R/bycatch.db.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
Defines functions
bycatch.db
#' @export
bycatch.db <- function(DS='redo.data',p=p,wd='C:/Users/HowseVJ/OneDrive - DFO-MPO/Bycatch Review'){
options(stringsAsFactors=F)
require(lubridate)
dir.create(file.path(wd,'data'),showWarnings = F)
dir.create(file.path(wd,'results'),showWarnings = F)
if(grepl('odbc',DS)) db.setup()
if(DS=='odbc.redo'){
xAll = connect.command(con,'select * from cooka.lobster_bycatch_assoc')
xAll$X = convert.dd.dddd(xAll$LONGDDMM)*-1
xAll$Y = convert.dd.dddd(xAll$LATDDMM)
saveRDS(xAll,file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
xAll = connect.command(con,'select * from cooka.bycatch_cbfha_2022')
xAll$X = convert.dd.dddd(xAll$LONGDDMM)*-1
xAll$Y = convert.dd.dddd(xAll$LATDDMM)
saveRDS(xAll,file.path(wd,'data/CBFHA_2021_atsea.rds'))
xAll = connect.command(con,'select * from cooka.bycatch_esfpa_2022')
xAll$X = convert.dd.dddd(xAll$LONGDDMM)*-1
xAll$Y = convert.dd.dddd(xAll$LATDDMM)
saveRDS(xAll,file.path(wd,'data/ESFPA_2019_atsea.rds'))
tr = connect.command(con,'select * from lobster.istraps')
se = connect.command(con,'select * from lobster.issets_mv')
de = connect.command(con,'select * from lobster.isdetails_mv')
saveRDS(list(tr,se,de),file=file.path(wd,'/data/ObserverInfo.rds'))
}
if(DS %in% c('logbook.merge.redo','logbook.merge')){
if(grepl('redo',DS)){
x = lobster.db('process.logs')
b = subset(x,LFA %in% c(33,34,35) & SYEAR %in% 2019:2021)
bb = subset(x, LFA %in% c(27) & SYEAR %in% 2019)
bbb = subset(x, LFA %in% c('31A','31B') & SYEAR %in% 2018:2019)
b = as.data.frame(rbind(rbind(b,bb),bbb))
gt = read.csv(file.path(wd,'data/Grids2Targets.csv'))
#logbook handling
b$mn = month(b$DATE_FISHED)
b$GridGroup = b$target = b$Period = NA
for(i in 1:nrow(b)){
pit = gt$GridGrouping[which(b$GRID_NUM[i]==gt$GRID_NUM & gt$LFA==b$LFA[i])]
if(length(pit)>0){
b$GridGroup[i] = pit
m = b$mn[i]
k = subset(gt,GRID_NUM==b$GRID_NUM[i]& gt$LFA==b$LFA[i])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
b$target[i] <- k[,ll]
b$Period[i] = lll
}
}
saveRDS(b,file=file.path(wd,'data/logbookReadyFILTERED.rds'))
return('complete')
}
return(readRDS(file.path(wd,'data/logbookReadyFILTERED.rds')))
}
if(DS=='targets'){
return( read.csv(file.path(wd,'data/Grids2Targets.csv'))
)
}
if(DS %in% c('SWLSS','SWLSS.redo')){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data','CompiledAtSeaMarch2022.rds'))
a = subset(a, OWNER_GROUP=='SWLSS')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$COMAREA_ID[which(a$TRIP== '107869-081219')] <- "L33"
ms = read.csv('data/SWLSSTripmatch.csv')
ms = subset(ms,select=c(TRIP,SD_LOG_ID_1,QUALITY))
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$JonahRtWt = ifelse(a$Jonah==1 & a$SEXCD_ID==1 & a$FISH_LENGTH>=130, a$JonahWt, 0)
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$Sz = round(a$FISH_LENGTH/5)*5
a$SP_SZ = paste(a$SPECCD_ID, a$Sz, sep="-")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
# season.dates = lobster.db('season.dates')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,JonahRtWt,LobsterWt)~UID+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
CDa = bio.utilities::rename.df(CDa, c('TRAP_ID', 'FISHSET_ID','STRATUM_ID','NUM_HOOK_HAUL','BOARD_DATE','CALWT_G'),c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT'))
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
saveRDS(CDa,file=file.path(wd,'data','SWLSSreshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','SWLSSreshape.rds')))
}
if(DS %in% c('ISDB.redo','ISDB')){
if(grepl('redo',DS)){
g = lobster.db('atSea.redo')
g = lobster.db('atSea.clean.redo')
g = lobster.db('atSea.clean')
gg = subset(g,DESCRIPTION=='ISDB' & SYEAR %in% (2019:2021) & LFA %in% 33:35)
gg$UID = paste(gg$TRIPNO,gg$TRAPNO,sep='_')
# LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
gt = t = bycatch.db('targets',wd=wd)
gg$GridGroup = gg$target = gg$Period = NA
gg$mn = month(gg$SDATE)
for(i in 1:nrow(gg)){
pit = gt$GridGrouping[which(gg$GRIDNO[i]==gt$GRID_NUM & gt$LFA==gg$LFA[i])]
if(length(pit)>0){
gg$GridGroup[i] = (pit)
m = gg$mn[i]
k = subset(gt,GRID_NUM==gg$GRIDNO[i] & LFA==gg$LFA[i])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
gg$target[i] <- as.numeric(k[,ll])
gg$Period[i] = lll
rm(k,m,ll,lll)
}
}
saveRDS(gg,file=file.path(wd,'data','ISDBclean.rds'))
return(gg)
}
return(readRDS(file=file.path(wd,'data','ISDBclean.rds')))
}
if(DS %in% c('ISDB.reshape.redo','ISDB.reshape')){
if(grepl('redo',DS)){
a = bycatch.db(DS='ISDB')
a$UID = paste(a$TRIPNO,a$TRAPNO,sep='_')
a$Legal = ifelse(a$SPECIESCODE == 2550 & a$CARLENGTH > 82 & a$SEX %in% 1:2,1,0)
a$Berried = ifelse(a$SPECIESCODE == 2550 & a$SEX %in% 3,1,0)
a$Lobster = ifelse(a$SPECIESCODE == 2550,1,0)
a$Cod = ifelse(a$SPECIESCODE == 10,1,0)
a$Cusk = ifelse(a$SPECIESCODE == 15,1,0)
a$Jonah = ifelse(a$SPECIESCODE == 2511,1,0)
a$SPECIESCODE = ifelse(is.na(a$SPECIESCODE),9999,a$SPECIESCODE)
a$Empty = ifelse(a$SPECIESCODE == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT/1000
a$CuskWt = a$Cusk * a$CALWT/1000
a$JonahWt = a$Jonah * a$CALWT/1000
a$JonahRtWt = ifelse(a$Jonah==1 & a$SEX==1 & a$CARLENGTH>=130, a$JonahWt, 0)
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT[which(is.na(a$CALWT))] <- 0
a$LobsterWt = a$Lobster * a$CALWT/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$Sz = round(a$CARLENGTH/5)*5
a$SP_SZ = paste(a$SPECIESCODE, a$Sz, sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT,CodWt,CuskWt,JonahWt,JonahRtWt,LobsterWt)~UID
+TRIPNO+X+Y+TRAPNO+NUM_HOOK_HAUL+LFA+GRIDNO+SDATE+SYEAR+WOS+Period+target+GridGroup, data=a,FUN=sum,na.rm=F)
BF = merge(ac,bb,by='UID')
BF$'P.9999-NA' = NULL
BF$P=1
names(BF)[c(2,6,8,9)] = c('TRIP','NUM_TRAPS','GRIDNUM','DATE_FISHED')
BF$DID = 'OBS'
BF$ll = paste(BF$X,BF$Y,sep='ll')
BF$Cluster = NA
cc = unique(BF$TRIP)
for(i in 1:length(cc)){
k = which(BF$TRIP == cc[i])
BF$Cluster[k] = create_seq_from_column(BF$ll[k])
}
BF$ll <- NULL
saveRDS(BF,file=file.path(wd,'data','ISDBreshape.rds'))
return(BF)
}
return(readRDS(file=file.path(wd,'data','ISDBreshape.rds')))
}
if(DS %in% c('ISDB.all.species.reshape.redo','ISDB.all.species.reshape')){
if(grepl('redo',DS)){
a = bycatch.db(DS='ISDB')
a$UID = paste(a$TRIPNO,a$TRAPNO,sep='_')
a$Legal = ifelse(a$SPECIESCODE == 2550 & a$CARLENGTH > 82 & a$SEX %in% 1:2,1,0)
a$Berried = ifelse(a$SPECIESCODE == 2550 & a$SEX %in% 3,1,0)
a$Lobster = ifelse(a$SPECIESCODE == 2550,1,0)
a$Cod = ifelse(a$SPECIESCODE == 10,1,0)
a$Cusk = ifelse(a$SPECIESCODE == 15,1,0)
a$Jonah = ifelse(a$SPECIESCODE == 2511,1,0)
a$SPECIESCODE = ifelse(is.na(a$SPECIESCODE),9999,a$SPECIESCODE)
a$Empty = ifelse(a$SPECIESCODE == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT/1000
a$CuskWt = a$Cusk * a$CALWT/1000
a$JonahWt = a$Jonah * a$CALWT/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT[which(is.na(a$CALWT))] <- 0
a$LobsterWt = a$Lobster * a$CALWT/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECIESCODE = bio.utilities::recode(a$SPECIESCODE, "12=193;13=193;200=211; 201=211; 202=211; 203=211; 204=211; 300=310; 301=310; 312=310; 636=122; 429=640; 648=640; 2521=2520")
a$P = 1
aa = aggregate(P~SPECIESCODE+UID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECIESCODE','P')],idvar='UID',timevar='SPECIESCODE', direction='wide')
bb = na.zero(bb)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIPNO+X+Y+TRAPNO+NUM_HOOK_HAUL+LFA+GRIDNO+SDATE+SYEAR+WOS+Period+target+GridGroup, data=a,FUN=sum,na.rm=F)
BF = merge(ac,bb,by='UID')
BF$'P.9999' = NULL
BF$P=1
