Data and code associated with "The evolution of male-female dominance relations in primate societies"

The files included in this repository contain the data and scripts required for the analyses presented in Huchard, Kappeler, Smit, Fichtel, Lukas (PNAS 2025) "The evolution of male-female dominance relations in primate societies". Please see the article for full details on the methods.

To repeat the analyses, download the files to a local folder on your computer. Place files 2-9 (files ending in .r) into a subfolder called "AnalysisCode" and files 10-13 (files ending in csv, txt, tre) into a subfolder called "data". Open the rmarkdown file Code_IntersexDominance.Rmd in the main folder and run the code. This markdown file refers to the data that is provided in the "data" folder and loads the additional code files from the "AnalysisCode" folder. Results will be saved as csv files in the "results" folder, and figures will be saved as pdf files in the "figures" folder. For file structure see https://github.com/dieterlukas/primate_power

Description of the files:
1) Code_IntersexDominance.Rmd: the annotated file to run the code to repeat the analyses presented in the manuscript
2) FemaleDominance_LoadData.r: script to load and prepare the data
3) FemaleDominance_PhylogeneticSignal.r: script to calculate the phylogenetic signal in the outcome variables
4) FemaleDominance_FunctionsPairwise.r: script that defines the statistical model for the pairwise analyses
5) FemaleDominance_Multivariate.r: script that defines the statistical model for the multivariate analyses
6) FemaleDominance_Figures.r: script to generate the figures
7) FemaleDominance_PrepareTablesPairwise.r: script to generate the output tables
8) FemaleDominance_VariationWithinSpecies.r: additional script to investigate variation in the outcome variables
9) FemaleDominance_Allometric.r: script for alternative analyses for allometric predictor variables
10) PrimatePhylogeny_IntersexDominance.tre: the phylogenetic tree in nexus format
11) PopulationData_IntersexDominance.csv: the data on the population level
12) SpeciesLevelPredictors_IntersexDominance.txt: the data for the species level predictor variables
13) VariableDescriptions_IntersexualDominance.txt: meta data describing all variables and their references