KenyaAtlasComparison

This repository contains the code and data used for the following publication:

Nussbaumer, R., Nussbaumer, A., Guchu, S., Hatfield, R.S., M. Kanga, E., Kung'u, G.N., Kuria, A., Miller, E., Ndang'ang'a, P.K., Njoroge, P., Ogada, D., Shema, S. and Jackson, C. (2024), Historical Bird Atlas and Contemporary Citizen Science Data Reveal Long-Term Changes in Geographic Range of Kenyan Birds. Diversity and Distribution. https://doi.org/10.1111/ddi.13935

The main output of this code can be visualized on kenyabirdtrends.co.ke

Code structure

Core analysis

You can reproduce the analysis by running the script in alphabetical order:

1. A_import_old_atlas.m: Process historical data (data/oldatlas/A Bird Atlas of Kenya_v5.xlsx) based on the species list data/species_base_list.xlsx into data/oldatlas.mat as well as the grid data (read from data/oldatlas/grid.geojson)
2. B_import_KBM.m: Process KBM data (downloaded from the ABAP API in data/kbm/geojson/) based on the species list data/kbm/sp_kbm.xlsx into data/kbmatlas.mat
3. C_import_ebird.m: Process eBird data (EBD file downloaded in data/eBird/ebd_KE_relOct-2023/) based on the species list data/eBird/sp_ebird.xlsx into data/ebirdatlas.mat
4. D_correction.m: Compute the confidence index into the corrected grid data/grid_corr.mat

Export

• E_export_figure.m: Generate figures for the paper
• E_export_website.m: Generate dataset in export/website/ for kenyabirdtrends.co.ke

Post-analysis for paper

F_analysis.m: More figures, some used in the paper, other not. F_phylo.m: Phyologenetic data

Other analysis and comparison not used in paper

• G_burns.m: Comparison with Burns et al. (2021)
• G_CSR8.m: Comparison with the CSR 8 population trends from AEWA
• G_Ngulia.m: Comparison with Pearson et al. (2017)
• G_sabap.m: Comparison with Underhill & Brooks (2014)
• G_scagenger.m:
• G_serengeti.m: Comparison with Henao-Diaz & Sinclair (2019)