names(BF)[c(2,6,8,9)] = c('TRIP','NUM_TRAPS','GRIDNUM','DATE_FISHED')
BF$DID = 'OBS'
saveRDS(BF,file=file.path(wd,'data','ISDB.all.species.reshape.rds'))
return(BF)
}
return(readRDS(file=file.path(wd,'data','ISDB.all.species.reshape.rds')))
}
if(DS %in% c('SWLSS.all.species','SWLSS.all.species.redo')){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data','CompiledAtSeaMarch2022.rds'))
a = subset(a, OWNER_GROUP=='SWLSS')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$COMAREA_ID[which(a$TRIP== '107869-081219')] <- "L33"
ms = read.csv('data/SWLSSTripmatch.csv')
ms = subset(ms,select=c(TRIP,SD_LOG_ID_1,QUALITY))
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "2=9991; 9=9991; 12=193; 13=193; 20=23; 54=9991; 92=9991; 112=193; 201=211;
204=211; 251=10; 300=310; 301=310; 302=310; 429=640;
440=640; 600=640; 620=640; 2551=2550;")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~SPECCD_ID+UID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECCD_ID','P')],idvar='UID',timevar='SPECCD_ID', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
# season.dates = lobster.db('season.dates')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:9,21)] =c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
saveRDS(CDa,file=file.path(wd,'data','SWLSS.all.species.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','SWLSS.all.species.reshape.rds')))
}
if(DS %in% c('CBFHA.redo','CBFHA') ){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='CBFHA')
aa = readRDS(file.path(wd,'data/CBFHA_2021_atsea.rds'))
aa$PORT_NAME = aa$VENT_CODE = aa$CULLS = NULL
a = as.data.frame(rbind(a,aa))
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$Cunner = ifelse(a$SPECCD_ID == 122,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CunnerWt = a$Cunner * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$CunnerWt[which(is.na(a$CunnerWt))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "300=310; 301=310; 302=310; 118=10;")
a$Sz = round(a$FISH_LENGTH/5)*5
a$SP_SZ = paste(a$SPECCD_ID, a$Sz, sep="-")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Cunner, Jonah, Legal, Berried,Empty,CunnerWt, LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:9,23)] =c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
CDa$SYEAR = year(CDa$DATE_FISHED)
saveRDS(CDa,file=file.path(wd,'data','CBFHA.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','CBFHA.reshape.rds')))
}
if(DS %in% c('CBFHA.all.species.redo','CBFHA.all.species') ){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='CBFHA')
aa = readRDS(file.path(wd,'data/CBFHA_2021_atsea.rds'))
aa$PORT_NAME = aa$VENT_CODE = aa$CULLS = NULL
a = as.data.frame(rbind(a,aa))
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "300=310; 301=310; 302=310; 118=10;")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SPECCD_ID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECCD_ID','P')],idvar='UID',timevar='SPECCD_ID', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:9,21)] =c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
CDa$SYEAR = year(CDa$DATE_FISHED)
saveRDS(CDa,file=file.path(wd,'data','CBFHA.all.species.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','CBFHA.all.species.reshape.rds')))
}
if(DS %in% c('GCIFA',"GCIFA.redo")){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='GCIFA')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$COMAREA_ID=='L31A' & a$FISH_LENGTH %in% 115:125 & a$SEXCD_ID %in% 2,0,a$Legal)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$Cunner = ifelse(a$SPECCD_ID == 122,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$CunnerWt = a$Cunner * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CunnerWt[which(is.na(a$CunnerWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "21=23; 65=9991; 120=122; 250=9991; 300=310; 455=640; 4250=4210; 301=310; 302=310; 118=10;")
