Optimizing laboratory cultures of <i>Gammarus fossarum</i> (Crustacea: Amphipoda) as a study organism in environmental sciences and ecotoxicology

Supplemental code and data for Alther, Krähenbühl, Bucher & Altermatt (2022) 'Optimizing laboratory cultures of Gammarus fossarum (Crustacea: Amphipoda) as a study organism in environmental sciences and ecotoxicology' (DOI: 10.1016/j.scitotenv.2022.158730). The repository folder contains three text files and a corresponding R script.

Rerunning the analysis and producing figures requires two raw data files: LabdataAK_v6_210616_Daylength_input.txt and Nutrition_Exp_KaplanMeier_v1_input.txt. In order to reproduce the analysis and figures, run 'AmphipodHusbandry_20220919.R'. Make sure that your working directory is the folder containing all data files, easily achieved by (re)starting R (or R Studio) by double-clicking the R script file in the folder. The analysis script will produce all the figures from the paper, organized in a folder 'Results' and a subfolder 'Supplement'. Figures are prepared as pixel graphics (PNG).

The R script was tested in R ver. 4.1.1 (Windows 10, version 21H1), 4.1.3 (macOS 11.6), and 4.2.0 (Ubuntu 22.04. Required packages are survival (version 3.2-13 worked), survminer (version 0.4.9 worked), and vioplot (version 0.3.7 worked).