other/Survdat_wgtATlen.r
In andybeet/survdat: Tools for working with NEFSC survey data
#Survdat_wgtATlen.r
#Add weight at length and size categories to survdat.RData
#7/14
#SML
#User parameters
if(Sys.info()['sysname']=="Windows"){
data.dir <- "L:\\EcoAP\\Data\\survey"
out.dir <- "L:\\EcoAP\\Data\\survey"
r.dir <- "L:\\Rworkspace\\RSurvey"
gis.dir <- "L:\\Rworkspace\\GIS_files"
}
if(Sys.info()['sysname']=="Linux"){
data.dir <- "/home/slucey/slucey/EcoAP/Data/survey"
out.dir <- "/home/slucey/slucey/EcoAP/Data/survey"
r.dir <- "/home/slucey/slucey/Rworkspace/RSurvey"
gis.dir <- "/home/slucey/slucey/Rworkspace/GIS_files"
uid <- 'slucey'
cat('Oracle Password:')
pwd <- readLines(n=1)
}
#-------------------------------------------------------------------------------
#Required packages
library(data.table); library(RODBC)
#-------------------------------------------------------------------------------
#User created functions
#-------------------------------------------------------------------------------
load(file.path(data.dir, "Survdat.RData"))
#Need a length/weight coefficients
if(Sys.info()['sysname']=="Windows") channel <- odbcDriverConnect()
if(Sys.info()['sysname']=="Linux") channel <- odbcConnect('sole', uid, pwd)
lw.qry <- "select svspp, sex, svlwexp, svlwcoeff,
svlwexp_spring, svlwcoeff_spring,
svlwexp_fall, svlwcoeff_fall,
svlwexp_winter, svlwcoeff_winter,
svlwexp_summer, svlwcoeff_summer
from length_weight_coefficients"
lw <- as.data.table(sqlQuery(channel, lw.qry))
#fix NAs
lw[is.na(SVLWEXP_SPRING), SVLWEXP_SPRING := SVLWEXP]
lw[is.na(SVLWEXP_FALL), SVLWEXP_FALL := SVLWEXP]
lw[is.na(SVLWEXP_WINTER), SVLWEXP_WINTER := SVLWEXP]
lw[is.na(SVLWEXP_SUMMER), SVLWEXP_SUMMER := SVLWEXP]
lw[is.na(SVLWCOEFF_SPRING), SVLWCOEFF_SPRING := SVLWCOEFF]
lw[is.na(SVLWCOEFF_FALL), SVLWCOEFF_FALL := SVLWCOEFF]
lw[is.na(SVLWCOEFF_WINTER), SVLWCOEFF_WINTER := SVLWCOEFF]
lw[is.na(SVLWCOEFF_SUMMER), SVLWCOEFF_SUMMER := SVLWCOEFF]
#Merge with survdat
setnames(lw, "SEX", "CATCHSEX")
survdat.lw <- merge(survdat, lw, by = c('SVSPP', 'CATCHSEX'), all.x = T)
#Calculate weight at length
survdat.lw[SEASON == 'SPRING', INDWT := exp(SVLWCOEFF_SPRING + SVLWEXP_SPRING * log(LENGTH))]
survdat.lw[SEASON == 'FALL', INDWT := exp(SVLWCOEFF_FALL + SVLWEXP_FALL * log(LENGTH))]
survdat.lw[SEASON == 'WINTER', INDWT := exp(SVLWCOEFF_WINTER + SVLWEXP_WINTER * log(LENGTH))]
survdat.lw[SEASON == 'SUMMER', INDWT := exp(SVLWCOEFF_SUMMER + SVLWEXP_SUMMER * log(LENGTH))]
#Calculate expanded weight at length
survdat.lw[, WGTLEN := INDWT * NUMLEN]
#Remove extra columns
survdat.lw[, c('SVLWEXP', 'SVLWCOEFF',
'SVLWEXP_SPRING', 'SVLWCOEFF_SPRING',
'SVLWEXP_FALL', 'SVLWCOEFF_FALL',
'SVLWEXP_WINTER', 'SVLWCOEFF_WINTER',
'SVLWEXP_SUMMER', 'SVLWCOEFF_SUMMER') := NULL]
#Assign size categories from FH
survdat.lw[, SIZECAT := factor(NA, levels = c('XS', 'S', 'M', 'L', 'XL'))]
survdat.lw[LENGTH <= 20, SIZECAT := 'S']
survdat.lw[LENGTH > 20 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[LENGTH > 50, SIZECAT := 'L']
#then set for specific taxa
#dogfish
#/*if (svspp>=013 and svspp<=015) and pdlen<=40 then sizecat='S ';
#else if (svspp>=013 and svspp<=015) and pdlen>40 and pdlen<=60 then sizecat='M ';
#else if (svspp>=013 and svspp<=015) and pdlen>60 and pdlen<=80 then sizecat='L ';*/
#new dogfish
survdat.lw[SVSPP %in% 13:15 & LENGTH < 36, SIZECAT := 'S']
survdat.lw[SVSPP %in% 13:15 & LENGTH >= 36 & LENGTH < 80, SIZECAT := 'M']
