Updating MH download files and expansion function

Examples/Gulf_reef_fish_CatchLimits_EDA.R

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+
+library(tidyverse)
+library(RColorBrewer)
+
+# MH dataset 
+mh <- readRDS("C:/Users/sarina.atkinson/Documents/GitHub/SEFSC/SEFSC-ODM-Management-History/ODM-MH-Data_log/data/results/MH_DL_2024Apr30.RDS")
+
+# Catch limits for Gulf Reef
+mh2 <- mh %>% filter(MANAGEMENT_CATEGORY == 'CATCH LIMITS',
+                    FMP == "REEF FISH RESOURCES OF THE GULF OF MEXICO")
+
+chk <- filter(mh, MANAGEMENT_TYPE == 'DEFINITION', 
+              FMP == "REEF FISH RESOURCES OF THE GULF OF MEXICO") %>% ungroup() %>% select(VALUE, FR_CITATION) %>% distinct()
+
+# Summarize management types by sector 
+plot1 <- ggplot(mh2 %>%
+                  group_by(SECTOR_USE, MANAGEMENT_TYPE_USE) %>%
+                  summarise(nrecs = n_distinct(REGULATION_ID)) %>%
+                  group_by(SECTOR_USE) %>% 
+                  mutate(tot = sum(nrecs), perc = nrecs/tot, labels = paste0(round(perc * 100,1), "%")), aes(x = "" , y = perc, fill = MANAGEMENT_TYPE_USE)) +
+  geom_col(width = 1, color = 1) +
+  coord_polar(theta = "y") +
+  #geom_text(aes(x = 1.7, label = labels), size=4.5, 
+  #          position = position_stack(vjust = 0.5))+
+  facet_wrap(~SECTOR_USE) +
+  scale_fill_brewer(palette = "Set3") +
+  guides(fill = guide_legend(title = "Management Type")) +
+  theme_void()
+
+# ACLs by species
+plot2 <- ggplot(mh2 %>%
+                  filter(MANAGEMENT_TYPE == 'ACL') %>%
+                  group_by(SECTOR_USE, SPP_NAME) %>%
+                  summarise(nrecs = n_distinct(REGULATION_ID)) %>%
+                  group_by(SECTOR_USE) %>% 
+                  mutate(tot = sum(nrecs), perc = nrecs/tot, labels = paste0(round(perc * 100,1), "%")), aes(x = "" , y = perc, fill = SPP_NAME)) +
+  geom_col(width = 1, color = 1) +
+  coord_polar(theta = "y") +
+  #geom_text(aes(x = 1.7, label = labels), size=4.5, 
+  #          position = position_stack(vjust = 0.5))+
+  facet_wrap(~SECTOR_USE) +
+  #scale_fill_brewer(palette = "Set3") +
+  guides(fill = guide_legend(title = "Species")) +
+  theme_void()
+
+unique(mh2$SPP_NAME)
+
+# DWG ACLS
+acl_dwg <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'ACL/ACT:  DEEP-WATER GROUPER (DWG) COMBINED') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+chk <- filter(mh2, MANAGEMENT_TYPE_USE == 'QUOTA', SPP_NAME == 'QUOTA: DEEP-WATER GROUPERS (DWG)')
+# SWG ACLS
+acl_swg <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'ACL/ACT:  OTHER SHALLOW-WATER GROUPER (OTHER SWG)') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+filter(mh2, SPP_NAME == 'ACL/ACT: SHALLOW-WATER GROUPER (SWG) COMBINED') %>% ungroup() %>% 
+  select(COMMON_NAME_USE) %>% distinct() %>% pull()
+
+# FRs for ACLS
+chk <- mh2 %>%
+  filter(MANAGEMENT_TYPE == 'ACL') %>%
+  group_by(FR_CITATION, SPP_NAME) %>%
+  summarise(nrecs = n_distinct(REGULATION_ID))
+
+filter(mh2, FR_CITATION == '73 FR 38139') %>% ungroup() %>% select(FR_URL) %>% distinct() %>% pull()
+
+# Gray Snapper ACLS
+acl_gs <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'SNAPPER, GRAY') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+# Tilefish ACLS
+acl_tile <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'ACL/ACT: TILEFISHES COMBINED') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+# Vermilion Snapper ACLS
+acl_vs <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'SNAPPER, VERMILION') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+# Mutton Snapper ACLS
+acl_ms <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'SNAPPER, MUTTON') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+# Yellowtail Snapper ACLS
+acl_ys <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'SNAPPER, YELLOWTAIL') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+# HOgfish ACLS
