R/clean.format.R
In rBatt/trawlData: Read and Clean Data from Bottom Trawl Surveys
Defines functions
clean.format
clean.format.ai
clean.format.ebs
clean.format.gmex
clean.format.goa
clean.format.neus
clean.format.newf
clean.format.ngulf
clean.format.sa
clean.format.sgulf
clean.format.shelf
clean.format.wcann
clean.format.wctri
Documented in
clean.format
#' Clean Format
#'
#' Clean by fixing data entry errors, and standardizing value formats
#'
#' @template X_reg
#'
#' @details
#' It is this function that makes specific corrections for data entry errors. For example, in one region a tow duration of 3 should have been 30. In another region some of the \code{effort} values were entered as \code{0} or \code{NA}, but should have had a particular value.
#'
#' This function also ensures that longitude and latitude are in the same format among regions.
#'
#' Other data entry errors or necessary corrections are implemented here, too.
#'
#' Dates are not thoroughly formatted here, except in some cases where getting a \code{year}, e.g., requires parsing values out of other columns. POSIX class dates not created.
#'
#' @template clean_seeAlso_template
#'
#' @import data.table
#' @export clean.format
clean.format <- function(X, reg=c("ai", "ebs", "gmex", "goa", "neus", "newf", "ngulf", "sa", "sgulf", "shelf", "wcann", "wctri")){
reg <- match.arg(reg)
clean.format0 <- function(x){
switch(x,
ai = clean.format.ai(X),
ebs = clean.format.ebs(X),
gmex = clean.format.gmex(X),
goa = clean.format.goa(X),
neus = clean.format.neus(X),
newf = clean.format.newf(X),
ngulf = clean.format.ngulf(X),
sa = clean.format.sa(X),
sgulf = clean.format.sgulf(X),
shelf = clean.format.shelf(X),
wcann = clean.format.wcann(X),
wctri = clean.format.wctri(X)
)
}
# ======================
# = Fix Column Classes =
# ======================
# standard column names that should be numeric
# can't do the lat/lon.start/end as numeric because newf needs them to stay as character
# in order for their conversion to decimal units to be simple
numeric.cols <- c("airtemp","areaswept","bdo", "bsalin", "btemp", "cnt", "cntcpue", "depth", "depth.end", "depth.max", "depth.min", "depth.start", "depth2.start", "effort", "lat", "lat.deg.end", "lat.deg.start", "lat.min.end", "lat.min.start", "length", "lon", "lon.deg.end", "lon.deg.start", "lon.min.end", "lon.min.start", "ssalin", "stemp", "stratumarea", "stratumarea2", "temperature", "towarea", "towdistance", "towduration", "towspeed", "weight", "wtcpue")
# standard column names that should be character
character.cols <- c("comment", "common", "cruise", "date", "date.end", "datetime", "geartype","genus", "haul", "haulid", "season", "set", "station", "station.comment", "stratum", "str", "survey.name", "time", "timel", "timezone", "towID", "vessel")
integer.cols <- c("day","dayl","month","monthl","year", "yearl")
# test <- copy(ai)
# X <- test
has.nc <- names(X)[names(X)%in%numeric.cols]
has.cc <- names(X)[names(X)%in%character.cols]
has.ic <- names(X)[names(X)%in%integer.cols]
# X[,c(has.nc):=eval(s2c(has.nc))]
as.n <- function(x){
x <- gsub("\\s|[O]*", "", x)
x[x==""] <- NA_real_
