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functions.R
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#######################################################
# Functions for use in GOAB files
# To pull these functions into a script, use source("functions.R")
#
# Created by CWM on 11/15/24
#######################################################
# Load in all .csv datasets from a designated file
get_data <- function(a) {
print(a)
files <- list.files(
path = a,
pattern = "*.csv",
full.names = F,
recursive = FALSE
)
for (i in seq(1, length(files))) {
print(files[[i]])
n <- gsub(".csv", "", files[[i]])
assign(n, read.csv(paste0(a, files[[i]])), envir = .GlobalEnv)
}
}
# Attribute data to Commercial Fisheries Management Units based on ADFG groudfish statistical areas.
# This code is written for GOAB bio data, with the column STATAREA containing statistical areas
area_split_cfmu <- function(a) {
a %>%
mutate(
CFMU = case_when(
!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(26) ~ "MAINLAND",
# Mainland salmon stat areas, Area Q/R!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(27, 576) ~ "CHIGNIK",
# Chignik salmon stat area, Area R!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(28) ~ "SAKPEN",
# South AK Peninsula Eastern District salmon stat areas, Area R!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(30, 664, 674, 684, 694) ~ "ALEUTIAN",
# Sotuh AK Peninsula Western District salmon stat areas, Area R!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(31) ~ "BERING",
# Any harvest in Bering Sea, salmon stat areas!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(445, 446, 455, 465) ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(496, 105) &
!STATAREA %in% c(496100, 496030) ~ "NG",
# North Gulf Coast, Area J, Stat Area in 2016 listed as 105932 but likely 505932
STATAREA %in% c(496100, 496030) ~ "CI",
# These areas have similar stat area to NG but are in CI!is.na(STATAREA) &
floor(STATAREA / 1000) %in% c(221, 223, 516, 526) ~ "CI",
# Cook Inlet, Area P!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25110 &
STATAREA <= 25235 ~ "AFOGNAK",
# Afognak salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25311 &
STATAREA <= 25640 ~ "WESTSIDE",
# Westside salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25710 &
STATAREA <= 25770 ~ "SOUTHWEST",
# Southwest salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25810 &
STATAREA <= 25830 ~ "EASTSIDE",
# Eastside salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25840 &
STATAREA <= 25870 ~ "SOUTHEAST",
# Southeast salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25880 &
STATAREA <= 25890 ~ "SOUTHWEST",
# Southwest salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25910 &
STATAREA <= 25940 ~ "NORTHEAST",
# Northeast salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 25 &
STATAREA >= 25941 &
STATAREA <= 25948 ~ "EASTSIDE",
# Eastside salmon stat areas, Area Q!is.na(STATAREA) &
floor(STATAREA / 1000) == 222 &
STATAREA >= 222000 &
STATAREA <= 222050 ~ "CI",
# Cook Inlet, Area P!is.na(STATAREA) &
floor(STATAREA / 1000) == 222 &
STATAREA %in% c(222060) ~ "NG",
# North Gulf Coast, Area P!is.na(STATAREA) &
floor(STATAREA / 1000) == 456 &
STATAREA >= 456001 &
STATAREA <= 456004 ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 456 &
STATAREA %in% c(456031, 456032) ~ "PWSI",
# PWS Inside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 466 &
STATAREA %in% c(466001, 466002, 466004, 466005) ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 466 &
STATAREA %in% c(466003, 466031, 466032, 466033, 466100) ~ "PWSI",
# PWS Inside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 475 &
(STATAREA >= 475500 &
STATAREA <= 475932 |
STATAREA %in% c(475934)) ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 475 &
STATAREA %in% c(475933) ~ "PWSI",
# PWS Inside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 476 &
STATAREA %in% c(476001, 476002) ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 476 &
(STATAREA >= 476003 &
STATAREA <= 476102) ~ "PWSI",
# PWS Inside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 485 &
(
STATAREA >= 485430 &
STATAREA <= 485831 |
STATAREA %in% c(485901, 485931, 485935)
) ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 485 &
