SOC_Irving_et_al_data

please cite:

Irving, K., Taniguchi-Quan, K. T. R., Aprahamian, A., Rivers, C., Sharp, G., Mazor, R.D., Theroux, S., Holt, A., Peek, R., Stein, E. D. (2022). Application of flow ecology analysis to inform prioritization for stream restoration and management actions. Frontiers in Environmental Science - Freshwater Science.

Code index

1 - 00_formatting_bug_algae_hydo.R 2a - 01_csci_median_logistic regression thresholds.R 2b - 01a_asci_median_logistic regression_thresholds.R 3 - 03_GLM_figures.R 4 - 04_correlation_matrix.R 5a - 05_csci_brts.R 5b - 05_asci_brts.R 6 - 06_relative_importance_figure.R 7 - 07_delta_h_limits.R 8 - 08_SOC_alteration.R 9 - 09_comparison_of_thresholds.R 10 - 10_Alteration_maps.R 11 - 11_final_alteration.R

code and data descriptions

1 - 00_formatting_bug_algae_hydo.R

Formatting raw CSCI and ASCI data extracted from SMC (By Liesl) Combining delta H FFM woth CSCI ASCI data Taking the median delta H over all years, sites/FFM with just one year removed Output is dataframe with bio (CSCI/ASCI) and hydro (delta H FFM) for GLMs:

00_csci_delta_formatted_median_updated_Nov2021.csv 00_asci_delta_formatted_median_Nov2021.csv

2a - 01_csci_median_logistic regression thresholds.R

Logistic regression (GLMs) for CSCI and FFM (delta H) output is predicted probability for all combinations, with input binary response and hydro

just CSCI

01_csci_neg_pos_logR_metrics_figures_April2021.csv

OoverE, MMI & CSCI

01_bugs_all_data_neg_pos_logR_metrics_figures_April2021.csv

2b - 01a_asci_median_logistic regression_thresholds.R

Same as above but with ASCI

Just Hybrid ASCI

01_h_asci_neg_pos_logR_metrics_figures_April2021.csv

Hybrid and Diatoms

01_algae_all_data_neg_pos_logR_metrics_figures_April2021.csv

3 - 03_GLM_figures.R

Figures for all FFM and bio indices with all index thresholds These figures are to be used in the FFM filtering process and are avilable in the manuscript supplementary material (Figures xxx)

4 - 04_correlation_matrix.R

Correlation of FFM delta H values at sites matched with CSCI and ASCI. Produces two correltion matrices:

04_ffm_cor_csci.csv 04_ffm_cor_asci.csv

5a - 05_csci_brts.R

brts for CSCI. Takes sveral parameter criteria to find the best model. results in relative importance for each FFM

05_rel_imp_csci_labels.csv

5b - 05_asci_brts.R

brts for ASCI. Takes sveral parameter criteria to find the best model. results in relative importance for each FFM

05_rel_imp_asci_labels.csv

6 - 06_relative_importance_figure.R

boxplot of both CSCI and ASCI relative importance

05_rel_imp_csci_asci_bar_plot_all_data.jpg

07_delta_h_limits.R

Extract delta H limits from curves for each threshold combination, FFM/index threshold/probability Produces 2 dataframes:

07_CSCI_delta_thresholds_scaled.csv 07_ASCI_delta_thresholds_scaled.csv

with delta h limits and number of observations per combinations

and combined data

07_ALL_delta_thresholds_scaled.csv

08_SOC_alteration.R

formatting delta h limits from regional curves:

08_all_delta_h_limits_all_combinations_thresh_combs.csv - all delta h limits 08_delta_H_all_years_and_subbasins.csv - all delta in SOC area, for supplementary material table xx 08_alteration_by_year_site_all_sites.csv - biologically relevant alteration

current conditions

08_altered_metrics_direction_current_by_year.csv - direction of alteration by year 08_altered_metrics_direction_current_overall.csv - direction of alteration overall 08_metric_suitability_tally_by_site_current.csv - number of years altered by site, threshold combo 08_sites_metrics_number_of_years_with_data.csv - number of years with data per site and FFM 08_metric_suitability_tally_condensed_all_sites_current.cs - % alteration per site, per combo

water conservation

08_altered_metrics_direction_watercon_by_year.csv - direction of alteration by year 08_altered_metrics_direction_watercon_overall.csv - direction of alteration overall 08_metric_suitability_tally_by_site_watercon.csv - number of years altered by site, threshold combo 08_metric_suitability_tally_condensed_all_sites_watercon.csv - % alteration per site, per combo

09_comparison_of_thresholds.R

A working script to find the best threshold combination. Produces summary tables and alteration over time plots:

09_subbasin_alteration_median_mean.csv - overall alteration per metric and combo

CSCI

CSCI_SP_Tim_Alt_over_time.jpg CSCI_DS_Dur_WS_Alt_over_time.jpg CSCI_Q99_Alt_over_time.jpg

ASCI

ASCI_SP_Dur_Alt_over_time.jpg ASCI_DS_Dur_WS_Alt_over_time.jpg ASCI_Q99_Alt_over_time.jpg

10_Alteration_maps.R

Alteration maps comparing threshold combos spatially. Produces 6 figures, one for each index/fmm

11_final_alteration.R

plots biological alteration with the final combinations for ASCI, ASCI and synthesis

11_SOC_CSCI_ASCI_HydroAlt_Synthesis_Summary_Current.csv