+acl_hog <- mh2 %>% ungroup() %>%
+  filter(SPP_NAME == 'HOGFISH') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, 
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE, NEVER_IMPLEMENTED) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION)
+
+# Catch limits for Gulf Reef
+mh3 <- mh %>% filter(MANAGEMENT_CATEGORY == 'CATCH LIMITS',
+                     FMP == "COASTAL MIGRATORY PELAGIC RESOURCES")
+# Cobia ACLS
+acl_cobia <- mh3 %>% ungroup() %>%
+  filter(SPP_NAME == 'COBIA', MANAGEMENT_TYPE_USE == 'ACL') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, ZONE_USE,
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION, REGULATION_ID)
+
+# Spanish Mackerel ACLS
+acl_sm <- mh3 %>% ungroup() %>%
+  filter(SPP_NAME == 'MACKEREL, SPANISH', ZONE_USE == 'GULF MIGRATORY GROUP SPANISH MACKEREL', MANAGEMENT_TYPE_USE == 'ACL') %>%
+  select(REGULATION_ID, MANAGEMENT_TYPE_USE, SECTOR, SECTOR_USE, FR_CITATION, ZONE_USE,
+         EFFECTIVE_DATE, START_YEAR, START_DATE2, END_DATE2,
+         VALUE, VALUE_TYPE, VALUE_UNITS, VALUE_RATE) %>% distinct() %>%
+  arrange(START_YEAR, FR_CITATION, REGULATION_ID)
+
+

ODM-MH-Analysis_ready/Catch Limits/CatchLimits.R

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+##### Catch Limits ####
+# Code to filter to all Catch Limit regulations for a species of interest
+
+##### Load packages ####
+librarian::shelf(here, tidyverse, gt, flextable, officer, dplyr, gt, officer, lubridate, htmltools, rmarkdown, tidyr)
+
+#### Load data ####
+# Load the MH Data Log
+mh <- readRDS(here("ODM-MH-Data_log", "data", "results", "MH_DL_2025Sep10.RDS"))
+
+#### Define species and region of interest ####
+species = c('SNAPPER, CUBERA', 'AMBERJACK, GREATER', 'AMBERJACK, LESSER', 'JACK, ALMACO', 'SNAPPER, SILK', 'SNAPPER, QUEEN', 'SNAPPER, BLACKFIN', 'WENCHMAN',
+            'DRUM, RED', 'COBIA', 'GROUPER, GAG', 'SNAPPER, GRAY', 'MACKEREL, KING', 'GROUPER, YELLOWEDGE', 'SNAPPER, LANE', 'GROUPER, RED', 'SNAPPER, RED', 
+            'SCAMP', 'MACKEREL, SPANISH','HOGFISH', 'SNAPPER, MUTTON', 'SNAPPER, YELLOWTAIL', 'SNAPPER, VERMILION', 'TRIGGERFISH, GRAY', 'TRIGGERFISH, QUEEN')
+region = 'GULF OF MEXICO'
+sector = 'RECREATIONAL'
+
+#### ACLs ####
+# Filter to species and region of interest
+# Remove non-detailed regulations and those that were never implemented
+# Filter to only include records that apply to the entire region (ZONE_USE = ALL) and sector of interest
+ACLs <- mh %>%
+  filter(COMMON_NAME_USE %in% species,
+         REGION %in% region,
+         SECTOR == sector,
+         DETAILED == "YES",
+         NEVER_IMPLEMENTED %in% c(0, NA),
+         REG_REMOVED == 0,
+         MANAGEMENT_TYPE_USE == "ACL") %>%
+  arrange(CLUSTER, START_DATE2) %>%
+  mutate(Species = case_when(str_detect(COMMON_NAME_USE, ",") ~ {parts <- str_split_fixed(COMMON_NAME_USE, ",", 2)
+  str_to_title(str_trim(parts[,2])) %>% paste(str_to_title(str_trim(parts[,1])))},
+                             TRUE ~ str_to_title(COMMON_NAME_USE)),
+         Fishery = str_to_title(paste0(SECTOR_USE, " ", SUBSECTOR_USE)),
+         `Region Affected` = str_to_title(paste0(REGION, " ", ZONE_USE)),
+         `First Year in Effect` = year(START_DATE2),
+         `Fishing Year Effective Date` = format(START_DATE2, "%m/%d/%Y"),
+         `FR Notice Effetive Date` = format(EFFECTIVE_DATE, "%m/%d/%Y"),
+         `FR Notice Ineffective Date` = format(INEFFECTIVE_DATE, "%m/%d/%Y"),
+         ACL = case_when(MANAGEMENT_TYPE_USE == "ACL" ~ paste0(VALUE, " ", tolower(VALUE_UNITS),ifelse(!is.na(VALUE_TYPE), paste0(" (", tolower(VALUE_TYPE), ")"), "")),
+                         TRUE ~ NA_character_),
+         `FR Reference` = case_when(MANAGEMENT_TYPE_USE == "ACL" ~ FR_CITATION,
+                                TRUE ~ NA_character_),