(STATAREA %in% c(485832, 485902, 485933, 485934)) ~ "NG",
# North Gulf Coast, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 485 &
(STATAREA %in% c(485932)) ~ "PWSI",
# PWS Inside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 486 &
(STATAREA %in% c(486002)) ~ "PWSO",
# PWS Outside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 486 &
(STATAREA %in% c(486001) |
(STATAREA >= 486003 &
STATAREA <= 486100)) ~ "PWSI",
# PWS Inside, Area J!is.na(STATAREA) &
floor(STATAREA / 1000) == 495 ~ case_when(
(STATAREA >= 495400 &
STATAREA <= 495700) ~ "EASTSIDE",
# Eastside, Area Q
(STATAREA >= 495901 &
STATAREA <= 495939 |
STATAREA == 495831) ~ "NG",
# North Gulf Coast, Area J
(STATAREA == 495730) ~ "NORTHEAST",
# Northeast, Area Q
(STATAREA %in% c(495800, 495832)) ~ "AFOGNAK" # Afognak, Area Q
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 505 ~ case_when(
(STATAREA >= 505330 & STATAREA <= 505700) ~ "EASTSIDE",
(STATAREA >= 505901 &
STATAREA <= 505934 | STATAREA == 505831) ~ "NG",
(STATAREA == 505730) ~ "NORTHEAST",
(STATAREA %in% c(505800, 505832)) ~ "AFOGNAK"
),!is.na(STATAREA) & floor(STATAREA / 1000) == 506 ~ "CI",!is.na(STATAREA) &
floor(STATAREA / 1000) == 515 ~ case_when(
(STATAREA >= 515300 & STATAREA <= 515700) ~ "EASTSIDE",
(
STATAREA >= 515901 &
STATAREA <= 515906 | STATAREA %in% c(515831, 515832)
) ~ "NG",
(STATAREA == 515730) ~ "NORTHEAST",
(STATAREA %in% c(515801, 515802, 515833)) ~ "AFOGNAK",
(STATAREA >= 515907 & STATAREA <= 515939) ~ "CI"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 525 ~ case_when(
(STATAREA >= 525230 & STATAREA <= 525703) ~ "EASTSIDE",
(STATAREA %in% c(525831, 525835, 525836, 525837)) ~ "NG",
(STATAREA %in% c(525731, 525732, 525733)) ~ "NORTHEAST",
(
STATAREA >= 525801 &
STATAREA <= 525807 |
STATAREA %in% c(525832, 525833, 525834)
) ~ "AFOGNAK",
(STATAREA >= 525901 & STATAREA <= 525932) ~ "CI"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 535 ~ case_when(
(
STATAREA >= 535230 &
STATAREA <= 535634 |
STATAREA %in% c(535703, 535704, 535705)
) ~ "SOUTHEAST",
(STATAREA %in% c(535635, 535702)) ~ "SOUTHWEST",
(STATAREA %in% c(535701, 535731, 535732, 535733, 535734)) ~ "WESTSIDE",
(STATAREA %in% c(535706, 535707)) ~ "EASTSIDE",
(STATAREA %in% c(535801, 535832)) ~ "MAINLAND",
# Mainland, Area R
(STATAREA %in% c(535802, 535803, 535831)) ~ "AFOGNAK",
(STATAREA %in% c(535833, 535834)) ~ "NG",
(STATAREA >= 535901 & STATAREA <= 535933) ~ "CI"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 545 ~ case_when(
(STATAREA >= 545200 &
STATAREA <= 545633 | STATAREA == 545704) ~ "SOUTHWEST",
(STATAREA %in% c(
545701, 545702, 545703, 545732, 545733, 545734
)) ~ "WESTSIDE",
(STATAREA %in% c(545731, 545801, 545802, 545803)) ~ "MAINLAND",
(STATAREA == 545804) ~ "AFOGNAK",
(STATAREA == 545900) ~ "CI"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 555 ~ case_when(
(STATAREA >= 555200 & STATAREA <= 555630) ~ "SOUTHWEST",
(STATAREA == 555701) ~ "WESTSIDE",
(STATAREA %in% c(555702, 555731, 555732, 555733)) ~ "MAINLAND"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 565 ~ case_when(
(STATAREA %in% c(
565131, 565201, 565231, 565301, 565331, 565401
)) ~ "SAKPEN",
(
STATAREA %in% c(
565132,
565202,
565232,
565302,
565333,
565403,
565432,
565502,
565534,
565604,
565635
)
) ~ "SOUTHWEST",
(
STATAREA %in% c(
565332,
565402,
565431,
565501,
565531,
565533,
565602,
565603,
565631,
565632,
565633,
565634,
565701,
565703
)
) ~ "CHIGNIK",
(STATAREA %in% c(565702, 565704)) ~ "MAINLAND"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 575 ~ case_when(
(
STATAREA >= 575131 &
STATAREA <= 575401 | STATAREA %in% c(575404, 575431)
) ~ "SAKPEN",
(STATAREA >= 575731 & STATAREA <= 575830) ~ "BERING",
(
STATAREA >= 575432 &
STATAREA <= 575635 | STATAREA %in% c(575402, 575403)
) ~ "CHIGNIK"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 585 ~ case_when(
(STATAREA >= 585100 &
STATAREA <= 585431 | STATAREA == 585501) ~ "SAKPEN",
(STATAREA >= 585631 & STATAREA <= 858830) ~ "BERING",
(
STATAREA %in% c(585432, 585502, 585531, 585532, 585601, 585602, 585603)
) ~ "CHIGNIK"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 595 ~ case_when(
(STATAREA >= 595100 & STATAREA <= 595533) ~ "SAKPEN",
(STATAREA >= 595631 & STATAREA <= 595833) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 605 ~ case_when(
