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.
|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)|
|Current Funding Organisation:||-|
|Research Foci:||Developing theories, methods, and tools|
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"
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.