as.numeric(x)
}
if(reg%in%c("newf")){
X[,c(has.nc):=lapply(eval(s2c(has.nc)), as.n)]
}else{
X[,c(has.nc):=lapply(eval(s2c(has.nc)), as.numeric)]
}
X[,c(has.cc):=lapply(eval(s2c(has.cc)), as.character)]
if(length(has.ic)){
X[,c(has.ic):=lapply(eval(s2c(has.ic)), as.integer)]
}
# Change factors to characters
isfactor <- sapply(X, is.factor)
if(any(isfactor)){
has.fc <- names(X)[isfactor]
invisible(X[,c(has.fc):=lapply(eval(s2c(has.fc)), as.character)])
}
# White Space & 9's to NA's
rmWhite(X) # remove whitespace in the elements of each column
rm9s(X) # check each column for 9999, and replace with NA
invisible(clean.format0(reg))
}
# ======
# = AI =
# ======
clean.format.ai <- function(X){
# Calculate a corrected longitude for Aleutians (all in western hemisphere coordinates)
if(X[,any(lon>0)]){
X[lon>0, lon:=(lon-360)]
}
}
# =======
# = EBS =
# =======
clean.format.ebs <- function(X){
# nothing to add beyond generic
}
# ========
# = GMEX =
# ========
clean.format.gmex <- function(X){
X[lat.deg.start==0, lat.deg.start:=NA_real_]
X[lon.deg.start==0, lon.deg.start:=NA_real_]
X[lat.deg.end==0, lat.deg.end:=NA_real_]
X[lon.deg.end==0, lon.deg.end:=NA_real_]
X[,depth:=depth*1.8288] # convert fathoms to meters
X[towspeed==30, towspeed:=3] # fix typo according to Jeff Rester: 30 = 3
X[btemp<0.01 | btemp > 100, btemp:=NA]
X[,time:=gsub("(?<=\\d)([\\d]{2})(?=$)", ":\\1", time, perl=TRUE)]
X[survey.name=='Summer SEAMAP Groundfish Suvey', survey.name:='Summer SEAMAP Groundfish Survey']
}
# =======
# = GOA =
# =======
clean.format.goa <- function(X){
# no changes to be made beyond what's
# already done in generic
}
# ========
# = NEUS =
# ========
clean.format.neus <- function(X){
X[,stratumarea:=stratumarea*3.429904] # convert square nautical miles to square kilometers
X[,season:=tolower(season)]
}
# ========
# = NEWF =
# ========
clean.format.newf <- function(X){
# The formatting below is for the
# "strata" data files in read.newf,
# but I currently don't bother with it
# because the information doesn't seem to be needed
# # Convert square nautical miles to square meters
# strat1$aream2 <- strat1$area*3429904
# strat2$aream2 <- strat2$area*3429904
# strat3$aream2 <- strat3$area*3429904
# strat4$aream2 <- strat4$area*3429904
#
# # Trim out spaces in NAFO division names
# strat1$nafo <- gsub(" ", "", strat1$nafo)
# strat2$nafo <- gsub(" ", "", strat2$nafo)
# strat3$nafo <- gsub(" ", "", strat3$nafo)
# strat4$nafo <- gsub(" ", "", strat4$nafo)
X[,year:=as.numeric(year)+1900]
X[year<1950, year:=year+100]
# # ==================
# # = Format lat/lon =
# # ==================
# # first, fix latitude
# lat.1 <- newf.raw[,(lat.start>0&lat.end>0)]
# lat.2 <- newf.raw[,(lat.start>0&lat.end==0)]
# # lat.3 <- newf.raw[,(latstart==0&latend>0)] # no instances of this case
#
# newf.raw[lat.1,lat:=(as.numeric(substr(lat.start, 1, 2)) + as.numeric(substr(lat.start, 3, 5))/600 + as.numeric(substr(latend, 1, 2)) + as.numeric(substr(latend, 3, 5))/600)/2]
#
# newf.raw[lat.2, lat:=as.numeric(substr(lat.start, 1, 2)) + as.numeric(substr(lat.start, 3, 5))/600]
conv.newf.lat <- function(x){