(STATAREA >= 605100 & STATAREA <= 605533) ~ "SAKPEN",
(STATAREA >= 605534 & STATAREA <= 605834) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 615 ~ case_when(
(STATAREA >= 615030 & STATAREA <= 615532) ~ "SAKPEN",
(STATAREA >= 615533 & STATAREA <= 615834) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 625 ~ case_when(
(STATAREA >= 625030 & STATAREA <= 625502) ~ "SAKPEN",
(STATAREA >= 625503 & STATAREA <= 625832) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 635 ~ case_when(
(STATAREA >= 635030 &
STATAREA <= 635436 | STATAREA == 635502) ~ "SAKPEN",
(STATAREA == 635501 |
STATAREA >= 635503 & STATAREA <= 635800) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 645 ~ case_when(
(
STATAREA >= 545500 &
STATAREA <= 645401 |
STATAREA %in% c(645403, 645404, 645405, 645432)
) ~ "SAKPEN",
(STATAREA == 645402 |
STATAREA >= 645406 & STATAREA <= 645431) ~ "ALEUTIAN",
(STATAREA >= 645433 & STATAREA <= 645730) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 655 ~ case_when(
(STATAREA >= 655000 & STATAREA <= 655413) ~ "ALEUTIAN",
(STATAREA >= 655430 & STATAREA <= 655700) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 665 ~ case_when(
(STATAREA >= 665000 & STATAREA <= 665405) ~ "ALEUTIAN",
(STATAREA >= 665430 & STATAREA <= 665600) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 675 ~ case_when(
(STATAREA >= 675000 & STATAREA <= 675400) ~ "ALEUTIAN",
(STATAREA >= 675430 & STATAREA <= 675600) ~ "BERING"
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 685 ~ case_when(
(STATAREA >= 685000 & STATAREA <= 685400) ~ "ALEUTIAN",
(STATAREA >= 685430 & STATAREA <= 685600) ~ "BERING",
),!is.na(STATAREA) &
floor(STATAREA / 1000) == 695 ~ case_when(
(STATAREA >= 695000 & STATAREA <= 695400) ~ "ALEUTIAN",
(STATAREA >= 695430 & STATAREA <= 695600) ~ "BERING"
),
TRUE ~ 'ZZZZ'
)
)
}
# Attribute data to Sport Fish Management Areas based on ADFG groudfish statistical areas.
# This code is written for GOAB bio data, with the column STATAREA containing statistical areas
area_split_sf <- function(a) {
a %>%
mutate(
SFmgmtarea = case_when(
STATAREA >= 440000 &
STATAREA < 480000 | STATAREA %in% c(
485430,
485500,
485530,
485600,
485630,
485700,
485730,
485800,
485831,
485901,
485931,
485932,
485935,
486001,
486002,
486003,
486004,
486005,
486031,
486032,
486033,
486034,
486100
) ~ 'PWS',
STATAREA %in% c(
485832,
485902,
485933,
485934,
485935,
486002,
495831,
495901,
495902,
495931,
495932,
495933,
495934,
495935,
495936,
495937,
495938,
495939,
496001,
496002,
505831,
505901,
505902,
505903,
505904,
505905,
505906,
505907,
505908,
505909,
505931,
505932,
505933,
505934
) ~ 'NG',
STATAREA %in% c(
495800,
495832,
505700,
505730,
505800,
505832,
515630,
515700,
515730,
515801,
515802,
515833,
525600,
525630,
525701,
525702,
525703,
525731,
525732,
525733,
525801,
525802,
525803,
525804,
525805,
525806,
525807,
525832,
525833,
525834,
535601,
535602,
535631,
535632,
535633,
535634,
535701,
535702,
535703,
535704,
535705,
535706,
535707,
535731,
535732,
535733,
535734,
535802,
535803,
535831,
545601,
545602,
545631,
545632,
545633,
545701,
545702,
545703,
545704,
545732,
545733,
545734,
545804,
555630,
555701,
555733
) ~ 'KOD',
STATAREA %in% c(555731, 555732, 545731, 545801, 545802, 545803, 535801, 535832) ~ 'AKPen',
STATAREA %in% c(
515831,
515832,
515901,
515902,
515903,
515904,
515905,
515906,
515907,
515908,
515931,
515932,
515933,
515934,
515935,
515936,
515937,
515938,
515939,
516001,
516002,
525831,
525835,
525836,
525837,
525901,
525902,
525931,
525932,
526002,
526003,
535833,
535834,
535901,
535902,
535903,
535904,
535905,
535906,
535931,
535932,
535933,
545900
) ~ 'CI',
TRUE ~ 'ZZZ'
),
SFmgmtarea = case_when(
is.na(SFmgmtarea) | SFmgmtarea == 'ZZZ' ~ case_when(
PORT %in% c('Homer', 'CCI') ~ 'CI',
PORT == 'Kodiak' ~ 'KOD',
PORT %in% c('Whittier', 'Valdez', 'Cordova') ~ 'PWS',
PORT == 'Seward' ~ 'NG',
TRUE ~ PORT
),
TRUE ~ SFmgmtarea
)
)
}
# Standard Error calculation
stderr <- function(values){ # Standard Error calculation
sd(values, na.rm = TRUE) / sqrt(length(values))
}
# Find mode of a variable. Used mainly for rockfish common year classes
mode <- function(x) {
x <- x[!is.na(x)] # Remove NAs
unique_x <- unique(x)
unique_x[which.max(tabulate(match(x, unique_x)))]
}