidymodels framework. The advantage of tidymodels is that the model syntax and the results returned to the user are standardised, thus providing a coherent interface to modelling.

`tidypopgen`

R

population genetics

tidypopgen provides a tidy grammar of population genetics, facilitating the manipulation and analysis of genetic data.

`geoGraph`

R

population genetics

graph theory

geoGraph implements graph approaches for geographic data, allowing to estimate distance costs and find shortest paths on complex geographic graphs.

`mtDNAcombine`

R

population genetics

mtDNA

An R package to collate mtDNA sequences from NCBI GenBank to generate Bayesian Skyline Plots, as described in Miller & Manica (2021).

Datasets

Palaeoclimate reconstructions

R

palaeoclimate

We have curated several time series of palaeoclimate reconstructions (e.g. Beyer et al. 2020 and Krapp et al. 2021). The easiest way to access these data is to use pastclim, but the raw data are also available from the repositories associated with those publications. See the pastclim website for details.

Ice sheet reconstructions

ice sheets

palaeoclimate

We generated estimates of extents of ice sheets during the Quaternary, with maps for every glaciation in Batchelor et al. 2019

Modern and ancient high-coverage human genomes

population genetics

A curated dataset of high-coverage shotgun data for population genomics modelling, from Maisano Delser et al. 2021

Biodiversity footprint of food production

biodiversity

agriculture

A consistent dataset of the biodiversity footprints (species richness, threatened species richness, and range rarity) of pasture and 175 crops at the global and national level., from Beyer and Manica 2021