inst/IP/StandardizedCPUE/SableWindGlorysTempGAMLFA29.r
In LobsterScience/bio.lobster: Lobster Stock Assessment Tools for DFO Maritimes
#wind data from Sable (source D Brickman 2020)
require(bio.lobster)
require(bio.utilities)
require(lubridate)
require(PBSmapping)
require(mgcv)
require(gratia)
dr = file.path(project.datadirectory('bio.lobster'),'data','wind')
a = read.table(file=file.path(dr, 'sable_daily.txt'),skip=13,header=T)
la()
#meterological direction is where it comes from to where it is going with N as 0, first line of data states direction 62.5 which is ENE wind meterologically
#(and thus -ve u and -ve v)
# this data is incorrectly coded for direction (i.e. west is 270 instead of 0 as is typical)-- correcting the direction and recalculating U and Vspeeds so need to use
# the wspd and dir (which are correct) to fix the Uspd and Vspd where Uspd is the xdirection and Vspd is the ydirection
a$mathDir = 270 - a$Dir
a$Uspd = a$Wspd * sin(a$mathDir*pi/180)
a$Vspd = a$Wspd * cos(a$mathDir*pi/180)
a$Date = as.Date(with(a, paste(Year, Mo, Dy, sep="-")), '%Y-%m-%d')
port_loc = lobster.db("port_location")
logs = lobster.db("process.logs")
vlog = lobster.db("process.vlog.redo")
logs = merge(logs,port_loc,by.y='PORT_CODE',by.x='COMMUNITY_CODE')
vlog$LICENCE_ID = paste(vlog$PORT_CODE, vlog$FCODE,sep="-")
tmp1 = subset(logs,select=c("DATE_FISHED","SYEAR","WEIGHT_KG","LFA.x","NUM_OF_TRAPS","GRID_NUM","COMMUNITY_CODE",'CENTLON','CENTLAT','LICENCE_ID'))
tmp1$type = 'mandatory'
tmp2 = subset(vlog,select=c("FDATE","SYEAR","W_KG","N_TRP","LFA","X","Y",'PORT_CODE',"LICENCE_ID"))
names(tmp2) = c("DATE_FISHED","SYEAR","WEIGHT_KG","NUM_OF_TRAPS","subarea","X","Y","COMMUNITY_CODE","LICENCE_ID")
tmp2$LFA.x = tmp2$subareas
tmp2 = assignArea(tmp2,coords=c("X","Y"))
tmp2 = subset(tmp2,select=c("DATE_FISHED","SYEAR","WEIGHT_KG","LFA","NUM_OF_TRAPS","LFA_GRID",'COMMUNITY_CODE','X',"Y","LICENCE_ID"))
tmp2$type = 'voluntary'
names(tmp2) = names(tmp1)
cpue.data = rbind(tmp2,tmp1)
#WIND
xx = merge(cpue.data,a[,c('Year','Date','Dir','Wspd','Uspd','Vspd')],by.x='DATE_FISHED',by.y='Date')
a$DL1 = a$Date+1
a = rename.df(a,c('Dir','Wspd','Uspd','Vspd'),c('Dir_L1','Wspd_L1','Uspd_L1','Vspd_L1'))
xx = merge(xx,a[,c('DL1','Dir_L1','Wspd_L1','Uspd_L1','Vspd_L1')],by.x='DATE_FISHED',by.y='DL1')
a$DL2 = a$Date+2
a = rename.df(a,c('Dir_L1','Wspd_L1','Uspd_L1','Vspd_L1'),c('Dir_L2','Wspd_L2','Uspd_L2','Vspd_L2'))
xx = merge(xx,a[,c('DL2','Dir_L2','Wspd_L2','Uspd_L2','Vspd_L2')],by.x='DATE_FISHED',by.y='DL2')
a$DL3 = a$Date+3
