Code

R scripts to fit hierarchical community distance sampling models

1. Virunga_HCDSM63.R: Contains code to format data and to fit a hierarchical community distance sampling model for 63 bird species relating their abundance along an elevation gradient.
2. Virunga_warblers_jsdm_elevation.R: Contains code to format data and to fit a hierarchical community distance sampling model to estimate residual correlations among five warbler species (Cisticolidae) after accounting for the effect of elevation.
3. Virunga_warblers_jsdm_null.R: Contains code to format data and to fit a hierarchical community distance sampling model to estimate residual correlations among five warbler species (Cisticolidae) - Null model.

Figures, and computation of niche overlap indices

1. Detection_probability.R: Contains code to generate community mean detection probabilities for birds in each vegetation type (Appendix S7:Figure S1).
2. Figures_niche_indices.R: Contains code to generate figures showing results from niche overlap indices, and to compute elevation, diet and foraging vertical strata niche overlap indices.
3. JSDM_output.R: Contains code to generate figures (4a,b) showing results from the community model extension used to estimate residual correlations among species pairs of warblers.

Body size variation

1. Body_size_null_model_code_n_Figure.R: Contains code to generate the null model distribution and figure for body size variation (Appendix S3: Figure S2).

Null model distributions

1. Null_model_elev.diet.strata.R: Contains code to generate niche overlap (Pianka) null distributions for a community of birds (63) along three niche axis: i) Elevation gradient, ii) Diet, and iii) Forest strata.

Supplementary Material - Appendix S1: Rank abundance plots

1. Rank_abundance_plots.R: Contains code to generate rank abundance plots to assess robustness of our single visit point count data (i.e., estimating abundance) in relation to a multi-year (i.e., 5 years) and longer duration point counts (10-min point counts).

Spatial site index

1. Spatial_site_index_detection_probability.R: Contains code to generate the null model distribution to assess whether detection probabilities for species within families are similar - Spatial site index.
2. Spatial_site_index_lantent_abundance.R: Contains code to estimate the Spatial Site index using latent abundance
3. Spatial_site_index_raw_counts.R: Contains code to estimate the Spatial Site index using raw counts(Table 1 - main text).