if(!is.character(x)){
message("already converted newf lat; no changes made")
return(x)
}
as.numeric(substr(x,1,2))+as.numeric(substr(x,3,5))/600
}
conv.newf.lon <- function(x){
if(!is.character(x)){
message("already converted newf lon; no changes made")
return(x)
}
-(as.numeric(substr(x,1,2))+as.numeric(substr(x,3,5))/600)
}
X[, lat.start:=conv.newf.lat(lat.start)]
X[, lat.end:=conv.newf.lat(lat.end)]
X[, lon.start:=conv.newf.lon(lon.start)]
X[, lon.end:=conv.newf.lon(lon.end)]
# # fix longitude
# lon.1 <- newf.raw[,(lonstart>0&lonend>0)]
# lon.2 <- newf.raw[,(lonstart>0&lonend==0)]
#
# newf.raw[lon.1, lon:=-(as.numeric(substr(lonstart, 1, 2)) + as.numeric(substr(lonstart, 3, 5))/600 + as.numeric(substr(lonend, 1, 2)) + as.numeric(substr(lonend, 3, 5))/600)/2]
#
# newf.raw[lon.2, lon:=-(as.numeric(substr(lonstart, 1, 2)) + as.numeric(substr(lonstart, 3, 5))/600)]
#
# ====================
# = Fix temperatures =
# ====================
# Fix the surface temp
fixT.surf <- X[,stemp >= 880 & !is.na(stemp)]
X[fixT.surf, stemp:= -(stemp - 900)/10]
fixT.surf2 <- X[,stemp < 880 & stemp > 0 & !is.na(stemp)]
X[fixT.surf2, stemp:=stemp/10]
# X[,summary(stempt)] # 379,007 NAs (of 383,710 rows): nearly all missing # Ryan gets 379,007 NA's too
# Fix the bottom temp
fixT.bot <- X[,btemp >= 880 & !is.na(btemp)]
X[fixT.bot, btemp:= -(btemp - 900)/10]
fixT.bot2 <- X[,btemp < 880 & btemp > 0 & !is.na(btemp)]
X[fixT.bot2, btemp:=btemp/10]
# summary(newf.raw$bottemp) # only 6459 NAs
}
# =========
# = NGULF =
# =========
clean.format.ngulf <- function(X){
message("Function not ready yet")
}
# ======
# = SA =
# ======
clean.format.sa <- function(X){
# =====================================================
# = Fix terrible ="asd" convention used in 10 columns =
# =====================================================
# Fix catch first
# names(sa.catch00)[grepl("[\"=]", head(sa.catch00)[1,])]
X[,PROJECTNAME:=gsub("[\"=]", "", PROJECTNAME)]
X[,PROJECTAGENCY:=gsub("[\"=]", "", PROJECTAGENCY)]
X[,haulid:=gsub("[\"=]", "", haulid)]
X[,GEARCODE:=gsub("[\"=]", "", GEARCODE)]
X[,spp:=gsub("[\"=]", "", spp)]
X[,common:=gsub("[\"=]", "", common)]
X[,LOCATION:=gsub("[\"=]", "", LOCATION)]
X[,REGION:=gsub("[\"=]", "", REGION)]
X[,DEPTHZONE:=gsub("[\"=]", "", DEPTHZONE)]
X[,stratum:=gsub("[\"=]", "", stratum)]
# Fix strata column
X[,haulid:=gsub("[\"=]", "", haulid)]
# ================================
# = Fix lat/lon, add stratumarea =
# ================================
# this was weird, so I took a guess
# Morley made similar corrections to this, but more direct rather than inferential
# End result is same
# But see Morley's corrections:
# https://github.com/mpinsky/OceanAdapt/blob/master/complete_r_script.R#L225-L348
X[lon.start > -782.000 & lon.start < -780.000, lon.start:=-79.0]
X[lon.end > -782.000 & lon.end < -780.000, lon.end:=-78.988]
X[lon.start > -802.000 & lon.start < -800.000, lon.start:= -81.006+0.01]
X[lat.end>40, lat.end:=lat.start+0.009]
# ==============
# = Fix Effort =
# ==============
# From Morley
# https://github.com/mpinsky/OceanAdapt/blob/master/complete_r_script.R#L225-L348
X[COLLECTIONNUMBER == 19910105, effort:=1.71273]