a = rename.df(a,c('Dir_L2','Wspd_L2','Uspd_L2','Vspd_L2'),c('Dir_L3','Wspd_L3','Uspd_L3','Vspd_L3'))
xx = merge(xx,a[,c('DL3','Dir_L3','Wspd_L3','Uspd_L3','Vspd_L3')],by.x='DATE_FISHED',by.y='DL3')
xx = rename.df(xx,c('CENTLON','CENTLAT'),c('X','Y'))
###
g = subset(xx,LFA.x ==29)
x = aggregate(cbind(WEIGHT_KG,NUM_OF_TRAPS)~DATE_FISHED+COMMUNITY_CODE+Uspd+Vspd+Year+Wspd+Dir+
Uspd_L1+Vspd_L1+Wspd_L1+Dir_L1+
Uspd_L2+Vspd_L2+Wspd_L2+Dir_L2+
Uspd_L3+Vspd_L3+Wspd_L3+Dir_L3
,data=g,FUN=sum)
x$CPUE = x$WEIGHT_KG / x$NUM_OF_TRAPS
x=x[order(x$DATE_FISHED),]
with(subset(x,Year==1985),plot(DATE_FISHED,CPUE,type='l'))
x$lWt = log(x$WEIGHT_KG)
x$lTr = log(x$NUM_OF_TRAPS)
x$Doy = yday(x$DATE_FISHED)
g$lWt = log(g$WEIGHT_KG)
g$lTr = log(g$NUM_OF_TRAPS)
g$Doy = yday(g$DATE_FISHED)
#does Wind affect effort on a given day?
## offset to max traps fished within season so that total reporting effort is captured
mT = aggregate(NUM_OF_TRAPS~Year+COMMUNITY_CODE,data=g, FUN=max)
names(mT)[2] = 'maxTraps'
x = merge(x,mT)
x$propMaxTraps = x$NUM_OF_TRAPS / x$maxTraps
#converting u and v to direction
uvToDir = function(u,v){
180+180/pi*atan2(v,u)
}
uvToSpeed = function(u,v){
sqrt(u^2+v^2)
}
#Add in Glorys Temperature Data
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
#Get the unique EIDS from GLORYS data
L = subset(LFAs,PID==29)
fd = file.path(project.datadirectory('bio.lobster'),'data','GLORYS','SummaryFiles')
gL = dir(fd,full.names=T)
gL = gL[grep('Isobath',gL)]
EIDs = readRDS(gL[1])
EIDs = EIDs[!duplicated(EIDs[,c('X','Y','EID')]),c('X','Y','EID')]
I = findPolys(EIDs,L)$EID
g = subset(xx,LFA.x==29)
#by LFA
out = list()
for(i in 1:length(gL)){
jk = readRDS(gL[i])
jk = subset(jk,EID %in% I & month(date) %in% 4:7 )
out[[i]] = jk
}
out = do.call(rbind,out)
aGL = aggregate(cbind(vo_surface,vo_bottom,thetao,uo_surface,uo_bottom,bottomT,zos)~date, data=out,FUN=median)
aGL$DATE = as.Date(aGL$date)
oo = merge(g,aGL, by.x='DATE_FISHED',by.y='DATE')
oo$lWt = log(oo$WEIGHT_KG)
oo$lTr = log(oo$NUM_OF_TRAPS)
oo$COMMUNITY_CODEf = as.factor(oo$COMMUNITY_CODE)
oo$Doy = yday(oo$DATE_FISHED)
oo$SoakDays = NA
iu = unique(oo$LICENCE_ID)
outt = list()
mm=0
for(i in 1:length(iu)){
u = subset(oo,LICENCE_ID ==iu[i])
ge = unique(u$SYEAR)
for(j in 1:length(ge)){
mm=mm+1
vc = subset(u,SYEAR==ge[j])
if(nrow(vc)>1){
vc$SoakDays = c(1,vc$DATE_FISHED[2:nrow(vc)] - vc$DATE_FISHED[1:(nrow(vc)-1)] )
outt[[mm]] = vc
}
}
}
outall = do.call(rbind,outt)
outall = subset(outall,SoakDays<10)
outall = subset(outall, is.finite(lWt))
###predators
