build/nss 2020/nss.2020.R
In TobieSurette/gulf.manage: Southern Gulf Data Management Functions
setwd("~/GitHub/gulf.manage")
source("R/gse.R")
library(gulf.data)
library(gulf.spatial)
year <- 2020
# Load raw data:
load(locate(file = paste0("nss.ese.", year)))
x <- PER2020150
rm(PER2020150)
x$set <- x$set[x$set$SETNO != 111, ] # Remove blank tow.
#New corrections - April 2021
index = x$detail$SETNO == 57 & x$detail$SPEC == "2550"
x$detail[which(index),]$SIZE_CLASS <- 1
index = x$basket$SETNO == 57 & x$basket$SPEC == "2550"
x$basket[which(index),]$SIZE_CLASS <- 1
index = x$catch$SETNO == 57 & x$catch$SPEC == "2550"
x$catch[which(index),]$SIZE_CLASS <- 1
index = x$set$GEAR == 13
x$set[which(index),]$GEAR <- 16
#Set corrections
x$set$ELONG[which(x$set$SETNO == 1)] <- 6426.14
index = x$set$SETNO == 9
x$set[which(index),]$ELAT <- 4638.53
index = x$set$SETNO == 10
x$set[which(index),]$SLAT <- 4644
index = x$set$SETNO == 10
x$set[which(index),]$EXPERIMENT_TYPE_CODE <- 1
index = x$set$SETNO == 12
x$set[which(index),]$ELONG <- 6426.3
index = x$set$SETNO == 18
x$set[which(index),]$CURNT <- 1
index = x$set$SETNO == 23
x$set[which(index),]$END_TIME <- 1316
index = x$set$SETNO == 23
x$set[which(index),]$ELAT <- 4643.3
index = x$set$SETNO == 23
x$set[which(index),]$ELONG <- 6436.96
index = x$set$SETNO == 24
x$set[which(index),]$ELAT <- 4648.52
index = x$set$SETNO == 27
x$set[which(index),]$FORCE <- 3
index = x$set$SETNO == 31
x$set[which(index),]$SLONG <- 6355.55
index = x$set$SETNO == 31
x$set[which(index),]$ELONG <- 6354.95
index = x$set$SETNO == 33
x$set[which(index),]$END_DEPTH <- 10
index = x$set$SETNO == 34
x$set[which(index),]$EXPERIMENT_TYPE_CODE <- 1
index = x$set$SETNO == 35
x$set[which(index),]$SLAT <- 4646.05
index = x$set$SETNO == 35
x$set[which(index),]$FORCE <- 3
index = x$set$SETNO == 37
x$set[which(index),]$ELONG <- 6446.18
index = x$set$SETNO == 41
x$set[which(index),]$ELAT <- 4700.13
index = x$set$SETNO == 43
x$set[which(index),]$START_DEPTH <- 36
index = x$set$SETNO == 48
x$set[which(index),]$SLONG <- 6429.3
index = x$set$SETNO == 51
x$set[which(index),]$END_DEPTH <- 10
index = x$set$SETNO == 53
x$set[which(index),]$START_DEPTH <- 16
index = x$set$SETNO == 54
x$set[which(index),]$END_DEPTH <- 12
index = x$set$SETNO == 55
x$set[which(index),]$START_DEPTH <- 10
index = x$set$SETNO == 56
x$set[which(index),]$START_TIME <- 1137
index = x$set$SETNO == 58
x$set[which(index),]$START_DEPTH <- 32
index = x$set$SETNO == 66
x$set[which(index),]$SLONG <- 6428.83
index = x$set$SETNO == 67
x$set[which(index),]$SLAT <- 4633.81
index = x$set$SETNO == 68
x$set[which(index),]$ELAT <- 4617.5
index = x$set$SETNO == 73
x$set[which(index),]$ELONG <- 6408.86
index = x$set$SETNO == 75
x$set[which(index),]$SLAT <- 4626.3
index = x$set$SETNO == 88
x$set[which(index),]$SLAT <- 4611.99
index = x$set$SETNO == 89
x$set[which(index),]$STATION <- "B1"
index = x$set$SETNO == 91
x$set[which(index),]$ELAT <- 4614.45
index = x$set$SETNO == 96
x$set[which(index),]$NOTE <- "Null - Caught chunk of mud"
index = x$set$SETNO == 102
x$set[which(index),]$STATION <- 331
index = x$set$SETNO == 104
x$set[which(index),]$ELONG <- 6400.69
index = x$set$SETNO == 110
x$set[which(index),]$END_DEPTH <- 19
#Basket corrections
index = x$basket$SPEC == 599
x$basket[which(index),]$SPEC <- 611
index = x$basket$SETNO == 63 & x$basket$SPEC == 8300
x$basket[which(index),]$SAMPLED <- "N"
index = x$basket$SETNO == 76 & x$basket$SPEC == 6511
x$basket[which(index),]$SAMPLED <- "N"