X[COLLECTIONNUMBER == 19990065, effort:=0.53648]
X[COLLECTIONNUMBER == 20070177, effort:=0.99936]
X[COLLECTIONNUMBER == 19950335, effort:=0.9775]
X[COLLECTIONNUMBER == 20110393, effort:=1.65726]
X[haulid == 2014325, effort:=1.755]
X[haulid == 1992219, effort:=1.796247]
X[COLLECTIONNUMBER == 19910423, effort:=0.50031]
X[COLLECTIONNUMBER == 20010431, effort:=0.25099]
# ================================
# = Fix Weights for Some Species =
# ================================
# Corrections from Morley
# https://github.com/mpinsky/OceanAdapt/blob/master/complete_r_script.R#L225-L348
X[COLLECTIONNUMBER==20010106 & SPECIESCODE==8713050104, weight:=31.9] # roughtail stingray
X[(is.na(weight) | weight==0) & SPECIESCODE==5802010101, weight:=(cnt*1.9)] # horseshoe crabs
X[COLLECTIONNUMBER==19940236 & SPECIESCODE == 9002050101, weight:=204] # leatherback sea turtle
X[(weight==0 | is.na(weight)) & SPECIESCODE==9002040101, weight:=46] # loggerhead
}
# =========
# = SGULF =
# =========
clean.format.sgulf <- function(X){
X[,time:=gsub("(?<=\\d)([\\d]{2})(?=$)", ":\\1", time, perl=TRUE)]
}
# =========
# = SHELF =
# =========
clean.format.shelf <- function(X){
X[,stratumarea:=stratumarea*1.852^2]
date.fix <- function(x){
as.POSIXct(gsub("-", "/", x), format="%y/%m/%d", tz="GMT")
}
X[,date:=date.fix(date)]
X[,date.end:=date.fix(date.end)]
X[,time:=gsub("(?<=\\d)([\\d]{2})(?=$)", ":\\1", time, perl=TRUE)]
fix.ll <- function(x){
as.numeric(substr(x,1,2))+as.numeric(substr(x,3,4))/60
}
X[,lat.start:=fix.ll(lat.start)]
X[,lon.start:= -fix.ll(lon.start)]
X[,lat.end:=fix.ll(lat.end)]
X[,lon.end:= -fix.ll(lon.end)]
}
# ==========
# = WC ANN =
# ==========
clean.format.wcann <- function(X){
# nothing to add beyond generic
# X[,year:=as.integer(gsub("Cycle ", "", year))]
}
# ==========
# = WC TRI =
# ==========
clean.format.wctri <- function(X){
X[towduration==0, towduration:=NA]
X[towdistance==0, towdistance:=NA]
}
rBatt/trawlData documentation built on May 26, 2019, 7:45 p.m.
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Defines functions clean.format clean.format.ai clean.format.ebs clean.format.gmex clean.format.goa clean.format.neus clean.format.newf clean.format.ngulf clean.format.sa clean.format.sgulf clean.format.shelf clean.format.wcann clean.format.wctri
Documented in clean.format
#' Clean Format
#'
#' Clean by fixing data entry errors, and standardizing value formats
#'
#' @template X_reg
#'
#' @details
#' It is this function that makes specific corrections for data entry errors. For example, in one region a tow duration of 3 should have been 30. In another region some of the \code{effort} values were entered as \code{0} or \code{NA}, but should have had a particular value.
#'
#' This function also ensures that longitude and latitude are in the same format among regions.
#'
#' Other data entry errors or necessary corrections are implemented here, too.
#'
#' Dates are not thoroughly formatted here, except in some cases where getting a \code{year}, e.g., requires parsing values out of other columns. POSIX class dates not created.
