Reproducibility Workflow for Analyses of Coral Species Richness, SST, Nestedness, and Regional Variation in Japan

Description

This repository contains the input data, intermediate datasets, and R scripts used to reproduce the data processing, statistical analyses, tables, and figures presented in this study. The workflow below describes the main steps from preparation of the coral occurrence and SST data to the analyses of regional species richness, SST thresholds, nestedness, and species distribution patterns. The steps are intended to be followed in numerical order.

Steps to reproduce

Step 1. Prepare the coral occurrence data Prepare "occurrence.txt". Step 2. Prepare the NOAA SST data Prepare "noaa_psl_55a2_880b_1f29_e977_a377_fe87.nc". Step 3. Prepare the 30-region boundary file Prepare "regions_rect30.csv" (Fig. 1; Table S1). Step 4. Generate the regional coral species list Run "create_coral_species_list_by_region_30regions_long.R": "Coral_species_list_by_region_30regions_long.csv" Step 5. Calculate coral species richness for the 30 study regions Run "calculate_coral_richness_30regions.R": "Coral_richness_by_region_30regions.csv" Step 6. Extract coldest-month mean SST for the 30 study regions Run "extract_coldest_month_sst_30regions.R": "SST_30regions_cold_1991_2020.csv" Step 7. Calculate the number of occurrence sites for the 30 study regions Run "calculate_occurrence_site_counts_30regions.R": "occurrence_site_counts_30regions.csv" Step 8. Create the combined 30-region dataset Run "merge_coral_richness_and_sst_30regions_and_occurrence.R": "coral_data_30regions_combined.csv" Step 9. Prepare the 13-region boundary file Prepare "regions_rect13.csv". Step 10. Analyze the relationship between winter SST and coral species richness and the influence of occurrence-site count Run "calculate_regional_regression_summary_30_and_13regions.R": "regional_regression_summary_30_and_13regions.txt" "Table_S4_13_Kuroshio_regions.csv" "Figure3_SST_species_richness_13regions.pdf" (Secs. 2.3–2.4, 3.2–3.3; Table S4; Fig. 3). Step 11. Generate the 1°C SST-bin species matrix Run "create_analysis_coral_species_by_1C_bins_nested_analysis.R": "AnalysisCoral_species_by_1C_bins_nested_analysis.csv" Step 12. Calculate cumulative species proportions and create Figure 2 Run "create_cumulative_species_proportion_data.R": "cumulative_species_proportion_data.csv" "cumulative_species_proportion_bar_step.pdf" Step 13. Detect an SST breakpoint in coral species richness across the 30 study regions Run "segmented_breakpoint_analysis_30regions.R": "segmented_breakpoint_analysis_30regions_summary.txt" Step 14. Evaluate a fixed 19.5°C threshold in coral species richness across the 30 study regions Run "fixed_threshold_analysis_30regions_19_5C.R": "fixed_threshold_analysis_30regions_19_5C_summary.txt" Step 15. Conduct the nestedness analysis using the complete dataset Run "nestedness_complete_dataset_c0.R": "nestedness_complete_dataset_c0_summary.txt" Step 16. Conduct the nestedness analysis standardized for occurrence-site count Run "nestedness_analysis_site_standardized_c0.R": "FINAL_1000x1000_nestedness_iterations.csv" "FINAL_1000x1000_nestedness_summary.csv" "FINAL_1000x1000_run_info.txt" Step 17. Classify coral species distribution patterns across SST bands Run "classify_species_distribution_patterns_5categories.R": "species_distribution_classification_5categories.csv" (Fig. 4).

Institutions

• Wakayama University

  Wakayama, Wakayama

Categories

Licence