p = bio.groundfish::load.groundfish.environment("BIOsurvey")
require(bio.survey)
fp1 = file.path(project.datadirectory('bio.lobster'),"analysis","LFA34-38")
p=list()
#loadfunctions('bio.groundfish')
p$strat=443:457
p$series =c('summer')# p$series =c('4vswcod');p$series =c('georges')
p$years.to.estimate = c(1970:2017)
p$functional.groups = T
yy = list()
yy[['LobPred']] = c(10,11,12,13,40,50,200,201,203,204,300)
p$species = 'LobPred'
p$yy = yy
p$vessel.correction = T
p$vessel.correction.fixed = 1.2
p$length.based = F
p$by.sex = p$sex.based = F
p$alpha = 0.05
p$strata.efficiencies=F
#out = groundfish.analysis(DS='ab.redo',p=p)
#MPA functional groups
p$functional.groups = T
p$bootstrapped.ci=F
p$strata.files.return=F
p$clusters = c( rep( "localhost", 7) )
p = make.list(list(v=p$species, yrs=p$years.to.estimate),Y=p)
p$runs = p$runs[order(p$runs$v),]
#parallel.run(groundfish.analysis,DS='stratified.estimates.redo',p=p,specific.allocation.to.clusters=T) #silly error arisingexit
aout= groundfish.analysis(DS='stratified.estimates.redo',out.dir = 'bio.lobster',p=p)
aout = subset(aout, select=c('yr','w.yst','n.yst'))
aout$SYEAR7 = aout$yr+7
aout$LBP = log(aout$w.yst)
outall = merge(outall, aout, by.x='Year', by.y='SYEAR7')
#best model Feb 16
outs = bam(lWt~ as.factor(Year)+
s(Uspd_L1,Vspd_L1)+
s(bottomT)+
s(Doy,bottomT)+
COMMUNITY_CODEf +
(SoakDays) +
# (LBP) + predators didnt really add anything
offset(lTr),data=subset(outall,month(DATE_FISHED)>4), method='REML')
#outall$yr = outall$n.yst = outall$w.yst = outall$LBP = NULL
require(gratia)
draw(outs, parametric=F)
savePlot('~/dellshared/lfa29CPUEFactors.png')
newD = data.frame(Year=as.factor(1993:2018), Uspd_L1=0, Vspd_L1=0, bottomT = 3.9, Doy = 112, COMMUNITY_CODEf = '10902', SoakDays=2, lTr = log(1), LBP=4)
predict(outs, newdata=newD)
a_lp_matrix = predict(object = outs, newD,
type = "lpmatrix")
n_sims =1000
a_coef_mean = coef(outs)
a_vcov = vcov(outs)
a_par_coef_posterior = rmvn(n = n_sims,
mu = a_coef_mean,
V = a_vcov)
ilink = family(outs)$linkinv
preds = ilink(a_lp_matrix %*% t(a_par_coef_posterior))
apreds = exp(as.data.frame(preds))
ag = apply(apreds[,1:1000],1,quantile,c(.025,0.5,.975))
par(mfrow = c(2,1), mar = c(1, 4, 1, 1), omi = c(0.2, 0.3, 0, 0.2))
#par(mfrow=c(1,2))
plot(1993:2018, ag[2,],type='b',pch=16,xlab='Year', ylab='Standardized CPUE',ylim=c(0,4.1), xlim=c(1986,2020))
arrows(1993:2018,y0=ag[3,], y1=ag[1,], length=0)
yrs =1993:2018
prs = seq( from=0.025, to=0.975, length.out=100)
Bq = apply(apreds[1:17,1:1000], 1, quantile, probs=prs, na.rm=T )