a$Sz = round(a$FISH_LENGTH/5)*5
a$SP_SZ = paste(a$SPECCD_ID, a$Sz, sep="-")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = (unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = c('31A','31B')
a = subset(a,LFA %in% lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cunner, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CunnerWt, CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$target = CDa$Period = NA
CDa$GridGroup = 1
for(i in 1:nrow(CDa)){
m = CDa$mn[i]
k = subset(gt, LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
k = k[1,]
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:8,22)] =c('TRAPNO','SETNO','GRIDNUM','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
saveRDS(CDa,file=file.path(wd,'data','GCIFA.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','GCIFA.reshape.rds')))
}
if(DS %in% c('GCIFA.all.species',"GCIFA.all.species.redo")){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='GCIFA')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$COMAREA_ID=='L31A' & a$FISH_LENGTH %in% 115:125 & a$SEXCD_ID %in% 2,0,a$Legal)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "21=23; 65=9991; 120=122; 250=9991; 300=310; 455=640; 4250=4210; 301=310; 302=310; 118=10;")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SPECCD_ID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECCD_ID','P')],idvar='UID',timevar='SPECCD_ID', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = (unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = c('31A','31B')
a = subset(a,LFA %in% lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$target = CDa$Period = NA
CDa$GridGroup = 1
for(i in 1:nrow(CDa)){
m = CDa$mn[i]
k = subset(gt, LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
k = k[1,]
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:8,20)] =c('TRAPNO','SETNO','GRIDNUM','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
saveRDS(CDa,file=file.path(wd,'data','GCIFA.all.species.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','GCIFA.all.species.reshape.rds')))
}
}
LobsterScience/bio.lobster documentation built on Feb. 14, 2025, 3:28 p.m.
R Package Documentation
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Defines functions bycatch.db
#' @export
bycatch.db <- function(DS='redo.data',p=p,wd='C:/Users/HowseVJ/OneDrive - DFO-MPO/Bycatch Review'){
options(stringsAsFactors=F)
require(lubridate)
dir.create(file.path(wd,'data'),showWarnings = F)
dir.create(file.path(wd,'results'),showWarnings = F)
if(grepl('odbc',DS)) db.setup()
if(DS=='odbc.redo'){
xAll = connect.command(con,'select * from cooka.lobster_bycatch_assoc')
xAll$X = convert.dd.dddd(xAll$LONGDDMM)*-1
xAll$Y = convert.dd.dddd(xAll$LATDDMM)
saveRDS(xAll,file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
xAll = connect.command(con,'select * from cooka.bycatch_cbfha_2022')
xAll$X = convert.dd.dddd(xAll$LONGDDMM)*-1
xAll$Y = convert.dd.dddd(xAll$LATDDMM)
saveRDS(xAll,file.path(wd,'data/CBFHA_2021_atsea.rds'))
xAll = connect.command(con,'select * from cooka.bycatch_esfpa_2022')
xAll$X = convert.dd.dddd(xAll$LONGDDMM)*-1
xAll$Y = convert.dd.dddd(xAll$LATDDMM)
saveRDS(xAll,file.path(wd,'data/ESFPA_2019_atsea.rds'))
tr = connect.command(con,'select * from lobster.istraps')
se = connect.command(con,'select * from lobster.issets_mv')
de = connect.command(con,'select * from lobster.isdetails_mv')
saveRDS(list(tr,se,de),file=file.path(wd,'/data/ObserverInfo.rds'))
}
if(DS %in% c('logbook.merge.redo','logbook.merge')){
if(grepl('redo',DS)){
x = lobster.db('process.logs')
b = subset(x,LFA %in% c(33,34,35) & SYEAR %in% 2019:2021)
bb = subset(x, LFA %in% c(27) & SYEAR %in% 2019)
bbb = subset(x, LFA %in% c('31A','31B') & SYEAR %in% 2018:2019)