survdat.lw[SVSPP %in% 13:15 & LENGTH >= 80, SIZECAT := 'L']
#skates
survdat.lw[SVSPP %in% 20:29 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP %in% 20:29 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP %in% 20:29 & LENGTH > 60 & LENGTH <= 80, SIZECAT := 'L']
survdat.lw[SVSPP %in% 20:29 & LENGTH > 80, SIZECAT := 'XL']
#anchovies, smelt, greeneyes, lanternfishes
survdat.lw[SVSPP %in% 38:56 & LENGTH <= 10, SIZECAT := 'S']
survdat.lw[SVSPP %in% 38:56 & LENGTH > 10 & LENGTH <= 25, SIZECAT := 'M']
survdat.lw[SVSPP %in% 38:56 & LENGTH > 25, SIZECAT := 'L']
#sandlance, hookear sculpin, pearlsides
survdat.lw[SVSPP %in% c(181, 159, 229) & LENGTH <= 10, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(181, 159, 229) & LENGTH > 10 & LENGTH <= 25, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(181, 159, 229) & LENGTH > 25, SIZECAT := 'L']
#clupeids
survdat.lw[SVSPP %in% 30:37 & LENGTH <= 10, SIZECAT := 'XS']
survdat.lw[SVSPP %in% 30:37 & LENGTH > 10 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 30:37 & LENGTH > 20 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP %in% 30:37 & LENGTH > 30, SIZECAT := 'L']
#Atlantic mackerel, butterfish
survdat.lw[SVSPP %in% c(121, 131) & LENGTH <= 10, SIZECAT := 'XS']
survdat.lw[SVSPP %in% c(121, 131) & LENGTH > 10 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP == 121 & LENGTH > 20 & LENGTH <= 35, SIZECAT := 'M']
survdat.lw[SVSPP == 121 & LENGTH > 35, SIZECAT := 'L']
survdat.lw[SVSPP == 131 & LENGTH > 20 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP == 131 & LENGTH > 30, SIZECAT := 'L']
#hakes
survdat.lw[SVSPP %in% 76:79 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 76:79 & LENGTH > 20 & LENGTH <= 40, SIZECAT := 'M']
survdat.lw[SVSPP %in% 76:79 & LENGTH > 40, SIZECAT := 'L']
survdat.lw[SVSPP %in% c(69, 72, 81, 86, 87) & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(69, 72, 81, 86, 87) & LENGTH > 20 & LENGTH <= 40, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(69, 72, 81, 86, 87) & LENGTH > 40, SIZECAT := 'L']
#cod, haddock, pollock
survdat.lw[SVSPP %in% 73:75 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 73:75 & LENGTH > 20 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[SVSPP %in% 73:75 & LENGTH > 50 & LENGTH <= 80, SIZECAT := 'L']
survdat.lw[SVSPP %in% 73:75 & LENGTH > 80, SIZECAT := 'XL']
#flatfish
survdat.lw[SVSPP %in% 102:110 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 102:110 & LENGTH > 20 & LENGTH <= 40, SIZECAT := 'M']
survdat.lw[SVSPP %in% 102:110 & LENGTH > 40 & LENGTH <= 70, SIZECAT := 'L']
survdat.lw[SVSPP %in% 102:110 & LENGTH > 70, SIZECAT := 'XL']
#halibut
survdat.lw[SVSPP == 101 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP == 101 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP == 101 & LENGTH > 60 & LENGTH <= 90, SIZECAT := 'L']
survdat.lw[SVSPP == 101 & LENGTH > 90, SIZECAT := 'XL']
#bluefish, striped bass
survdat.lw[SVSPP %in% c(135, 139) & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(135, 139) & LENGTH > 30 & LENGTH <= 70, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(135, 139) & LENGTH > 70, SIZECAT := 'L']
#croaker, black sea bass, weakfish
survdat.lw[SVSPP %in% c(136, 141, 145) & LENGTH <= 25, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(136, 141, 145) & LENGTH > 25 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(136, 141, 145) & LENGTH > 50, SIZECAT := 'L']