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
for ( j in 1:length(prs) ) {
abline( h=median(Bq[j,])*.4, lwd=4, col=cols2[j] )
}
abline( h=median(Bq[50,])*.4, lwd=1, col='red' )
lines(1993:2018, ag[2,],type='b',pch=16)
arrows(1993:2018,y0=ag[3,], y1=ag[1,], length=0)
cD = aggregate(cbind(WEIGHT_KG,NUM_OF_TRAPS)~SYEAR, data=subset(cpue.data, LFA.x==29),FUN=sum)
cD$CPUE = cD$WEIGHT_KG / cD$NUM_OF_TRAPS
#x11()
plot(cD$CPUE~cD$SYEAR,type='b',xlab='Year',pch=16,ylab='Raw CPUE')
abline(h=median(cD$CPUE[1:24])*.4,lwd=2,col='red')
savePlot('dellshared/LFA29CPUE.png')
##MLS 81 1997, 1998 82.5, 1999 84
cl=70:100
g = cbind(cl,1/(1+(exp(14.173+(-.1727*cl)))))
#from hcrs inc mls
tt = data.frame(cbind(c(1,3.5,6), c(24,43,76)))
names(tt) = c('Size','Eggs')
gg = lm(Eggs~Size+0,data=tt)
predict(gg,newdata=data.frame(Size=c(-3,-1.5,0,1,3.5,6)))
#20% increase in egg prod with each size increase
plot(1994:2018,(ag[2,2:ncol(ag)] - ag[2,1:(ncol(ag)-1)])/ag[2,1:(ncol(ag)-1)])
abline(v=c(1998,1999,2005,2006))
pred = aggregate(LBP~Year,data=outall, FUN=mean)
temp = aggregate(bottomT~Year,data=outall, FUN=mean)
cor.test((pred[,2]),(ag[2,]))
cor.test((temp[1:19,2]),(ag[2,8:ncol(ag)]))
plot((pred[,2]),(ag[2,]))
plot((temp[1:19,2]),(ag[2,8:ncol(ag)]))
plot(1993:2018, ag[2,],type='b',pch=16,xlab='Year', ylab='Standardized CPUE',ylim=c(0,4.1), xlim=c(1986,2020))
arrows(1993:2018,y0=ag[3,], y1=ag[1,], length=0)
abline(v=c(1998,1999,2005,2006),col=c('blue','blue','red','red'))
savePlot('dellshared/LFA29MLSinc.png')
#offset to max traps fished within season so that total reporting effort is captured
ooo = aggregate(NUM_OF_TRAPS~Year+COMMUNITY_CODE+DATE_FISHED+Doy+Uspd+Uspd_L1+Uspd_L2+Uspd_L3+Vspd+Vspd_L1+Vspd_L2+Vspd_L3,data=outall, FUN=sum)
mT = aggregate(NUM_OF_TRAPS~Year+COMMUNITY_CODE,data=ooo, FUN=max)
names(mT)[3] = 'maxTraps'
oo = merge(ooo,mT)
oo$propMaxTraps = oo$NUM_OF_TRAPS / oo$maxTraps
oo$COMMUNITY_CODEf = as.factor(oo$COMMUNITY_CODE)
outsEffort = gam(propMaxTraps~ s(Year)+
s(Doy)+
s(Uspd,Vspd, by=COMMUNITY_CODEf)
,data=subset(oo,Year>1991), family = betar(link='logit'), method='REML')
draw(outsEffort)
savePlot('~/tmp/lfa29Effort.png')
outT = gam(bottomT~ s(Year)+
s(Uspd_L1,Vspd_L1)+s(Doy),
data=outall, method='REML')
draw(outT)
savePlot('~/tmp/lfa29bottomT.png')
outW = gam(Uspd~ s(Year)+
s(Doy),
data=outall, method='REML')
draw(outW)
savePlot('~/tmp/lfa29WU.png')
outV = gam(Vspd~ s(Year)+
s(Doy),
data=outall, method='REML')
draw(outV)
savePlot('~/tmp/lfa29WV.png')