b = as.data.frame(rbind(rbind(b,bb),bbb))
gt = read.csv(file.path(wd,'data/Grids2Targets.csv'))
#logbook handling
b$mn = month(b$DATE_FISHED)
b$GridGroup = b$target = b$Period = NA
for(i in 1:nrow(b)){
pit = gt$GridGrouping[which(b$GRID_NUM[i]==gt$GRID_NUM & gt$LFA==b$LFA[i])]
if(length(pit)>0){
b$GridGroup[i] = pit
m = b$mn[i]
k = subset(gt,GRID_NUM==b$GRID_NUM[i]& gt$LFA==b$LFA[i])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
b$target[i] <- k[,ll]
b$Period[i] = lll
}
}
saveRDS(b,file=file.path(wd,'data/logbookReadyFILTERED.rds'))
return('complete')
}
return(readRDS(file.path(wd,'data/logbookReadyFILTERED.rds')))
}
if(DS=='targets'){
return( read.csv(file.path(wd,'data/Grids2Targets.csv'))
)
}
if(DS %in% c('SWLSS','SWLSS.redo')){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data','CompiledAtSeaMarch2022.rds'))
a = subset(a, OWNER_GROUP=='SWLSS')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$COMAREA_ID[which(a$TRIP== '107869-081219')] <- "L33"
ms = read.csv('data/SWLSSTripmatch.csv')
ms = subset(ms,select=c(TRIP,SD_LOG_ID_1,QUALITY))
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$JonahRtWt = ifelse(a$Jonah==1 & a$SEXCD_ID==1 & a$FISH_LENGTH>=130, a$JonahWt, 0)
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$Sz = round(a$FISH_LENGTH/5)*5
a$SP_SZ = paste(a$SPECCD_ID, a$Sz, sep="-")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
# season.dates = lobster.db('season.dates')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,JonahRtWt,LobsterWt)~UID+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
CDa = bio.utilities::rename.df(CDa, c('TRAP_ID', 'FISHSET_ID','STRATUM_ID','NUM_HOOK_HAUL','BOARD_DATE','CALWT_G'),c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT'))
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
saveRDS(CDa,file=file.path(wd,'data','SWLSSreshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','SWLSSreshape.rds')))
}
if(DS %in% c('ISDB.redo','ISDB')){
if(grepl('redo',DS)){
g = lobster.db('atSea.redo')
g = lobster.db('atSea.clean.redo')
g = lobster.db('atSea.clean')
gg = subset(g,DESCRIPTION=='ISDB' & SYEAR %in% (2019:2021) & LFA %in% 33:35)
gg$UID = paste(gg$TRIPNO,gg$TRAPNO,sep='_')
# LFAgrid<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","GridPolys.csv"))
gt = t = bycatch.db('targets',wd=wd)
gg$GridGroup = gg$target = gg$Period = NA
gg$mn = month(gg$SDATE)
for(i in 1:nrow(gg)){
pit = gt$GridGrouping[which(gg$GRIDNO[i]==gt$GRID_NUM & gt$LFA==gg$LFA[i])]
if(length(pit)>0){
gg$GridGroup[i] = (pit)
m = gg$mn[i]
k = subset(gt,GRID_NUM==gg$GRIDNO[i] & LFA==gg$LFA[i])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
gg$target[i] <- as.numeric(k[,ll])
gg$Period[i] = lll
rm(k,m,ll,lll)
}
}
saveRDS(gg,file=file.path(wd,'data','ISDBclean.rds'))
return(gg)
}
return(readRDS(file=file.path(wd,'data','ISDBclean.rds')))
}
if(DS %in% c('ISDB.reshape.redo','ISDB.reshape')){
if(grepl('redo',DS)){
a = bycatch.db(DS='ISDB')
a$UID = paste(a$TRIPNO,a$TRAPNO,sep='_')
a$Legal = ifelse(a$SPECIESCODE == 2550 & a$CARLENGTH > 82 & a$SEX %in% 1:2,1,0)
a$Berried = ifelse(a$SPECIESCODE == 2550 & a$SEX %in% 3,1,0)
a$Lobster = ifelse(a$SPECIESCODE == 2550,1,0)
a$Cod = ifelse(a$SPECIESCODE == 10,1,0)
a$Cusk = ifelse(a$SPECIESCODE == 15,1,0)
a$Jonah = ifelse(a$SPECIESCODE == 2511,1,0)
a$SPECIESCODE = ifelse(is.na(a$SPECIESCODE),9999,a$SPECIESCODE)
a$Empty = ifelse(a$SPECIESCODE == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT/1000
a$CuskWt = a$Cusk * a$CALWT/1000
a$JonahWt = a$Jonah * a$CALWT/1000
a$JonahRtWt = ifelse(a$Jonah==1 & a$SEX==1 & a$CARLENGTH>=130, a$JonahWt, 0)
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT[which(is.na(a$CALWT))] <- 0
