GitHub - OBAMANEXT/pelagic_fish_assemblages: Code for the manuscript Community-level modelling of pelagic fish assemblages in the Baltic Sea reveals temporal shifts and effects of environmental drivers

This repository presents the code for the manuscript

Community-level modelling of pelagic fish assemblages in the Baltic Sea reveals temporal shifts and effects of environmental drivers

The algorithm consists of the following steps:

Running scripts starting with 1 would aggregate data for the analysis. Alternatively, one can upload the data files from https://doi.org/10.5281/zenodo.22027768
Run main.py, which runs MCMC analysing the data
Run files starting with 2_ for the analysis.
Run files starting with 3_ for some extra analysis.

Some other scripts are used for supportive functions / visualisation

dependencies:

Name		Name	Last commit message	Last commit date
data		data
data_figures		data_figures
input_data		input_data
internal_results		internal_results
new_artist		new_artist
probabilistic_programming		probabilistic_programming
result_files		result_files
results_appendix		results_appendix
results_main_text		results_main_text
samples		samples
1_1_make_obs_list.ipynb		1_1_make_obs_list.ipynb
1_2_make_map.ipynb		1_2_make_map.ipynb
1_2b_correct_map.ipynb		1_2b_correct_map.ipynb
1_3_map_transparency_oxygen.ipynb		1_3_map_transparency_oxygen.ipynb
1_4_map_salinity_temperature.ipynb		1_4_map_salinity_temperature.ipynb
1_5_make_data.ipynb		1_5_make_data.ipynb
1_6_make_anchor_points.ipynb		1_6_make_anchor_points.ipynb
2_1_check_whats_up.ipynb		2_1_check_whats_up.ipynb
2_2_make_predictions.py		2_2_make_predictions.py
2_3_all_responces.ipynb		2_3_all_responces.ipynb
2_4_by_species.ipynb		2_4_by_species.ipynb
2_5_clustering_map.ipynb		2_5_clustering_map.ipynb
2_6_richness.ipynb		2_6_richness.ipynb
3_1_rhat.ipynb		3_1_rhat.ipynb
3_2_estimate_variance_partitioning.py		3_2_estimate_variance_partitioning.py
3_3_show_variance_partitioning.ipynb		3_3_show_variance_partitioning.ipynb
LICENSE		LICENSE
README.md		README.md
anchor_points.py		anchor_points.py
data_pers.py		data_pers.py
load_data.py		load_data.py
main.py		main.py
main_test.py		main_test.py
map_23.png		map_23.png
model.py		model.py
plot_data_hauls.ipynb		plot_data_hauls.ipynb
plot_data_species.ipynb		plot_data_species.ipynb
plot_map.ipynb		plot_map.ipynb
plots.py		plots.py
profiling.py		profiling.py
read_data.py		read_data.py
useful.py		useful.py

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