#'
#' @template clean_seeAlso_template
#'
#' @import data.table
#' @export clean.format
clean.format <- function(X, reg=c("ai", "ebs", "gmex", "goa", "neus", "newf", "ngulf", "sa", "sgulf", "shelf", "wcann", "wctri")){
reg <- match.arg(reg)
clean.format0 <- function(x){
switch(x,
ai = clean.format.ai(X),
ebs = clean.format.ebs(X),
gmex = clean.format.gmex(X),
goa = clean.format.goa(X),
neus = clean.format.neus(X),
newf = clean.format.newf(X),
ngulf = clean.format.ngulf(X),
sa = clean.format.sa(X),
sgulf = clean.format.sgulf(X),
shelf = clean.format.shelf(X),
wcann = clean.format.wcann(X),
wctri = clean.format.wctri(X)
)
}
# ======================
# = Fix Column Classes =
# ======================
# standard column names that should be numeric
# can't do the lat/lon.start/end as numeric because newf needs them to stay as character
# in order for their conversion to decimal units to be simple
numeric.cols <- c("airtemp","areaswept","bdo", "bsalin", "btemp", "cnt", "cntcpue", "depth", "depth.end", "depth.max", "depth.min", "depth.start", "depth2.start", "effort", "lat", "lat.deg.end", "lat.deg.start", "lat.min.end", "lat.min.start", "length", "lon", "lon.deg.end", "lon.deg.start", "lon.min.end", "lon.min.start", "ssalin", "stemp", "stratumarea", "stratumarea2", "temperature", "towarea", "towdistance", "towduration", "towspeed", "weight", "wtcpue")
# standard column names that should be character
character.cols <- c("comment", "common", "cruise", "date", "date.end", "datetime", "geartype","genus", "haul", "haulid", "season", "set", "station", "station.comment", "stratum", "str", "survey.name", "time", "timel", "timezone", "towID", "vessel")
integer.cols <- c("day","dayl","month","monthl","year", "yearl")
# test <- copy(ai)
# X <- test
has.nc <- names(X)[names(X)%in%numeric.cols]
has.cc <- names(X)[names(X)%in%character.cols]
has.ic <- names(X)[names(X)%in%integer.cols]
# X[,c(has.nc):=eval(s2c(has.nc))]
as.n <- function(x){
x <- gsub("\\s|[O]*", "", x)
x[x==""] <- NA_real_
as.numeric(x)
}
if(reg%in%c("newf")){
X[,c(has.nc):=lapply(eval(s2c(has.nc)), as.n)]
}else{
X[,c(has.nc):=lapply(eval(s2c(has.nc)), as.numeric)]
}
X[,c(has.cc):=lapply(eval(s2c(has.cc)), as.character)]
if(length(has.ic)){
X[,c(has.ic):=lapply(eval(s2c(has.ic)), as.integer)]
}
# Change factors to characters
isfactor <- sapply(X, is.factor)
if(any(isfactor)){
has.fc <- names(X)[isfactor]
invisible(X[,c(has.fc):=lapply(eval(s2c(has.fc)), as.character)])
}
# White Space & 9's to NA's
rmWhite(X) # remove whitespace in the elements of each column
rm9s(X) # check each column for 9999, and replace with NA
invisible(clean.format0(reg))
}
# ======
# = AI =
# ======
clean.format.ai <- function(X){
# Calculate a corrected longitude for Aleutians (all in western hemisphere coordinates)
if(X[,any(lon>0)]){
X[lon>0, lon:=(lon-360)]
}
}
# =======
# = EBS =
# =======
clean.format.ebs <- function(X){
# nothing to add beyond generic
}
# ========
# = GMEX =
# ========
clean.format.gmex <- function(X){
X[lat.deg.start==0, lat.deg.start:=NA_real_]
X[lon.deg.start==0, lon.deg.start:=NA_real_]
X[lat.deg.end==0, lat.deg.end:=NA_real_]
X[lon.deg.end==0, lon.deg.end:=NA_real_]
X[,depth:=depth*1.8288] # convert fathoms to meters
X[towspeed==30, towspeed:=3] # fix typo according to Jeff Rester: 30 = 3
X[btemp<0.01 | btemp > 100, btemp:=NA]
X[,time:=gsub("(?<=\\d)([\\d]{2})(?=$)", ":\\1", time, perl=TRUE)]