a$LobsterWt = a$Lobster * a$CALWT/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$Sz = round(a$CARLENGTH/5)*5
a$SP_SZ = paste(a$SPECIESCODE, a$Sz, sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT,CodWt,CuskWt,JonahWt,JonahRtWt,LobsterWt)~UID
+TRIPNO+X+Y+TRAPNO+NUM_HOOK_HAUL+LFA+GRIDNO+SDATE+SYEAR+WOS+Period+target+GridGroup, data=a,FUN=sum,na.rm=F)
BF = merge(ac,bb,by='UID')
BF$'P.9999-NA' = NULL
BF$P=1
names(BF)[c(2,6,8,9)] = c('TRIP','NUM_TRAPS','GRIDNUM','DATE_FISHED')
BF$DID = 'OBS'
BF$ll = paste(BF$X,BF$Y,sep='ll')
BF$Cluster = NA
cc = unique(BF$TRIP)
for(i in 1:length(cc)){
k = which(BF$TRIP == cc[i])
BF$Cluster[k] = create_seq_from_column(BF$ll[k])
}
BF$ll <- NULL
saveRDS(BF,file=file.path(wd,'data','ISDBreshape.rds'))
return(BF)
}
return(readRDS(file=file.path(wd,'data','ISDBreshape.rds')))
}
if(DS %in% c('ISDB.all.species.reshape.redo','ISDB.all.species.reshape')){
if(grepl('redo',DS)){
a = bycatch.db(DS='ISDB')
a$UID = paste(a$TRIPNO,a$TRAPNO,sep='_')
a$Legal = ifelse(a$SPECIESCODE == 2550 & a$CARLENGTH > 82 & a$SEX %in% 1:2,1,0)
a$Berried = ifelse(a$SPECIESCODE == 2550 & a$SEX %in% 3,1,0)
a$Lobster = ifelse(a$SPECIESCODE == 2550,1,0)
a$Cod = ifelse(a$SPECIESCODE == 10,1,0)
a$Cusk = ifelse(a$SPECIESCODE == 15,1,0)
a$Jonah = ifelse(a$SPECIESCODE == 2511,1,0)
a$SPECIESCODE = ifelse(is.na(a$SPECIESCODE),9999,a$SPECIESCODE)
a$Empty = ifelse(a$SPECIESCODE == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT/1000
a$CuskWt = a$Cusk * a$CALWT/1000
a$JonahWt = a$Jonah * a$CALWT/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT[which(is.na(a$CALWT))] <- 0
a$LobsterWt = a$Lobster * a$CALWT/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECIESCODE = bio.utilities::recode(a$SPECIESCODE, "12=193;13=193;200=211; 201=211; 202=211; 203=211; 204=211; 300=310; 301=310; 312=310; 636=122; 429=640; 648=640; 2521=2520")
a$P = 1
aa = aggregate(P~SPECIESCODE+UID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECIESCODE','P')],idvar='UID',timevar='SPECIESCODE', direction='wide')
bb = na.zero(bb)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIPNO+X+Y+TRAPNO+NUM_HOOK_HAUL+LFA+GRIDNO+SDATE+SYEAR+WOS+Period+target+GridGroup, data=a,FUN=sum,na.rm=F)
BF = merge(ac,bb,by='UID')
BF$'P.9999' = NULL
BF$P=1
names(BF)[c(2,6,8,9)] = c('TRIP','NUM_TRAPS','GRIDNUM','DATE_FISHED')
BF$DID = 'OBS'
saveRDS(BF,file=file.path(wd,'data','ISDB.all.species.reshape.rds'))
return(BF)
}
return(readRDS(file=file.path(wd,'data','ISDB.all.species.reshape.rds')))
}
if(DS %in% c('SWLSS.all.species','SWLSS.all.species.redo')){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data','CompiledAtSeaMarch2022.rds'))
a = subset(a, OWNER_GROUP=='SWLSS')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$COMAREA_ID[which(a$TRIP== '107869-081219')] <- "L33"
ms = read.csv('data/SWLSSTripmatch.csv')
ms = subset(ms,select=c(TRIP,SD_LOG_ID_1,QUALITY))
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "2=9991; 9=9991; 12=193; 13=193; 20=23; 54=9991; 92=9991; 112=193; 201=211;
204=211; 251=10; 300=310; 301=310; 302=310; 429=640;
440=640; 600=640; 620=640; 2551=2550;")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~SPECCD_ID+UID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECCD_ID','P')],idvar='UID',timevar='SPECCD_ID', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
# season.dates = lobster.db('season.dates')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:9,21)] =c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
saveRDS(CDa,file=file.path(wd,'data','SWLSS.all.species.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','SWLSS.all.species.reshape.rds')))
}
if(DS %in% c('CBFHA.redo','CBFHA') ){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='CBFHA')
aa = readRDS(file.path(wd,'data/CBFHA_2021_atsea.rds'))