index = x$basket$SETNO == 57 & x$basket$SPEC == 2550
x$basket[which(index),]$SIZE_CLASS <- 1
index = x$basket$SETNO == 5 & x$basket$SPEC == 2539
x$basket[which(index),]$SAMPLED <- "Y"
# Check these svp:
x$basket[is.na(x$basket$SPEC), ]
x$basket[is.na(x$basket$SAMPLED), ]
# Detail corrections
index = x$detail$SETNO == 66 & x$detail$SPECIMEN_ID == 21733
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 87 & x$detail$SPECIMEN_ID == 32083
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 83 & x$detail$SPECIMEN_ID == 30070
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 35 & x$detail$SPECIMEN_ID == 14057
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 35 & x$detail$SPECIMEN_ID == 13878
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 70 & x$detail$SPECIMEN_ID == 24129
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 49 & x$detail$SPECIMEN_ID == 18389
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 68 & x$detail$SPECIMEN_ID == 22641
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 70 & x$detail$SPECIMEN_ID == 23868
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 52 & x$detail$SPECIMEN_ID == 18798
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 54 & x$detail$SPECIMEN_ID == 19197
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 73 & x$detail$SPECIMEN_ID == 26240
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 70 & x$detail$SPECIMEN_ID == 23991
x$detail[which(index),]$SEX <- 1
index = x$detail$SETNO == 32 & x$detail$SPECIMEN_ID == 12016
x$detail[which(index),]$LOBSTER_EGG_CONDITION <- NA
#x$detail[which(x$detail$SEX),]
# Check :
ix <- x$detail$SETNO == 17 & x$detail$SPEC == 60 # Size class 2 change to 1:
# Check herring length units
x$detail$LENGTH[x$detail$SPEC == 60] <- x$detail$LENGTH[x$detail$SPEC == 60] / 10
# Reformat:
y <- ese2gsd(x, survey = "nss")
y <- lapply(y, squeeze)
# Calculate tow distance:
y$set$distance <- (1 / 1.852) * distance(-dmm2deg(y$set$longitude.start), dmm2deg(y$set$latitude.start), -dmm2deg(y$set$longitude.stop), dmm2deg(y$set$latitude.stop), pairwise = FALSE)
y$set$distance <- round(y$set$distance, 3)
# Check tow distance below 0.25nm svp:
# Generate catch table:
key.cat <- c("date", "cruise", "set.number", "species", "size.class")
tmp <- stats::aggregate(list(weight.caught = y$basket$weight), by = y$basket[key.cat], sum)
y$cat$weight.caught <- tmp$weight.caught[match(y$cat[key.cat], tmp[key.cat])]
index <- which(y$basket$sampled == "Y")
tmp <- stats::aggregate(list(sample.weight = y$basket$weight[index]), by = y$basket[index, key.cat], sum)
y$cat$weight.sampled <- tmp$sample.weight[match(y$cat[key.cat], tmp[key.cat])]
tmp <- stats::aggregate(list(n = y$basket$set.number), by = y$basket[key.cat], length)
y$cat$number.basket <- tmp$n[match(y$cat[key.cat], tmp[key.cat])]
y$cat$weight.sampled[is.na(y$cat$weight.sampled)] <- 0
y$cat <- y$cat[c(setdiff(names(y$cat), "comment"), "comment")]
y$cat$comment <- gulf.utils::deblank(y$cat$comment)
# Write data gulf.data:
path <- gsub("gulf.manage", "gulf.data", getwd())
path <- paste0(path, "/inst/extdata")
if (file.exists(path)){
year <- sort(unique(year(y$set)))
write.csv(y$set, file = paste0(path, "/", "nss.set.", year, ".csv"), row.names = FALSE)
write.csv(y$cat, file = paste0(path, "/", "nss.cat.", year, ".csv"), row.names = FALSE)
write.csv(y$bio, file = paste0(path, "/", "nss.bio.", year, ".csv"), row.names = FALSE)
}
TobieSurette/gulf.manage documentation built on Feb. 10, 2024, 10:51 p.m.
