Novel computational methods in wildlife research

Many of our research projects require new computational methods for processing and evaluating the data obtained. We develop these analysis tools either ourselves or in cooperation with partners, and also make them available to third parties.

Project details

Duration:	since 09/2016
Third-party funded:	no
Involved Department(s):	Dept Evolutionary Genetics
Leibniz-IZW Project Leader(s):	Alexandre Courtiol (Dept Evolutionary Genetics)
Leibniz-IZW Project Team:	Liam Bailey, Colin Vullioud (all: Dept Evolutionary Genetics)
Consortium Partner(s):	-
Current Funding Organisation:	-
Research Foci:	Developing theories, methods, and tools

Many of our research projects require new approaches for processing and evaluating the data obtained. We develop computational methods to solve outstanding problems for ecologists and evolutionary biologists, which we distribute to the community by means of packages in the open source statistical software R. We identify challenging computational tasks in the research projects in which we are involved and implement general solutions that can be used by others. To complete these tasks, we combine our detailed biological knowledge on the topics with our practical knowledge of computer programming. Some of the tools we have created (or significantly contributed to) are used by many scientists all around the world (e.g. camtrapR, climwin).

Selection of already established methods and tools:

camtrapR (https://cran.r-project.org/web/packages/camtrapR/index.html): a toolkit for the management and data extraction of camera trap photographs in wildlife studies
IsoriX (https://cran.r-project.org/web/packages/IsoriX/index.html): a toolkit for building isoscapes using mixed models and inferring the geographic origin of organisms based on their isotopic ratios.
spaMM (https://cran.r-project.org/web/packages/spaMM/index.html): a toolkit to efficiently fit linear models of varying complexity, including mixed models with spatial autocorrelation.
climwin (https://cran.r-project.org/web/packages/climwin/index.html): a toolkit to detect and visualise periods of climate sensitivity (climate windows) for a given biological response.

Methods and tools in preparation:

torpor: a Bayesian method to assign metabolic rate measurements to either the torpor or the euthermia state, in heterothermic endotherm species.
hyenaR: a toolkit to manage the data of Leibniz-IZW Ngorongoro Hyena Project and help to prepare data for downstream analyses. This package also serves as a model for other long-term projects.
Rato: an adaptation of hyenaR tailored for the study of the Damaraland mole rats of the Kalahari Meerkat Project (University of Cambridge).
estiMate: a toolkit to estimate various aspects of mate choice from the observations of mating pairs in natural populations or genetic parentage analyses.
simulMate: a toolkit to simulate pair formation according to specific mating rules and population constraints.
SPI-Birds (https://nioo.knaw.nl/en/spi-birds): a project to convert individual level bird breeding data into a standard community data to facilitate collaboration and data transparency.

2021: Presentation "Using R6 object-oriented programming to build agent-based models"

Selected Publications

Courtiol A, Rousset F, Rohwäder M-S, Soto DX, Lehnert LS, Voigt CC, Hobson KA, Wassenaar LI, Kramer-Schadt S (2019): Isoscape computation and inference of spatial origins with mixed models using the R package IsoriX. Tracking Animal Migration with Stable Isotopes (Eds. Hobson K & Wassenaar LI, Academic Press), Chapter 9, 207-236. doi:10.1016/B978-0-12-814723-8.00009-X.

Rousset F, Gouy A, Martinez-Almoyna C, Courtiol A (2017): The summary likelihood method and its implementation in the Infusion package. MOL ECOL RESOUR 17, 110-119. doi:10.1111/1755-0998.12627

Niedballa J, Sollmann R, Courtiol A, Wilting A (2016): camtrapR: An R package for efficient camera trap data management. METHODS ECOL EVOL 7, 1457-1462. doi:10.1111/2041-210X.12600.