#longhorn sculpin, sea raven, redfish
survdat.lw[SVSPP %in% c(155, 163, 164) & LENGTH <= 25, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(155, 163, 164) & LENGTH > 25 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(155, 163, 164) & LENGTH > 50, SIZECAT := 'L']
#sea robins
survdat.lw[SVSPP %in% 171:174 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 171:174 & LENGTH > 20 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP %in% 171:174 & LENGTH > 30, SIZECAT := 'L']
#goosefish
survdat.lw[SVSPP == 197 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP == 197 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP == 197 & LENGTH > 60 & LENGTH <= 90, SIZECAT := 'L']
survdat.lw[SVSPP == 197 & LENGTH > 90, SIZECAT := 'XL']
#pouts, wolffish
survdat.lw[SVSPP %in% 189:193 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP %in% 189:193 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP %in% 189:193 & LENGTH > 60, SIZECAT := 'L']
#squids
survdat.lw[SVSPP %in% c(502, 503) & LENGTH <= 15, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(502, 503) & LENGTH > 15 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(502, 503) & LENGTH > 30, SIZECAT := 'L']
#Sum biomass by size category
setkey(survdat.lw, CRUISE6, STRATUM, STATION, SVSPP, CATCHSEX, SIZECAT)
survdat.lw[, WGTCAT := sum(WGTLEN), by = key(survdat.lw)]
survdat.lw[, NUMCAT := sum(NUMLEN), by = key(survdat.lw)]
survdat.lw <- unique(survdat.lw, by = key(survdat.lw))
#Drop individual columns
survdat.lw[, c('LENGTH', 'NUMLEN', 'INDWT', 'WGTLEN') := NULL]
save(survdat.lw, file = file.path(out.dir, "survdat_lw.RData"))
andybeet/survdat documentation built on Nov. 9, 2023, 10:11 a.m.
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#Survdat_wgtATlen.r
#Add weight at length and size categories to survdat.RData
#7/14
#SML
#User parameters
if(Sys.info()['sysname']=="Windows"){
data.dir <- "L:\\EcoAP\\Data\\survey"
out.dir <- "L:\\EcoAP\\Data\\survey"
r.dir <- "L:\\Rworkspace\\RSurvey"
gis.dir <- "L:\\Rworkspace\\GIS_files"
}
if(Sys.info()['sysname']=="Linux"){
data.dir <- "/home/slucey/slucey/EcoAP/Data/survey"
out.dir <- "/home/slucey/slucey/EcoAP/Data/survey"
r.dir <- "/home/slucey/slucey/Rworkspace/RSurvey"
gis.dir <- "/home/slucey/slucey/Rworkspace/GIS_files"
uid <- 'slucey'
cat('Oracle Password:')
pwd <- readLines(n=1)
}
#-------------------------------------------------------------------------------
#Required packages
library(data.table); library(RODBC)
#-------------------------------------------------------------------------------
#User created functions
#-------------------------------------------------------------------------------
load(file.path(data.dir, "Survdat.RData"))
#Need a length/weight coefficients
if(Sys.info()['sysname']=="Windows") channel <- odbcDriverConnect()
if(Sys.info()['sysname']=="Linux") channel <- odbcConnect('sole', uid, pwd)
lw.qry <- "select svspp, sex, svlwexp, svlwcoeff,
svlwexp_spring, svlwcoeff_spring,
svlwexp_fall, svlwcoeff_fall,
svlwexp_winter, svlwcoeff_winter,
svlwexp_summer, svlwcoeff_summer
from length_weight_coefficients"
lw <- as.data.table(sqlQuery(channel, lw.qry))
#fix NAs
lw[is.na(SVLWEXP_SPRING), SVLWEXP_SPRING := SVLWEXP]
lw[is.na(SVLWEXP_FALL), SVLWEXP_FALL := SVLWEXP]
lw[is.na(SVLWEXP_WINTER), SVLWEXP_WINTER := SVLWEXP]
lw[is.na(SVLWEXP_SUMMER), SVLWEXP_SUMMER := SVLWEXP]
