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workflow.r
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## -----------------------------------------------------------------------------
##
## IR Assessment Workflow
## for Toxics Reevaluation Analysis
##
## -----------------------------------------------------------------------------
devtools::load_all()
# ------------------------------------------------------------------------------
# 0. Load Processed Data & Update Variables
# ------------------------------------------------------------------------------
ir_data <- all_processed_data
# Categories of pollutant_group - Updates also required in pollutant crosswalk spreadsheet
metals <- c("ARSENIC", "COPPER", "LEAD", "MERCURY", "ZINC")
organics <- c("CHLORDANE_TECHNICAL", "DDD", "DDE", "DDT", "DIELDRIN", "HEPTACHLOR_EPOXIDE", "PAH1", "PAH2","PAH3", "PCB_TOTAL")
# Timeframe for analysis - Update as needed
start_date_5yr <- "07/01/2018"
end_date_5yr <- "06/30/2023"
start_date_10yr <- "07/01/2013"
end_date_10yr <- "06/30/2023"
# ------------------------------------------------------------------------------
# 1. Lookup Criteria
# ------------------------------------------------------------------------------
ir_data <- lookup_criteria(ir_data)
# ------------------------------------------------------------------------------
# 2. Evaluate Criteria
# ------------------------------------------------------------------------------
criteria_results <- evaluate_criteria(ir_data)
write.csv(criteria_results, "output/criteria_results.csv")
# ------------------------------------------------------------------------------
# 3. Summarize Basic Summary
# ------------------------------------------------------------------------------
# 3a. Metals only (take into account test_fraction in analysis)
my_basic_summary_metals <- summarize_basic_metals(criteria_results)
# 3b. Other (non Metal) parameters
my_basic_summary_other <- summarize_basic(criteria_results)
# 3c. Compile All Basic Summaries
my_basic_summary <- compile_basic(my_basic_summary_other, my_basic_summary_metals)
# ------------------------------------------------------------------------------
# 4. Summarize Basic Recent Summary (Last 10 Years)
# ------------------------------------------------------------------------------
# 4a. Metals Only
my_basic_summary_10yr_metals <- summarize_basic_recent_metals(criteria_results = criteria_results, start_date = start_date_10yr, end_date = end_date_10yr)
# 4b. Other (non Metal) parameters
my_basic_summary_10yr_other <- summarize_basic_recent(criteria_results = criteria_results, start_date = start_date_10yr, end_date = end_date_10yr)
# 4c. Compile All Last 5 Year Summaries
my_basic_summary_10yr <- compile_basic_recent(my_basic_summary_10yr_metals, my_basic_summary_10yr_other)
# ------------------------------------------------------------------------------
# 5. Summarize Basic Recent Summary (Last 5 Years)
# ------------------------------------------------------------------------------
# 5a. Metals Only
my_basic_summary_5yr_metals <- summarize_basic_recent_metals(criteria_results = criteria_results, start_date = start_date_5yr, end_date = end_date_5yr)
# 5b. Other (non Metal) parameters
my_basic_summary_5yr_other <- summarize_basic_recent(criteria_results = criteria_results, start_date = start_date_5yr, end_date = end_date_5yr)
# 5c. Compile All Last 5 Year Summaries
my_basic_summary_5yr <- compile_basic_recent(my_basic_summary_5yr_metals, my_basic_summary_5yr_other)
# ------------------------------------------------------------------------------
# 6. Compile Summaries
# ------------------------------------------------------------------------------
# Consolidate Summaries
my_compiled_summaries <- compile_summaries(my_basic_summary, my_basic_summary_10yr, my_basic_summary_5yr, five_year_start_date = start_date_5yr, five_year_end_date = end_date_5yr, ten_year_start_date = start_date_10yr, ten_year_end_date = end_date_10yr)
# ------------------------------------------------------------------------------
# 7. Create Decision Logic
# ------------------------------------------------------------------------------
# 7a. Class C
my_decision_logic_class_c <- create_decision_logic_class_c(my_compiled_summaries, five_year_start_date = start_date_5yr, five_year_end_date = end_date_5yr, ten_year_start_date = start_date_10yr, ten_year_end_date = end_date_10yr)
# 7b. Class D
my_decision_logic_class_d <- create_decision_logic_class_d(my_compiled_summaries, five_year_start_date = start_date_5yr, five_year_end_date = end_date_5yr, ten_year_start_date = start_date_10yr, ten_year_end_date = end_date_10yr)
# ------------------------------------------------------------------------------
# 8. Create Results Tables
# ------------------------------------------------------------------------------
# 8a. Consolidate for Results - Class C
my_results_class_c <- create_results_class_c(my_decision_logic_class_c, five_year_start_date = start_date_5yr, five_year_end_date = end_date_5yr, ten_year_start_date = start_date_10yr, ten_year_end_date = end_date_10yr)
write.csv(my_results_class_c, file = "output/results_class_c.csv", row.names = F)
# 8b. Consolidate for Results - Class D
my_results_class_d <- create_results_class_d(my_decision_logic_class_d, five_year_start_date = start_date_5yr, five_year_end_date = end_date_5yr, ten_year_start_date = start_date_10yr, ten_year_end_date = end_date_10yr)
write.csv(my_results_class_d, file = "output/results_class_d.csv", row.names = F)
# 8c. Reconcile Class C and Class D decisions
my_results_reconciliation <- create_results_reconciliation(my_decision_logic_class_c, my_decision_logic_class_d)
write.csv(my_results_reconciliation, file = "output/results_reconciliation.csv", row.names = F)
# 8d. Recreate Results - Class C tables with merge formatting
my_results_class_c_merge <- create_results_class_c_merge(my_results_class_c)
# 8e. Recreate Results - Class D tables with merge formatting
my_results_class_d_merge <- create_results_class_d_merge(my_results_class_d)