+         `FR URL` = case_when(MANAGEMENT_TYPE_USE == "ACL" ~ FR_URL,
+                          TRUE ~ NA_character_),
+         `Amendment Number or Rule Type` = case_when(!is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE, " ", AMENDMENT_NUMBER)),
+                                                     !is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", AMENDMENT_NUMBER)),
+                                                     is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE)),
+                                                     is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(ACTION)),
+         `Cluster` = CLUSTER) %>%
+  select(CLUSTER, Species, Fishery, `Region Affected`,
+        `First Year in Effect`, `Fishing Year Effective Date`, `FR Notice Effetive Date`, `FR Notice Ineffective Date`, `ACL`,
+         `FR Reference`, `FR URL`, `Amendment Number or Rule Type`) %>%
+  arrange(Species, CLUSTER, `First Year in Effect`)
+
+# Quota
+Quotas <- mh %>%
+  filter(COMMON_NAME_USE %in% species,
+         REGION %in% region,
+         SECTOR == sector,
+         DETAILED == "YES",
+         NEVER_IMPLEMENTED %in% c(0, NA),
+         REG_REMOVED == 0,
+         MANAGEMENT_TYPE_USE == "QUOTA") %>%
+  arrange(CLUSTER, START_DATE2) %>%
+  mutate(Species = case_when(str_detect(COMMON_NAME_USE, ",") ~ {parts <- str_split_fixed(COMMON_NAME_USE, ",", 2)
+  str_to_title(str_trim(parts[,2])) %>% paste(str_to_title(str_trim(parts[,1])))},
+  TRUE ~ str_to_title(COMMON_NAME_USE)),
+  Fishery = str_to_title(paste0(SECTOR_USE, " ", SUBSECTOR_USE)),
+  `Region Affected` = str_to_title(paste0(REGION, " ", ZONE_USE)),
+  `First Year in Effect` = year(START_DATE2),
+  `Fishing Year Effective Date` = format(START_DATE2, "%m/%d/%Y"),
+  `FR Notice Effetive Date` = format(EFFECTIVE_DATE, "%m/%d/%Y"),
+  `FR Notice Ineffective Date` = format(INEFFECTIVE_DATE, "%m/%d/%Y"),
+  Quota = case_when(MANAGEMENT_TYPE_USE == "QUOTA" ~ paste0(VALUE, " ", tolower(VALUE_UNITS),ifelse(!is.na(VALUE_TYPE), paste0(" (", tolower(VALUE_TYPE), ")"), "")),
+                  TRUE ~ NA_character_),
+  `FR Reference` = case_when(MANAGEMENT_TYPE_USE == "QUOTA" ~ FR_CITATION,
+                             TRUE ~ NA_character_),
+  `FR URL` = case_when(MANAGEMENT_TYPE_USE == "QUOTA" ~ FR_URL,
+                       TRUE ~ NA_character_),
+  `Amendment Number or Rule Type` = case_when(!is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE, " ", AMENDMENT_NUMBER)),
+                                              !is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", AMENDMENT_NUMBER)),
+                                              is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE)),
+                                              is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(ACTION)),
+  `Cluster` = CLUSTER) %>%
+  select(CLUSTER, Species, Fishery, `Region Affected`,
+         `First Year in Effect`, `Fishing Year Effective Date`, `FR Notice Effetive Date`, `FR Notice Ineffective Date`, `Quota`,
+         `FR Reference`, `FR URL`, `Amendment Number or Rule Type`) %>%
+  arrange(Species, CLUSTER, `First Year in Effect`)
+
+# ACT
+ACTs <- mh %>%
+  filter(COMMON_NAME_USE %in% species,
+         REGION %in% region,
+         SECTOR == sector,
+         DETAILED == "YES",
+         NEVER_IMPLEMENTED %in% c(0, NA),
+         MANAGEMENT_TYPE_USE == "ACT") %>%
+  arrange(CLUSTER, START_DATE2) %>%
+  mutate(Species = case_when(str_detect(COMMON_NAME_USE, ",") ~ {parts <- str_split_fixed(COMMON_NAME_USE, ",", 2)
+         str_to_title(str_trim(parts[,2])) %>% paste(str_to_title(str_trim(parts[,1])))},
+         TRUE ~ str_to_title(COMMON_NAME_USE)),
+         Fishery = str_to_title(paste0(SECTOR_USE, " ", SUBSECTOR_USE)),
+         `Region Affected` = str_to_title(paste0(REGION, " ", ZONE_USE)),