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#wind data from Sable (source D Brickman 2020)
require(bio.lobster)
require(bio.utilities)
require(lubridate)
require(PBSmapping)
require(mgcv)
require(gratia)
dr = file.path(project.datadirectory('bio.lobster'),'data','wind')
a = read.table(file=file.path(dr, 'sable_daily.txt'),skip=13,header=T)
la()
#meterological direction is where it comes from to where it is going with N as 0, first line of data states direction 62.5 which is ENE wind meterologically
#(and thus -ve u and -ve v)
# this data is incorrectly coded for direction (i.e. west is 270 instead of 0 as is typical)-- correcting the direction and recalculating U and Vspeeds so need to use
# the wspd and dir (which are correct) to fix the Uspd and Vspd where Uspd is the xdirection and Vspd is the ydirection
a$mathDir = 270 - a$Dir
a$Uspd = a$Wspd * sin(a$mathDir*pi/180)
a$Vspd = a$Wspd * cos(a$mathDir*pi/180)
a$Date = as.Date(with(a, paste(Year, Mo, Dy, sep="-")), '%Y-%m-%d')
port_loc = lobster.db("port_location")
logs = lobster.db("process.logs")
vlog = lobster.db("process.vlog.redo")
logs = merge(logs,port_loc,by.y='PORT_CODE',by.x='COMMUNITY_CODE')
vlog$LICENCE_ID = paste(vlog$PORT_CODE, vlog$FCODE,sep="-")
tmp1 = subset(logs,select=c("DATE_FISHED","SYEAR","WEIGHT_KG","LFA.x","NUM_OF_TRAPS","GRID_NUM","COMMUNITY_CODE",'CENTLON','CENTLAT','LICENCE_ID'))
tmp1$type = 'mandatory'
tmp2 = subset(vlog,select=c("FDATE","SYEAR","W_KG","N_TRP","LFA","X","Y",'PORT_CODE',"LICENCE_ID"))
names(tmp2) = c("DATE_FISHED","SYEAR","WEIGHT_KG","NUM_OF_TRAPS","subarea","X","Y","COMMUNITY_CODE","LICENCE_ID")
tmp2$LFA.x = tmp2$subareas
tmp2 = assignArea(tmp2,coords=c("X","Y"))
tmp2 = subset(tmp2,select=c("DATE_FISHED","SYEAR","WEIGHT_KG","LFA","NUM_OF_TRAPS","LFA_GRID",'COMMUNITY_CODE','X',"Y","LICENCE_ID"))
tmp2$type = 'voluntary'
names(tmp2) = names(tmp1)
cpue.data = rbind(tmp2,tmp1)
#WIND
xx = merge(cpue.data,a[,c('Year','Date','Dir','Wspd','Uspd','Vspd')],by.x='DATE_FISHED',by.y='Date')
a$DL1 = a$Date+1
a = rename.df(a,c('Dir','Wspd','Uspd','Vspd'),c('Dir_L1','Wspd_L1','Uspd_L1','Vspd_L1'))
xx = merge(xx,a[,c('DL1','Dir_L1','Wspd_L1','Uspd_L1','Vspd_L1')],by.x='DATE_FISHED',by.y='DL1')
a$DL2 = a$Date+2
a = rename.df(a,c('Dir_L1','Wspd_L1','Uspd_L1','Vspd_L1'),c('Dir_L2','Wspd_L2','Uspd_L2','Vspd_L2'))
xx = merge(xx,a[,c('DL2','Dir_L2','Wspd_L2','Uspd_L2','Vspd_L2')],by.x='DATE_FISHED',by.y='DL2')
a$DL3 = a$Date+3
a = rename.df(a,c('Dir_L2','Wspd_L2','Uspd_L2','Vspd_L2'),c('Dir_L3','Wspd_L3','Uspd_L3','Vspd_L3'))
