R/fishery_model.r
In jae0/snowcrab: Snow crab assessment suite for aegis* and associated projects.
Defines functions
fishery_model
fishery_model = function( p=NULL, DS="plot",
plotresults=TRUE, tag="default", areas=c("cfanorth", "cfasouth", "cfa4x"),
vname="", type="density", res=NULL, fit=NULL, fn=NULL, aulabels=c("N-ENS","S-ENS","4X"), save.plot=TRUE, ... ) {
# sb = bio.snowcrab::fishery_model( DS="data_aggregated_timeseries", p=p )
if (tag=="default") {
if (!is.null(p)) if (exists("tag", p)) tag = p$tag
}
if (DS=="logistic_parameters") {
p = parameters_add(p, list(...)) # add passed args to parameter list, priority to args
out = list()
if (!exists("method", out)) out$method = "stan" # "jags", etc.
if (!exists("carstm_model_label", p)) p$carstm_model_label = "default"
if (!exists("outdir", out)) out$outdir = file.path( p$modeldir, p$carstm_model_label, "fishery_model_results", tag )
if (!exists("fnres", out)) out$fnres = file.path( out$outdir, paste( "logistics_model_results", p$year.assessment, out$method, tag, "RDS", sep=".") )
if (!exists("fnfit", out)) out$fnfit = file.path( out$outdir, paste( "logistics_model_fit", p$year.assessment, out$method, tag, "RDS", sep=".") )
dir.create( out$outdir, showWarnings = FALSE, recursive = TRUE )
message( "Results will be saved to:", out$outdir)
# observations
if (!exists("fmdata", out)) {
out$fmdata = fishery_model( DS="data_aggregated_timeseries", p=p )
oo = apply( out$fmdata$IOA, 2, range, na.rm=TRUE )
for (i in 1:ncol(oo)) {
out$fmdata$IOA[,i] = (out$fmdata$IOA[,i] - oo[1,i] )/ diff(oo[,i]) # force median 0.5 with most data inside 0,1
}
# out$fmdata$IOA_min = apply( out$fmdata$IOA, 2, min, na.rm=TRUE )
}
if (!exists("er", out$fmdata)) out$fmdata$er = 0.2 # target exploitation rate
if (!exists("U", out$fmdata)) out$fmdata$U = ncol( out$fmdata$IOA) # number of regions
if (!exists("N", out$fmdata)) out$fmdata$N = nrow( out$fmdata$IOA) # no years with data
if (!exists("M", out$fmdata)) out$fmdata$M = 3 # no years for projections
if (!exists("ty", out$fmdata)) out$fmdata$ty = which(p$yrs == 2004) # index of the transition year (2004) between spring and fall surveys
if (!exists("cfa4x", out$fmdata)) out$fmdata$cfa4x = 3 # column index of cfa4x
if (!exists("eps", out$fmdata)) out$fmdata$eps = 1e-9 # small non-zero number
out$fmdata$missing = ifelse( is.finite(out$fmdata$IOA), 0, 1)
out$fmdata$missing_n = colSums(out$fmdata$missing)
out$fmdata$missing_ntot = sum(out$fmdata$missing_n)
# this must be done last
out$fmdata$IOA[ which(!is.finite(out$fmdata$IOA)) ] = 0 # reset NAs to 0 as stan does not take NAs
out$fmdata$CAT[ which(!is.finite(out$fmdata$CAT)) ] = out$fmdata$eps # remove NA's
# priors
if (!exists("Kmu", out$fmdata)) out$fmdata$Kmu = c( 5.5, 65.0, 2.0 ) ## based upon prior historical analyses (when stmv and kriging were attempted)
if (!exists("rmu", out$fmdata)) out$fmdata$rmu = c( 1.0, 1.0, 1.0 ) ## biological constraint
if (!exists("qmu", out$fmdata)) out$fmdata$qmu = c( 1.0, 1.0, 1.0 ) ## based upon video observations q is close to 1 .. but sampling locations can of course cause bias (avoiding rocks and bedrock)
if (!exists("Ksd", out$fmdata)) out$fmdata$Ksd = c( 0.25, 0.25, 0.25 ) * out$fmdata$Kmu
if (!exists("rsd", out$fmdata)) out$fmdata$rsd = c( 0.1, 0.1, 0.1 ) * out$fmdata$rmu # smaller SD's to encourage solutions closer to prior means
if (!exists("qsd", out$fmdata)) out$fmdata$qsd = c( 0.1, 0.1, 0.1 ) * out$fmdata$qmu
return(out)
}
if (DS=="stan_surplus_production_2019_model") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.0> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=eps, upper=1.0> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps, upper=1.0> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps, upper=1.25> [M+N,U] bm; // permit overshoot bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ beta( 8, 2 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ beta( 1, 100000 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] / K[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] /K[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3]/K[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j]/K[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3]/ K[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] / K[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( fmax(fmin(b0,0.99),eps), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_variation1_wider_qc_uniform") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ uniform( -0.5, 0.5 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 2 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_uniform") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=0, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.25> [U] bosd; // observation error
vector <lower=eps, upper=0.25> [U] bpsd; // process error
// vector <lower=eps, upper=0.25> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coefficient
qc ~ uniform( 0, 1 ) ; // i.e., Y:b offset constant ;
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_variation1_wider_qc_normal") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ normal( 0, 0.25 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_variation1_wider_qc_normal_0") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ normal( 0, 0.000001 ) ; // i.e.,force to be 0
