These analyses focuses on three aspect of functional diversity: Functional richness, functional evenness and functional divergence. We analysed the response of the whole community, as well as for three functional groups: urban exploiters, urban adapters and urban avoiders, to the urbanization gradient at three spatial scales and accounting for indirect effects.
The scripts are prepared to run from the R project FD_BerlinBirds and are found in the folder rscripts . For the code to work properly, it is recomended to run first the ordination scripts and then, the SEMs scripts.
Folder data :
Contains the data necessary for the analyses:
- grid_birds_abundance_corrected: Abundance of bird species from the breeding bird monitoring program in Berlin.
- birds_all_traits: functional traits for the species.
- species_groups_responses: classification of the species into the functional groups.
- grids_environmental_variables: environmental data extracted at monitoring grid scale (1km resolution).
- territories_environmental_variables: environmental data extracted at the centroid of the bird territory scale (100m resolution).
- locations_environmental_variables_20m: environmental data extracted at the exact location of the birds (20m resolution).
Folder rscripts :
- source_packages.R: contains all the R packages to run the scripts.
- source_functions.R: self-made functions to use in the scripts.
- FD_ordination_allbirds.Rmd: Ordination analysis of the whole bird community, functional traits and environmental effects.
- FD_ordination_groups.Rmd: Ordination analysis of the three functional groups, functional traits and environmental effects.
- SEMs_allbirds.Rmd: Structural Equation Models for the whole bird community, analysing direct and indirect effects of human disturbance in the urbanization gradient, mediated by vegetation structure.
- SEMs_groups.Rmd: Structural Equation Models for the three functional groups, analysing direct and indirect effects of human disturbance in the urbanization gradient, mediated by vegetation structure.