lw[is.na(SVLWCOEFF_SPRING), SVLWCOEFF_SPRING := SVLWCOEFF]
lw[is.na(SVLWCOEFF_FALL), SVLWCOEFF_FALL := SVLWCOEFF]
lw[is.na(SVLWCOEFF_WINTER), SVLWCOEFF_WINTER := SVLWCOEFF]
lw[is.na(SVLWCOEFF_SUMMER), SVLWCOEFF_SUMMER := SVLWCOEFF]
#Merge with survdat
setnames(lw, "SEX", "CATCHSEX")
survdat.lw <- merge(survdat, lw, by = c('SVSPP', 'CATCHSEX'), all.x = T)
#Calculate weight at length
survdat.lw[SEASON == 'SPRING', INDWT := exp(SVLWCOEFF_SPRING + SVLWEXP_SPRING * log(LENGTH))]
survdat.lw[SEASON == 'FALL', INDWT := exp(SVLWCOEFF_FALL + SVLWEXP_FALL * log(LENGTH))]
survdat.lw[SEASON == 'WINTER', INDWT := exp(SVLWCOEFF_WINTER + SVLWEXP_WINTER * log(LENGTH))]
survdat.lw[SEASON == 'SUMMER', INDWT := exp(SVLWCOEFF_SUMMER + SVLWEXP_SUMMER * log(LENGTH))]
#Calculate expanded weight at length
survdat.lw[, WGTLEN := INDWT * NUMLEN]
#Remove extra columns
survdat.lw[, c('SVLWEXP', 'SVLWCOEFF',
'SVLWEXP_SPRING', 'SVLWCOEFF_SPRING',
'SVLWEXP_FALL', 'SVLWCOEFF_FALL',
'SVLWEXP_WINTER', 'SVLWCOEFF_WINTER',
'SVLWEXP_SUMMER', 'SVLWCOEFF_SUMMER') := NULL]
#Assign size categories from FH
survdat.lw[, SIZECAT := factor(NA, levels = c('XS', 'S', 'M', 'L', 'XL'))]
survdat.lw[LENGTH <= 20, SIZECAT := 'S']
survdat.lw[LENGTH > 20 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[LENGTH > 50, SIZECAT := 'L']
#then set for specific taxa
#dogfish
#/*if (svspp>=013 and svspp<=015) and pdlen<=40 then sizecat='S ';
#else if (svspp>=013 and svspp<=015) and pdlen>40 and pdlen<=60 then sizecat='M ';
#else if (svspp>=013 and svspp<=015) and pdlen>60 and pdlen<=80 then sizecat='L ';*/
#new dogfish
survdat.lw[SVSPP %in% 13:15 & LENGTH < 36, SIZECAT := 'S']
survdat.lw[SVSPP %in% 13:15 & LENGTH >= 36 & LENGTH < 80, SIZECAT := 'M']
survdat.lw[SVSPP %in% 13:15 & LENGTH >= 80, SIZECAT := 'L']
#skates
survdat.lw[SVSPP %in% 20:29 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP %in% 20:29 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP %in% 20:29 & LENGTH > 60 & LENGTH <= 80, SIZECAT := 'L']
survdat.lw[SVSPP %in% 20:29 & LENGTH > 80, SIZECAT := 'XL']
#anchovies, smelt, greeneyes, lanternfishes
survdat.lw[SVSPP %in% 38:56 & LENGTH <= 10, SIZECAT := 'S']
survdat.lw[SVSPP %in% 38:56 & LENGTH > 10 & LENGTH <= 25, SIZECAT := 'M']
survdat.lw[SVSPP %in% 38:56 & LENGTH > 25, SIZECAT := 'L']
#sandlance, hookear sculpin, pearlsides
survdat.lw[SVSPP %in% c(181, 159, 229) & LENGTH <= 10, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(181, 159, 229) & LENGTH > 10 & LENGTH <= 25, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(181, 159, 229) & LENGTH > 25, SIZECAT := 'L']
#clupeids
survdat.lw[SVSPP %in% 30:37 & LENGTH <= 10, SIZECAT := 'XS']
survdat.lw[SVSPP %in% 30:37 & LENGTH > 10 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 30:37 & LENGTH > 20 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP %in% 30:37 & LENGTH > 30, SIZECAT := 'L']
#Atlantic mackerel, butterfish
survdat.lw[SVSPP %in% c(121, 131) & LENGTH <= 10, SIZECAT := 'XS']
survdat.lw[SVSPP %in% c(121, 131) & LENGTH > 10 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP == 121 & LENGTH > 20 & LENGTH <= 35, SIZECAT := 'M']
survdat.lw[SVSPP == 121 & LENGTH > 35, SIZECAT := 'L']
survdat.lw[SVSPP == 131 & LENGTH > 20 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP == 131 & LENGTH > 30, SIZECAT := 'L']
#hakes
survdat.lw[SVSPP %in% 76:79 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 76:79 & LENGTH > 20 & LENGTH <= 40, SIZECAT := 'M']
