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).

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.
torpor (https://github.com/vullioud/torpor): a toolkit to fit thermoregulatory curves in heterothermic endotherm animals, while assigning metabolic rate measurements to either the torpor or the euthermia state.
timevarcorr (https://cran.r-project.org/web/packages/timevarcorr/index.html): a toolkit to compute how the correlation between 2 time-series changes over time.

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.

Fasel N, Vullioud C, Genoud M (2022): Assigning metabolic rate measurements to torpor and euthermy in heterothermic endotherms: "torpor", a new package for R. BIOL OPEN 11, bio059064. doi:10.1242/bio.059064.

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.