X[survey.name=='Summer SEAMAP Groundfish Suvey', survey.name:='Summer SEAMAP Groundfish Survey']
}
# =======
# = GOA =
# =======
clean.format.goa <- function(X){
# no changes to be made beyond what's
# already done in generic
}
# ========
# = NEUS =
# ========
clean.format.neus <- function(X){
X[,stratumarea:=stratumarea*3.429904] # convert square nautical miles to square kilometers
X[,season:=tolower(season)]
}
# ========
# = NEWF =
# ========
clean.format.newf <- function(X){
# The formatting below is for the
# "strata" data files in read.newf,
# but I currently don't bother with it
# because the information doesn't seem to be needed
# # Convert square nautical miles to square meters
# strat1$aream2 <- strat1$area*3429904
# strat2$aream2 <- strat2$area*3429904
# strat3$aream2 <- strat3$area*3429904
# strat4$aream2 <- strat4$area*3429904
#
# # Trim out spaces in NAFO division names
# strat1$nafo <- gsub(" ", "", strat1$nafo)
# strat2$nafo <- gsub(" ", "", strat2$nafo)
# strat3$nafo <- gsub(" ", "", strat3$nafo)
# strat4$nafo <- gsub(" ", "", strat4$nafo)
X[,year:=as.numeric(year)+1900]
X[year<1950, year:=year+100]
# # ==================
# # = Format lat/lon =
# # ==================
# # first, fix latitude
# lat.1 <- newf.raw[,(lat.start>0&lat.end>0)]
# lat.2 <- newf.raw[,(lat.start>0&lat.end==0)]
# # lat.3 <- newf.raw[,(latstart==0&latend>0)] # no instances of this case
#
# newf.raw[lat.1,lat:=(as.numeric(substr(lat.start, 1, 2)) + as.numeric(substr(lat.start, 3, 5))/600 + as.numeric(substr(latend, 1, 2)) + as.numeric(substr(latend, 3, 5))/600)/2]
#
# newf.raw[lat.2, lat:=as.numeric(substr(lat.start, 1, 2)) + as.numeric(substr(lat.start, 3, 5))/600]
conv.newf.lat <- function(x){
if(!is.character(x)){
message("already converted newf lat; no changes made")
return(x)
}
as.numeric(substr(x,1,2))+as.numeric(substr(x,3,5))/600
}
conv.newf.lon <- function(x){
if(!is.character(x)){
message("already converted newf lon; no changes made")
return(x)
}
-(as.numeric(substr(x,1,2))+as.numeric(substr(x,3,5))/600)
}
X[, lat.start:=conv.newf.lat(lat.start)]
X[, lat.end:=conv.newf.lat(lat.end)]
X[, lon.start:=conv.newf.lon(lon.start)]
X[, lon.end:=conv.newf.lon(lon.end)]
# # fix longitude
# lon.1 <- newf.raw[,(lonstart>0&lonend>0)]
# lon.2 <- newf.raw[,(lonstart>0&lonend==0)]
#
# newf.raw[lon.1, lon:=-(as.numeric(substr(lonstart, 1, 2)) + as.numeric(substr(lonstart, 3, 5))/600 + as.numeric(substr(lonend, 1, 2)) + as.numeric(substr(lonend, 3, 5))/600)/2]
#
# newf.raw[lon.2, lon:=-(as.numeric(substr(lonstart, 1, 2)) + as.numeric(substr(lonstart, 3, 5))/600)]
#
# ====================
# = Fix temperatures =
# ====================
# Fix the surface temp
fixT.surf <- X[,stemp >= 880 & !is.na(stemp)]
X[fixT.surf, stemp:= -(stemp - 900)/10]
fixT.surf2 <- X[,stemp < 880 & stemp > 0 & !is.na(stemp)]
X[fixT.surf2, stemp:=stemp/10]
# X[,summary(stempt)] # 379,007 NAs (of 383,710 rows): nearly all missing # Ryan gets 379,007 NA's too
# Fix the bottom temp
fixT.bot <- X[,btemp >= 880 & !is.na(btemp)]
X[fixT.bot, btemp:= -(btemp - 900)/10]
fixT.bot2 <- X[,btemp < 880 & btemp > 0 & !is.na(btemp)]
X[fixT.bot2, btemp:=btemp/10]
# summary(newf.raw$bottemp) # only 6459 NAs
}
# =========
# = NGULF =
# =========
clean.format.ngulf <- function(X){
message("Function not ready yet")
}
# ======
# = SA =
# ======
clean.format.sa <- function(X){