survdat.lw[SVSPP %in% 76:79 & LENGTH > 40, SIZECAT := 'L']
survdat.lw[SVSPP %in% c(69, 72, 81, 86, 87) & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(69, 72, 81, 86, 87) & LENGTH > 20 & LENGTH <= 40, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(69, 72, 81, 86, 87) & LENGTH > 40, SIZECAT := 'L']
#cod, haddock, pollock
survdat.lw[SVSPP %in% 73:75 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 73:75 & LENGTH > 20 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[SVSPP %in% 73:75 & LENGTH > 50 & LENGTH <= 80, SIZECAT := 'L']
survdat.lw[SVSPP %in% 73:75 & LENGTH > 80, SIZECAT := 'XL']
#flatfish
survdat.lw[SVSPP %in% 102:110 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 102:110 & LENGTH > 20 & LENGTH <= 40, SIZECAT := 'M']
survdat.lw[SVSPP %in% 102:110 & LENGTH > 40 & LENGTH <= 70, SIZECAT := 'L']
survdat.lw[SVSPP %in% 102:110 & LENGTH > 70, SIZECAT := 'XL']
#halibut
survdat.lw[SVSPP == 101 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP == 101 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP == 101 & LENGTH > 60 & LENGTH <= 90, SIZECAT := 'L']
survdat.lw[SVSPP == 101 & LENGTH > 90, SIZECAT := 'XL']
#bluefish, striped bass
survdat.lw[SVSPP %in% c(135, 139) & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(135, 139) & LENGTH > 30 & LENGTH <= 70, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(135, 139) & LENGTH > 70, SIZECAT := 'L']
#croaker, black sea bass, weakfish
survdat.lw[SVSPP %in% c(136, 141, 145) & LENGTH <= 25, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(136, 141, 145) & LENGTH > 25 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(136, 141, 145) & LENGTH > 50, SIZECAT := 'L']
#longhorn sculpin, sea raven, redfish
survdat.lw[SVSPP %in% c(155, 163, 164) & LENGTH <= 25, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(155, 163, 164) & LENGTH > 25 & LENGTH <= 50, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(155, 163, 164) & LENGTH > 50, SIZECAT := 'L']
#sea robins
survdat.lw[SVSPP %in% 171:174 & LENGTH <= 20, SIZECAT := 'S']
survdat.lw[SVSPP %in% 171:174 & LENGTH > 20 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP %in% 171:174 & LENGTH > 30, SIZECAT := 'L']
#goosefish
survdat.lw[SVSPP == 197 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP == 197 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP == 197 & LENGTH > 60 & LENGTH <= 90, SIZECAT := 'L']
survdat.lw[SVSPP == 197 & LENGTH > 90, SIZECAT := 'XL']
#pouts, wolffish
survdat.lw[SVSPP %in% 189:193 & LENGTH <= 30, SIZECAT := 'S']
survdat.lw[SVSPP %in% 189:193 & LENGTH > 30 & LENGTH <= 60, SIZECAT := 'M']
survdat.lw[SVSPP %in% 189:193 & LENGTH > 60, SIZECAT := 'L']
#squids
survdat.lw[SVSPP %in% c(502, 503) & LENGTH <= 15, SIZECAT := 'S']
survdat.lw[SVSPP %in% c(502, 503) & LENGTH > 15 & LENGTH <= 30, SIZECAT := 'M']
survdat.lw[SVSPP %in% c(502, 503) & LENGTH > 30, SIZECAT := 'L']
#Sum biomass by size category
setkey(survdat.lw, CRUISE6, STRATUM, STATION, SVSPP, CATCHSEX, SIZECAT)
survdat.lw[, WGTCAT := sum(WGTLEN), by = key(survdat.lw)]
survdat.lw[, NUMCAT := sum(NUMLEN), by = key(survdat.lw)]
survdat.lw <- unique(survdat.lw, by = key(survdat.lw))
#Drop individual columns
survdat.lw[, c('LENGTH', 'NUMLEN', 'INDWT', 'WGTLEN') := NULL]
save(survdat.lw, file = file.path(out.dir, "survdat_lw.RData"))
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