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setwd("~/GitHub/gulf.manage")
source("R/gse.R")
library(gulf.data)
library(gulf.spatial)
year <- 2020
# Load raw data:
load(locate(file = paste0("nss.ese.", year)))
x <- PER2020150
rm(PER2020150)
x$set <- x$set[x$set$SETNO != 111, ] # Remove blank tow.
#New corrections - April 2021
index = x$detail$SETNO == 57 & x$detail$SPEC == "2550"
x$detail[which(index),]$SIZE_CLASS <- 1
index = x$basket$SETNO == 57 & x$basket$SPEC == "2550"
x$basket[which(index),]$SIZE_CLASS <- 1
index = x$catch$SETNO == 57 & x$catch$SPEC == "2550"
x$catch[which(index),]$SIZE_CLASS <- 1
index = x$set$GEAR == 13
x$set[which(index),]$GEAR <- 16
#Set corrections
x$set$ELONG[which(x$set$SETNO == 1)] <- 6426.14
index = x$set$SETNO == 9
x$set[which(index),]$ELAT <- 4638.53
index = x$set$SETNO == 10
x$set[which(index),]$SLAT <- 4644
index = x$set$SETNO == 10
x$set[which(index),]$EXPERIMENT_TYPE_CODE <- 1
index = x$set$SETNO == 12
x$set[which(index),]$ELONG <- 6426.3
index = x$set$SETNO == 18
x$set[which(index),]$CURNT <- 1
index = x$set$SETNO == 23
x$set[which(index),]$END_TIME <- 1316
index = x$set$SETNO == 23
x$set[which(index),]$ELAT <- 4643.3
index = x$set$SETNO == 23
x$set[which(index),]$ELONG <- 6436.96
index = x$set$SETNO == 24
x$set[which(index),]$ELAT <- 4648.52
index = x$set$SETNO == 27
x$set[which(index),]$FORCE <- 3
index = x$set$SETNO == 31
x$set[which(index),]$SLONG <- 6355.55
index = x$set$SETNO == 31
x$set[which(index),]$ELONG <- 6354.95
index = x$set$SETNO == 33
x$set[which(index),]$END_DEPTH <- 10
index = x$set$SETNO == 34
x$set[which(index),]$EXPERIMENT_TYPE_CODE <- 1
index = x$set$SETNO == 35
x$set[which(index),]$SLAT <- 4646.05
index = x$set$SETNO == 35
x$set[which(index),]$FORCE <- 3
index = x$set$SETNO == 37
x$set[which(index),]$ELONG <- 6446.18
index = x$set$SETNO == 41
x$set[which(index),]$ELAT <- 4700.13
index = x$set$SETNO == 43
x$set[which(index),]$START_DEPTH <- 36
index = x$set$SETNO == 48
x$set[which(index),]$SLONG <- 6429.3
index = x$set$SETNO == 51
x$set[which(index),]$END_DEPTH <- 10
index = x$set$SETNO == 53
x$set[which(index),]$START_DEPTH <- 16
index = x$set$SETNO == 54
x$set[which(index),]$END_DEPTH <- 12
index = x$set$SETNO == 55
x$set[which(index),]$START_DEPTH <- 10
index = x$set$SETNO == 56
x$set[which(index),]$START_TIME <- 1137
index = x$set$SETNO == 58
x$set[which(index),]$START_DEPTH <- 32
index = x$set$SETNO == 66
x$set[which(index),]$SLONG <- 6428.83
index = x$set$SETNO == 67
x$set[which(index),]$SLAT <- 4633.81
index = x$set$SETNO == 68
x$set[which(index),]$ELAT <- 4617.5
index = x$set$SETNO == 73
x$set[which(index),]$ELONG <- 6408.86
index = x$set$SETNO == 75
x$set[which(index),]$SLAT <- 4626.3
index = x$set$SETNO == 88
x$set[which(index),]$SLAT <- 4611.99
index = x$set$SETNO == 89
x$set[which(index),]$STATION <- "B1"
index = x$set$SETNO == 91
x$set[which(index),]$ELAT <- 4614.45
index = x$set$SETNO == 96
x$set[which(index),]$NOTE <- "Null - Caught chunk of mud"
index = x$set$SETNO == 102
x$set[which(index),]$STATION <- 331
index = x$set$SETNO == 104
x$set[which(index),]$ELONG <- 6400.69
index = x$set$SETNO == 110
x$set[which(index),]$END_DEPTH <- 19
#Basket corrections
index = x$basket$SPEC == 599
x$basket[which(index),]$SPEC <- 611
index = x$basket$SETNO == 63 & x$basket$SPEC == 8300
x$basket[which(index),]$SAMPLED <- "N"
index = x$basket$SETNO == 76 & x$basket$SPEC == 6511
x$basket[which(index),]$SAMPLED <- "N"