# =====================================================
# = Fix terrible ="asd" convention used in 10 columns =
# =====================================================
# Fix catch first
# names(sa.catch00)[grepl("[\"=]", head(sa.catch00)[1,])]
X[,PROJECTNAME:=gsub("[\"=]", "", PROJECTNAME)]
X[,PROJECTAGENCY:=gsub("[\"=]", "", PROJECTAGENCY)]
X[,haulid:=gsub("[\"=]", "", haulid)]
X[,GEARCODE:=gsub("[\"=]", "", GEARCODE)]
X[,spp:=gsub("[\"=]", "", spp)]
X[,common:=gsub("[\"=]", "", common)]
X[,LOCATION:=gsub("[\"=]", "", LOCATION)]
X[,REGION:=gsub("[\"=]", "", REGION)]
X[,DEPTHZONE:=gsub("[\"=]", "", DEPTHZONE)]
X[,stratum:=gsub("[\"=]", "", stratum)]
# Fix strata column
X[,haulid:=gsub("[\"=]", "", haulid)]
# ================================
# = Fix lat/lon, add stratumarea =
# ================================
# this was weird, so I took a guess
# Morley made similar corrections to this, but more direct rather than inferential
# End result is same
# But see Morley's corrections:
# https://github.com/mpinsky/OceanAdapt/blob/master/complete_r_script.R#L225-L348
X[lon.start > -782.000 & lon.start < -780.000, lon.start:=-79.0]
X[lon.end > -782.000 & lon.end < -780.000, lon.end:=-78.988]
X[lon.start > -802.000 & lon.start < -800.000, lon.start:= -81.006+0.01]
X[lat.end>40, lat.end:=lat.start+0.009]
# ==============
# = Fix Effort =
# ==============
# From Morley
# https://github.com/mpinsky/OceanAdapt/blob/master/complete_r_script.R#L225-L348
X[COLLECTIONNUMBER == 19910105, effort:=1.71273]
X[COLLECTIONNUMBER == 19990065, effort:=0.53648]
X[COLLECTIONNUMBER == 20070177, effort:=0.99936]
X[COLLECTIONNUMBER == 19950335, effort:=0.9775]
X[COLLECTIONNUMBER == 20110393, effort:=1.65726]
X[haulid == 2014325, effort:=1.755]
X[haulid == 1992219, effort:=1.796247]
X[COLLECTIONNUMBER == 19910423, effort:=0.50031]
X[COLLECTIONNUMBER == 20010431, effort:=0.25099]
# ================================
# = Fix Weights for Some Species =
# ================================
# Corrections from Morley
# https://github.com/mpinsky/OceanAdapt/blob/master/complete_r_script.R#L225-L348
X[COLLECTIONNUMBER==20010106 & SPECIESCODE==8713050104, weight:=31.9] # roughtail stingray
X[(is.na(weight) | weight==0) & SPECIESCODE==5802010101, weight:=(cnt*1.9)] # horseshoe crabs
X[COLLECTIONNUMBER==19940236 & SPECIESCODE == 9002050101, weight:=204] # leatherback sea turtle
X[(weight==0 | is.na(weight)) & SPECIESCODE==9002040101, weight:=46] # loggerhead
}
# =========
# = SGULF =
# =========
clean.format.sgulf <- function(X){
X[,time:=gsub("(?<=\\d)([\\d]{2})(?=$)", ":\\1", time, perl=TRUE)]
}
# =========
# = SHELF =
# =========
clean.format.shelf <- function(X){
X[,stratumarea:=stratumarea*1.852^2]
date.fix <- function(x){
as.POSIXct(gsub("-", "/", x), format="%y/%m/%d", tz="GMT")
}
X[,date:=date.fix(date)]
X[,date.end:=date.fix(date.end)]
X[,time:=gsub("(?<=\\d)([\\d]{2})(?=$)", ":\\1", time, perl=TRUE)]
fix.ll <- function(x){
as.numeric(substr(x,1,2))+as.numeric(substr(x,3,4))/60
}
X[,lat.start:=fix.ll(lat.start)]
X[,lon.start:= -fix.ll(lon.start)]
X[,lat.end:=fix.ll(lat.end)]
X[,lon.end:= -fix.ll(lon.end)]
}
# ==========
# = WC ANN =
# ==========
clean.format.wcann <- function(X){
# nothing to add beyond generic
# X[,year:=as.integer(gsub("Cycle ", "", year))]
}
# ==========
# = WC TRI =
# ==========
clean.format.wctri <- function(X){
X[towduration==0, towduration:=NA]
X[towdistance==0, towdistance:=NA]
}
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