xx = merge(xx,a[,c('DL3','Dir_L3','Wspd_L3','Uspd_L3','Vspd_L3')],by.x='DATE_FISHED',by.y='DL3')
xx = rename.df(xx,c('CENTLON','CENTLAT'),c('X','Y'))
###
g = subset(xx,LFA.x ==29)
x = aggregate(cbind(WEIGHT_KG,NUM_OF_TRAPS)~DATE_FISHED+COMMUNITY_CODE+Uspd+Vspd+Year+Wspd+Dir+
Uspd_L1+Vspd_L1+Wspd_L1+Dir_L1+
Uspd_L2+Vspd_L2+Wspd_L2+Dir_L2+
Uspd_L3+Vspd_L3+Wspd_L3+Dir_L3
,data=g,FUN=sum)
x$CPUE = x$WEIGHT_KG / x$NUM_OF_TRAPS
x=x[order(x$DATE_FISHED),]
with(subset(x,Year==1985),plot(DATE_FISHED,CPUE,type='l'))
x$lWt = log(x$WEIGHT_KG)
x$lTr = log(x$NUM_OF_TRAPS)
x$Doy = yday(x$DATE_FISHED)
g$lWt = log(g$WEIGHT_KG)
g$lTr = log(g$NUM_OF_TRAPS)
g$Doy = yday(g$DATE_FISHED)
#does Wind affect effort on a given day?
## offset to max traps fished within season so that total reporting effort is captured
mT = aggregate(NUM_OF_TRAPS~Year+COMMUNITY_CODE,data=g, FUN=max)
names(mT)[2] = 'maxTraps'
x = merge(x,mT)
x$propMaxTraps = x$NUM_OF_TRAPS / x$maxTraps
#converting u and v to direction
uvToDir = function(u,v){
180+180/pi*atan2(v,u)
}
uvToSpeed = function(u,v){
sqrt(u^2+v^2)
}
#Add in Glorys Temperature Data
LFAs<-read.csv(file.path( project.datadirectory("bio.lobster"), "data","maps","LFAPolys.csv"))
#Get the unique EIDS from GLORYS data
L = subset(LFAs,PID==29)
fd = file.path(project.datadirectory('bio.lobster'),'data','GLORYS','SummaryFiles')
gL = dir(fd,full.names=T)
gL = gL[grep('Isobath',gL)]
EIDs = readRDS(gL[1])
EIDs = EIDs[!duplicated(EIDs[,c('X','Y','EID')]),c('X','Y','EID')]
I = findPolys(EIDs,L)$EID
g = subset(xx,LFA.x==29)
#by LFA
out = list()
for(i in 1:length(gL)){
jk = readRDS(gL[i])
jk = subset(jk,EID %in% I & month(date) %in% 4:7 )
out[[i]] = jk
}
out = do.call(rbind,out)
aGL = aggregate(cbind(vo_surface,vo_bottom,thetao,uo_surface,uo_bottom,bottomT,zos)~date, data=out,FUN=median)
aGL$DATE = as.Date(aGL$date)
oo = merge(g,aGL, by.x='DATE_FISHED',by.y='DATE')
oo$lWt = log(oo$WEIGHT_KG)
oo$lTr = log(oo$NUM_OF_TRAPS)
oo$COMMUNITY_CODEf = as.factor(oo$COMMUNITY_CODE)
oo$Doy = yday(oo$DATE_FISHED)
oo$SoakDays = NA
iu = unique(oo$LICENCE_ID)
outt = list()
mm=0
for(i in 1:length(iu)){
u = subset(oo,LICENCE_ID ==iu[i])
ge = unique(u$SYEAR)
for(j in 1:length(ge)){
mm=mm+1
vc = subset(u,SYEAR==ge[j])
if(nrow(vc)>1){
vc$SoakDays = c(1,vc$DATE_FISHED[2:nrow(vc)] - vc$DATE_FISHED[1:(nrow(vc)-1)] )
outt[[mm]] = vc
}
}
}
outall = do.call(rbind,outt)
outall = subset(outall,SoakDays<10)
outall = subset(outall, is.finite(lWt))
###predators
p = bio.groundfish::load.groundfish.environment("BIOsurvey")