index = x$basket$SETNO == 57 & x$basket$SPEC == 2550
x$basket[which(index),]$SIZE_CLASS <- 1
index = x$basket$SETNO == 5 & x$basket$SPEC == 2539
x$basket[which(index),]$SAMPLED <- "Y"
# Check these svp:
x$basket[is.na(x$basket$SPEC), ]
x$basket[is.na(x$basket$SAMPLED), ]
# Detail corrections
index = x$detail$SETNO == 66 & x$detail$SPECIMEN_ID == 21733
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 87 & x$detail$SPECIMEN_ID == 32083
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 83 & x$detail$SPECIMEN_ID == 30070
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 35 & x$detail$SPECIMEN_ID == 14057
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 35 & x$detail$SPECIMEN_ID == 13878
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 70 & x$detail$SPECIMEN_ID == 24129
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 49 & x$detail$SPECIMEN_ID == 18389
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 68 & x$detail$SPECIMEN_ID == 22641
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 70 & x$detail$SPECIMEN_ID == 23868
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 52 & x$detail$SPECIMEN_ID == 18798
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 54 & x$detail$SPECIMEN_ID == 19197
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 73 & x$detail$SPECIMEN_ID == 26240
x$detail[which(index),]$LENGTH <- NA
index = x$detail$SETNO == 70 & x$detail$SPECIMEN_ID == 23991
x$detail[which(index),]$SEX <- 1
index = x$detail$SETNO == 32 & x$detail$SPECIMEN_ID == 12016
x$detail[which(index),]$LOBSTER_EGG_CONDITION <- NA
#x$detail[which(x$detail$SEX),]
# Check :
ix <- x$detail$SETNO == 17 & x$detail$SPEC == 60 # Size class 2 change to 1:
# Check herring length units
x$detail$LENGTH[x$detail$SPEC == 60] <- x$detail$LENGTH[x$detail$SPEC == 60] / 10
# Reformat:
y <- ese2gsd(x, survey = "nss")
y <- lapply(y, squeeze)
# Calculate tow distance:
y$set$distance <- (1 / 1.852) * distance(-dmm2deg(y$set$longitude.start), dmm2deg(y$set$latitude.start), -dmm2deg(y$set$longitude.stop), dmm2deg(y$set$latitude.stop), pairwise = FALSE)
y$set$distance <- round(y$set$distance, 3)
# Check tow distance below 0.25nm svp:
# Generate catch table:
key.cat <- c("date", "cruise", "set.number", "species", "size.class")
tmp <- stats::aggregate(list(weight.caught = y$basket$weight), by = y$basket[key.cat], sum)
y$cat$weight.caught <- tmp$weight.caught[match(y$cat[key.cat], tmp[key.cat])]
index <- which(y$basket$sampled == "Y")
tmp <- stats::aggregate(list(sample.weight = y$basket$weight[index]), by = y$basket[index, key.cat], sum)
y$cat$weight.sampled <- tmp$sample.weight[match(y$cat[key.cat], tmp[key.cat])]
tmp <- stats::aggregate(list(n = y$basket$set.number), by = y$basket[key.cat], length)
y$cat$number.basket <- tmp$n[match(y$cat[key.cat], tmp[key.cat])]
y$cat$weight.sampled[is.na(y$cat$weight.sampled)] <- 0
y$cat <- y$cat[c(setdiff(names(y$cat), "comment"), "comment")]
y$cat$comment <- gulf.utils::deblank(y$cat$comment)
# Write data gulf.data:
path <- gsub("gulf.manage", "gulf.data", getwd())
path <- paste0(path, "/inst/extdata")
if (file.exists(path)){
year <- sort(unique(year(y$set)))
write.csv(y$set, file = paste0(path, "/", "nss.set.", year, ".csv"), row.names = FALSE)
write.csv(y$cat, file = paste0(path, "/", "nss.cat.", year, ".csv"), row.names = FALSE)
write.csv(y$bio, file = paste0(path, "/", "nss.bio.", year, ".csv"), row.names = FALSE)
}
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