aa$PORT_NAME = aa$VENT_CODE = aa$CULLS = NULL
a = as.data.frame(rbind(a,aa))
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$Cunner = ifelse(a$SPECCD_ID == 122,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CunnerWt = a$Cunner * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$CunnerWt[which(is.na(a$CunnerWt))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "300=310; 301=310; 302=310; 118=10;")
a$Sz = round(a$FISH_LENGTH/5)*5
a$SP_SZ = paste(a$SPECCD_ID, a$Sz, sep="-")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Cunner, Jonah, Legal, Berried,Empty,CunnerWt, LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:9,23)] =c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
CDa$SYEAR = year(CDa$DATE_FISHED)
saveRDS(CDa,file=file.path(wd,'data','CBFHA.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','CBFHA.reshape.rds')))
}
if(DS %in% c('CBFHA.all.species.redo','CBFHA.all.species') ){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='CBFHA')
aa = readRDS(file.path(wd,'data/CBFHA_2021_atsea.rds'))
aa$PORT_NAME = aa$VENT_CODE = aa$CULLS = NULL
a = as.data.frame(rbind(a,aa))
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "300=310; 301=310; 302=310; 118=10;")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SPECCD_ID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECCD_ID','P')],idvar='UID',timevar='SPECCD_ID', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = as.numeric(unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = unique(a$LFA)
lfa = na.omit(lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
m=m+1
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+NUM_HOOK_HAUL+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$GridGroup = CDa$target = CDa$Period = NA
for(i in 1:nrow(CDa)){
pit = gt$GridGrouping[which(CDa$STRATUM_ID[i]==gt$GRID_NUM & gt$LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])]
if(length(pit)>0){
CDa$GridGroup[i] = (pit)
m = CDa$mn[i]
k = subset(gt,GRID_NUM==CDa$STRATUM_ID[i] & LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:9,21)] =c('TRAPNO','SETNO','GRIDNUM','NUM_TRAPS','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
CDa$SYEAR = year(CDa$DATE_FISHED)
saveRDS(CDa,file=file.path(wd,'data','CBFHA.all.species.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','CBFHA.all.species.reshape.rds')))
}
if(DS %in% c('GCIFA',"GCIFA.redo")){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='GCIFA')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$COMAREA_ID=='L31A' & a$FISH_LENGTH %in% 115:125 & a$SEXCD_ID %in% 2,0,a$Legal)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$Cunner = ifelse(a$SPECCD_ID == 122,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$CunnerWt = a$Cunner * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CunnerWt[which(is.na(a$CunnerWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "21=23; 65=9991; 120=122; 250=9991; 300=310; 455=640; 4250=4210; 301=310; 302=310; 118=10;")
a$Sz = round(a$FISH_LENGTH/5)*5
a$SP_SZ = paste(a$SPECCD_ID, a$Sz, sep="-")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SP_SZ,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SP_SZ','P')],idvar='UID',timevar='SP_SZ', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = (unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = c('31A','31B')
a = subset(a,LFA %in% lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cunner, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CunnerWt, CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$target = CDa$Period = NA
CDa$GridGroup = 1
for(i in 1:nrow(CDa)){
m = CDa$mn[i]
k = subset(gt, LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
k = k[1,]
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:8,22)] =c('TRAPNO','SETNO','GRIDNUM','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