+         `First Year in Effect` = year(START_DATE2),
+         `Fishing Year Effective Date` = format(START_DATE2, "%m/%d/%Y"),
+         `FR Notice Effetive Date` = format(EFFECTIVE_DATE, "%m/%d/%Y"),
+         `FR Notice Ineffective Date` = format(INEFFECTIVE_DATE, "%m/%d/%Y"),
+         ACT = case_when(MANAGEMENT_TYPE_USE == "ACT" ~ paste0(VALUE, " ", tolower(VALUE_UNITS),ifelse(!is.na(VALUE_TYPE), paste0(" (", tolower(VALUE_TYPE), ")"), "")),
+                           TRUE ~ NA_character_),
+         `FR Reference` = case_when(MANAGEMENT_TYPE_USE == "ACT" ~ FR_CITATION,
+                                    TRUE ~ NA_character_),
+         `FR URL` = case_when(MANAGEMENT_TYPE_USE == "ACT" ~ FR_URL,
+                              TRUE ~ NA_character_),
+         `Amendment Number or Rule Type` = case_when(!is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE, " ", AMENDMENT_NUMBER)),
+                                                     !is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", AMENDMENT_NUMBER)),
+                                                     is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE)),
+                                                     is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(ACTION)),
+         `Cluster` = CLUSTER) %>%
+  select(CLUSTER, Species, Fishery, `Region Affected`,
+         `First Year in Effect`, `Fishing Year Effective Date`, `FR Notice Effetive Date`, `FR Notice Ineffective Date`, `ACT`,
+         `FR Reference`, `FR URL`, `Amendment Number or Rule Type`) %>%
+  arrange(Species, CLUSTER, `First Year in Effect`)
+
+# TAC
+TACs <- mh %>%
+  filter(COMMON_NAME_USE %in% species,
+         REGION %in% region,
+         SECTOR == sector,
+         DETAILED == "YES",
+         NEVER_IMPLEMENTED %in% c(0, NA),
+         REG_REMOVED == 0,
+         MANAGEMENT_TYPE_USE == "TAC") %>%
+  arrange(CLUSTER, START_DATE2) %>%
+  mutate(Species = case_when(str_detect(COMMON_NAME_USE, ",") ~ {parts <- str_split_fixed(COMMON_NAME_USE, ",", 2)
+  str_to_title(str_trim(parts[,2])) %>% paste(str_to_title(str_trim(parts[,1])))},
+  TRUE ~ str_to_title(COMMON_NAME_USE)),
+  Fishery = str_to_title(paste0(SECTOR_USE, " ", SUBSECTOR_USE)),
+  `Region Affected` = str_to_title(paste0(REGION, " ", ZONE_USE)),
+  `First Year in Effect` = year(START_DATE2),
+  `Fishing Year Effective Date` = format(START_DATE2, "%m/%d/%Y"),
+  `FR Notice Effetive Date` = format(EFFECTIVE_DATE, "%m/%d/%Y"),
+  `FR Notice Ineffective Date` = format(INEFFECTIVE_DATE, "%m/%d/%Y"),
+  TAC = case_when(MANAGEMENT_TYPE_USE == "TAC" ~ paste0(VALUE, " ", tolower(VALUE_UNITS),ifelse(!is.na(VALUE_TYPE), paste0(" (", tolower(VALUE_TYPE), ")"), "")),
+                  TRUE ~ NA_character_),
+  `FR Reference` = case_when(MANAGEMENT_TYPE_USE == "TAC" ~ FR_CITATION,
+                             TRUE ~ NA_character_),
+  `FR URL` = case_when(MANAGEMENT_TYPE_USE == "TAC" ~ FR_URL,
+                       TRUE ~ NA_character_),
+  `Amendment Number or Rule Type` = case_when(!is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE, " ", AMENDMENT_NUMBER)),
+                                              !is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", AMENDMENT_NUMBER)),
+                                              is.na(AMENDMENT_NUMBER) & !is.na(ACTION_TYPE) ~ str_to_title(paste0(ACTION, " ", ACTION_TYPE)),
+                                              is.na(AMENDMENT_NUMBER) &  is.na(ACTION_TYPE) ~ str_to_title(ACTION)),
+  `Cluster` = CLUSTER) %>%
+  select(CLUSTER, Species, Fishery, `Region Affected`,
+         `First Year in Effect`, `Fishing Year Effective Date`, `FR Notice Effetive Date`, `FR Notice Ineffective Date`, `TAC`,
+         `FR Reference`, `FR URL`, `Amendment Number or Rule Type`) %>%
+  arrange(Species, CLUSTER, `First Year in Effect`)