require(bio.survey)
fp1 = file.path(project.datadirectory('bio.lobster'),"analysis","LFA34-38")
p=list()
#loadfunctions('bio.groundfish')
p$strat=443:457
p$series =c('summer')# p$series =c('4vswcod');p$series =c('georges')
p$years.to.estimate = c(1970:2017)
p$functional.groups = T
yy = list()
yy[['LobPred']] = c(10,11,12,13,40,50,200,201,203,204,300)
p$species = 'LobPred'
p$yy = yy
p$vessel.correction = T
p$vessel.correction.fixed = 1.2
p$length.based = F
p$by.sex = p$sex.based = F
p$alpha = 0.05
p$strata.efficiencies=F
#out = groundfish.analysis(DS='ab.redo',p=p)
#MPA functional groups
p$functional.groups = T
p$bootstrapped.ci=F
p$strata.files.return=F
p$clusters = c( rep( "localhost", 7) )
p = make.list(list(v=p$species, yrs=p$years.to.estimate),Y=p)
p$runs = p$runs[order(p$runs$v),]
#parallel.run(groundfish.analysis,DS='stratified.estimates.redo',p=p,specific.allocation.to.clusters=T) #silly error arisingexit
aout= groundfish.analysis(DS='stratified.estimates.redo',out.dir = 'bio.lobster',p=p)
aout = subset(aout, select=c('yr','w.yst','n.yst'))
aout$SYEAR7 = aout$yr+7
aout$LBP = log(aout$w.yst)
outall = merge(outall, aout, by.x='Year', by.y='SYEAR7')
#best model Feb 16
outs = bam(lWt~ as.factor(Year)+
s(Uspd_L1,Vspd_L1)+
s(bottomT)+
s(Doy,bottomT)+
COMMUNITY_CODEf +
(SoakDays) +
# (LBP) + predators didnt really add anything
offset(lTr),data=subset(outall,month(DATE_FISHED)>4), method='REML')
#outall$yr = outall$n.yst = outall$w.yst = outall$LBP = NULL
require(gratia)
draw(outs, parametric=F)
savePlot('~/dellshared/lfa29CPUEFactors.png')
newD = data.frame(Year=as.factor(1993:2018), Uspd_L1=0, Vspd_L1=0, bottomT = 3.9, Doy = 112, COMMUNITY_CODEf = '10902', SoakDays=2, lTr = log(1), LBP=4)
predict(outs, newdata=newD)
a_lp_matrix = predict(object = outs, newD,
type = "lpmatrix")
n_sims =1000
a_coef_mean = coef(outs)
a_vcov = vcov(outs)
a_par_coef_posterior = rmvn(n = n_sims,
mu = a_coef_mean,
V = a_vcov)
ilink = family(outs)$linkinv
preds = ilink(a_lp_matrix %*% t(a_par_coef_posterior))
apreds = exp(as.data.frame(preds))
ag = apply(apreds[,1:1000],1,quantile,c(.025,0.5,.975))
par(mfrow = c(2,1), mar = c(1, 4, 1, 1), omi = c(0.2, 0.3, 0, 0.2))
#par(mfrow=c(1,2))
plot(1993:2018, ag[2,],type='b',pch=16,xlab='Year', ylab='Standardized CPUE',ylim=c(0,4.1), xlim=c(1986,2020))
arrows(1993:2018,y0=ag[3,], y1=ag[1,], length=0)
yrs =1993:2018
prs = seq( from=0.025, to=0.975, length.out=100)
Bq = apply(apreds[1:17,1:1000], 1, quantile, probs=prs, na.rm=T )