saveRDS(CDa,file=file.path(wd,'data','GCIFA.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','GCIFA.reshape.rds')))
}
if(DS %in% c('GCIFA.all.species',"GCIFA.all.species.redo")){
if(grepl('redo',DS)){
a = readRDS(file.path(wd,'data/CompiledAtSeaMarch2022.rds'))
a = subset(a,OWNER_GROUP=='GCIFA')
a$COMAREA_ID = toupper(a$COMAREA_ID)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$FISH_LENGTH > 82 & a$SEXCD_ID %in% 1:2,1,0)
a$Legal = ifelse(a$SPECCD_ID == 2550 & a$COMAREA_ID=='L31A' & a$FISH_LENGTH %in% 115:125 & a$SEXCD_ID %in% 2,0,a$Legal)
a$Berried = ifelse(a$SPECCD_ID == 2550 & a$SEXCD_ID %in% 3,1,0)
a$Lobster = ifelse(a$SPECCD_ID == 2550,1,0)
a$Cod = ifelse(a$SPECCD_ID == 10,1,0)
a$Cusk = ifelse(a$SPECCD_ID == 15,1,0)
a$Jonah = ifelse(a$SPECCD_ID == 2511,1,0)
a$SPECCD_ID = ifelse(is.na(a$SPECCD_ID),9999,a$SPECCD_ID)
a$Empty = ifelse(a$SPECCD_ID == 9999,1,0)
a$LegalWt = a$Legal * a$CALWT_G/1000
a$LegalWt[which(is.na(a$LegalWt))] <- 0
a$CodWt = a$Cod * a$CALWT_G/1000
a$CuskWt = a$Cusk * a$CALWT_G/1000
a$JonahWt = a$Jonah * a$CALWT_G/1000
a$CodWt[which(is.na(a$CodWt))] <- 0
a$CuskWt[which(is.na(a$CuskWt))] <- 0
a$JonahWt[which(is.na(a$JonahWt))] <- 0
a$CALWT_G[which(is.na(a$CALWT_G))] <- 0
a$LobsterWt = a$Lobster * a$CALWT_G/1000
a$LobsterWt[which(is.na(a$LobsterWt))] <- 0
a$SPECCD_ID = bio.utilities::recode(a$SPECCD_ID, "21=23; 65=9991; 120=122; 250=9991; 300=310; 455=640; 4250=4210; 301=310; 302=310; 118=10;")
a$UID = paste(a$TRIP, a$FISHSET_ID, a$TRAP_ID,sep="-")
a$P = 1
aa = aggregate(P~UID+SPECCD_ID,data=a,FUN=sum)
bb = reshape(aa[,c('UID','SPECCD_ID','P')],idvar='UID',timevar='SPECCD_ID', direction='wide')
bb = na.zero(bb)
season.dates = backFillSeasonDates(lobster.db('season.dates'),eyr=year(Sys.time()))
a = subset(a, !is.na(BOARD_DATE))
a$LFA = (unlist(lapply(strsplit(a$COMAREA_ID,'L'),"[[",2)))
a = addSYEAR(a,date.field = 'BOARD_DATE')
a$WOS = NA
m=0
lfa = c('31A','31B')
a = subset(a,LFA %in% lfa)
for(i in 1:length(lfa)) {
h = season.dates[season.dates$LFA==lfa[i],]
k = na.omit(unique(a$SYEAR[a$LFA==lfa[i]]))
#h = na.omit(h)
k = intersect(k,h$SYEAR)
for(j in k){
ll = which(a$LFA==lfa[i] & a$SYEAR==j)
a$WOS[ll] = floor(as.numeric(a$BOARD_DATE[ll]-min(h$START_DATE[h$SYEAR==j]))/7)+1
}
}
if(any(!is.finite(a$WOS))) {kl = which(!is.finite(a$WOS)); a$WOS[kl] = NA}
a = subset(a,WOS>0)
#per trap
ac = aggregate(cbind(Lobster, Cod, Cusk, Jonah, Legal, Berried,Empty,LegalWt,CALWT_G,CodWt,CuskWt,JonahWt,LobsterWt)~UID
+TRIP+X+Y+TRAP_ID+FISHSET_ID+COMAREA_ID+STRATUM_ID+BOARD_DATE+WOS+LFA+SYEAR, data=a,FUN=sum,na.rm=F)
CDa = merge(ac,bb,by='UID')
CDa$'P.9999-NA' = NULL
CDa$P=1
CDa$mn = month(CDa$BOARD_DATE)
gt = bycatch.db('targets',wd=wd)
CDa$target = CDa$Period = NA
CDa$GridGroup = 1
for(i in 1:nrow(CDa)){
m = CDa$mn[i]
k = subset(gt, LFA==strsplit(CDa$COMAREA_ID[i],'L')[[1]][2])
k = k[1,]
ll = ifelse(m >=k$Period1.Start & m<=k$Period1.End,'Period1',ifelse(m >=k$Period2.Start & m<=k$Period2.End,'Period2',ifelse(m >=k$Period3.Start & m<=k$Period3.End,'Period3','Period4')))
lll = as.numeric(strsplit(ll,'Period')[[1]][2])
CDa$target[i] <- as.numeric(k[,ll])
CDa$Period[i] = lll
# rm(k,m,ll,lll)
}
CDa$COMAREA_ID = NULL
names(CDa)[c(5:8,20)] =c('TRAPNO','SETNO','GRIDNUM','DATE_FISHED','CALWT')
CDa$DID = 'ASSOC'
CDa$ll = paste(CDa$X,CDa$Y,sep='ll')
CDa$Cluster = NA
cc = unique(CDa$TRIP)
for(i in 1:length(cc)){
k = which(CDa$TRIP == cc[i])
CDa$Cluster[k] = create_seq_from_column(CDa$ll[k])
}
CDa$ll <- NULL
saveRDS(CDa,file=file.path(wd,'data','GCIFA.all.species.reshape.rds'))
return(CDa)
}
return(readRDS(file=file.path(wd,'data','GCIFA.all.species.reshape.rds')))
}
}
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