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
for ( j in 1:length(prs) ) {
abline( h=median(Bq[j,])*.4, lwd=4, col=cols2[j] )
}
abline( h=median(Bq[50,])*.4, lwd=1, col='red' )
lines(1993:2018, ag[2,],type='b',pch=16)
arrows(1993:2018,y0=ag[3,], y1=ag[1,], length=0)
cD = aggregate(cbind(WEIGHT_KG,NUM_OF_TRAPS)~SYEAR, data=subset(cpue.data, LFA.x==29),FUN=sum)
cD$CPUE = cD$WEIGHT_KG / cD$NUM_OF_TRAPS
#x11()
plot(cD$CPUE~cD$SYEAR,type='b',xlab='Year',pch=16,ylab='Raw CPUE')
abline(h=median(cD$CPUE[1:24])*.4,lwd=2,col='red')
savePlot('dellshared/LFA29CPUE.png')
##MLS 81 1997, 1998 82.5, 1999 84
cl=70:100
g = cbind(cl,1/(1+(exp(14.173+(-.1727*cl)))))
#from hcrs inc mls
tt = data.frame(cbind(c(1,3.5,6), c(24,43,76)))
names(tt) = c('Size','Eggs')
gg = lm(Eggs~Size+0,data=tt)
predict(gg,newdata=data.frame(Size=c(-3,-1.5,0,1,3.5,6)))
#20% increase in egg prod with each size increase
plot(1994:2018,(ag[2,2:ncol(ag)] - ag[2,1:(ncol(ag)-1)])/ag[2,1:(ncol(ag)-1)])
abline(v=c(1998,1999,2005,2006))
pred = aggregate(LBP~Year,data=outall, FUN=mean)
temp = aggregate(bottomT~Year,data=outall, FUN=mean)
cor.test((pred[,2]),(ag[2,]))
cor.test((temp[1:19,2]),(ag[2,8:ncol(ag)]))
plot((pred[,2]),(ag[2,]))
plot((temp[1:19,2]),(ag[2,8:ncol(ag)]))
plot(1993:2018, ag[2,],type='b',pch=16,xlab='Year', ylab='Standardized CPUE',ylim=c(0,4.1), xlim=c(1986,2020))
arrows(1993:2018,y0=ag[3,], y1=ag[1,], length=0)
abline(v=c(1998,1999,2005,2006),col=c('blue','blue','red','red'))
savePlot('dellshared/LFA29MLSinc.png')
#offset to max traps fished within season so that total reporting effort is captured
ooo = aggregate(NUM_OF_TRAPS~Year+COMMUNITY_CODE+DATE_FISHED+Doy+Uspd+Uspd_L1+Uspd_L2+Uspd_L3+Vspd+Vspd_L1+Vspd_L2+Vspd_L3,data=outall, FUN=sum)
mT = aggregate(NUM_OF_TRAPS~Year+COMMUNITY_CODE,data=ooo, FUN=max)
names(mT)[3] = 'maxTraps'
oo = merge(ooo,mT)
oo$propMaxTraps = oo$NUM_OF_TRAPS / oo$maxTraps
oo$COMMUNITY_CODEf = as.factor(oo$COMMUNITY_CODE)
outsEffort = gam(propMaxTraps~ s(Year)+
s(Doy)+
s(Uspd,Vspd, by=COMMUNITY_CODEf)
,data=subset(oo,Year>1991), family = betar(link='logit'), method='REML')
draw(outsEffort)
savePlot('~/tmp/lfa29Effort.png')
outT = gam(bottomT~ s(Year)+
s(Uspd_L1,Vspd_L1)+s(Doy),
data=outall, method='REML')
draw(outT)
savePlot('~/tmp/lfa29bottomT.png')
outW = gam(Uspd~ s(Year)+
s(Doy),
data=outall, method='REML')
draw(outW)
savePlot('~/tmp/lfa29WU.png')
outV = gam(Vspd~ s(Year)+
s(Doy),
data=outall, method='REML')
draw(outV)
savePlot('~/tmp/lfa29WV.png')
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