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_beta") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=0, upper=0.5> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ beta( 1, 2 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_cauchy") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=0, upper=1.0> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ cauchy( 0, 0.1 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_cauchy_wider") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1.0, upper=1.0> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ cauchy( 0, 0.1 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_catch_observation") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
MN = M+N ;
N1 = N+1;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=eps, upper=0.5> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] catsd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
matrix <lower=eps> [N,U] cat; // estimated catch
vector <lower=eps, upper=0.5> [U] catQ; // multiplicative factor .. fraction misreported
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
catsd ~ cauchy( 0, 0.1 ) ;
catQ ~ beta( 1, 5 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ beta( 1, 5 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// catch observation model -- cat = CAT/K *catQ
// spring surveys
for (j in 1:2) {
( CAT[1,j]/K[j] ) * (1.0 + catQ[j]) ~ normal( cat[1,j], catsd[j] );
for (i in 2:(ty-1) ){
( CAT[i-1,j]/K[j] ) * (1.0 + catQ[j]) ~ normal( cat[i-1,j], catsd[j] );
}
}
for (i in 1:(ty-1) ){
( CAT[i,3]/K[3] ) * (1.0 + catQ[3]) ~ normal( cat[i,3], catsd[3] );
}
// transition year (ty)
for (j in 1:2) {
( CAT[ty-1,j] + CAT[ty,j] ) / ( 2.0* K[j] ) * (1.0 + catQ[j]) ~ normal( cat[ty,j], catsd[j] );
}
( CAT[ty,3] / K[3] ) * (1.0 + catQ[3]) ~ normal( cat[ty,3], catsd[3] );
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( CAT[i,j]/K[j] ) * (1.0 + catQ[j]) ~ normal( cat[i,j], catsd[j] );
}
}
// biomass observation model
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - cat[1,j], eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - cat[i-1,j], eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - cat[i,3], eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:3) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - cat[ty,j], eps) ) ) , bosd[j] ) ;
}
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - cat[i,j], eps) ) ), bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - cat[i-1,j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
}
"
)
}
if (DS=="stan_surplus_production_2020") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] qsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
MN = M+N ;
N1 = N+1;
}
parameters {
vector <lower=eps>[U] K;
vector <lower=eps>[U] r;
vector <lower=eps>[U] q;
vector <lower=eps>[U] qs;
vector <lower=eps,upper=(1-eps)>[U] bosd; // observation error
vector <lower=eps,upper=(1-eps)>[U] bpsd; // process error
vector <lower=eps,upper=(1-eps)>[U] b0;
vector <lower=eps>[missing_ntot] IOAmissing;
matrix <lower=eps>[M+N,U] bm;
}
transformed parameters {
matrix[N,U] Y; // index of abundance
matrix[N,U] Ymu; // collator used to force positive values for lognormal
matrix[MN,U] bmmu; // collator used to force positive values for lognormal
matrix[MN,U] rem; // observed catch
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j];
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
// -------------------
// removals (catch) observation model, standardized to K (assuming no errors in observation of catch!)
for (j in 1:U) {
rem[1:N,j] = CAT[1:N,j]/K[j] ;
rem[(N+1):MN,j] = er*bm[ N:(MN-1),j] ; // forecasts
}
// -------------------
// observation model calcs and contraints:
// Ymu = 'surveyed/observed' residual biomass at time of survey (Bsurveyed)
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
for (j in 1:2) {
Ymu[1,j] = qs[j] * bm[1,j] - rem[1,j] ; // starting year approximation
Ymu[2:(ty-1),j] = qs[j] * bm[2:(ty-1),j] - rem[1:(ty-2),j] ; //spring surveys
Ymu[ty,j] = q[j] * bm[ty,j] - (rem[(ty-1),j] + rem[ty,j] )/2.0 ; // transition year .. approximation
Ymu[(ty+1):N,j] = q[j] * bm[(ty+1):N,j] - rem[(ty+1):N,j] ; // fall surveys
}
{
int k;
k=3;
Ymu[1,k] = q[k] * bm[1,k] - rem[1,k] ; // starting year approximation ymu[1991] = bm[1991]-rem[1991]
Ymu[2:(ty-1),k] = q[k] * bm[2:(ty-1),k] - rem[2:(ty-1),k];
Ymu[ty:N,k] = q[k] * bm[ty:N,k] - rem[ty:N,k];
}
for (j in 1:U) {
for (i in 1:N) {
Ymu[i,j] = K[j] * fmax( Ymu[i,j], eps); // force positive value
}
}
// -------------------
// process model calcs and constraints
for (j in 1:U) {
bmmu[1,j] = b0[j] ; // biomass at first year
for (i in 2:MN) {
bmmu[i,j] = bm[i-1,j] * ( 1.0 + r[j]*(1-bm[i-1,j]) ) - rem[i-1,j] ;
}
}
for (j in 1:U) {
for (i in 1:MN) {
bmmu[i,j] = fmax(bmmu[i,j], eps); // force positive value
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
q ~ normal( qmu, qsd ) ;
qs ~ normal( qmu, qsd ) ;
b0 ~ beta( 8, 2 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
// -------------------
// biomass observation model
for (j in 1:U) {
log(Y[1:N,j]) ~ normal( log(Ymu[1:N,j]), bosd[j] ) ; // stan thinks Y is being transformed due to attempt to impute missing values .. ignore
}
// -------------------
// biomass process model
for (j in 1:U) {
log(bm[1:MN,j]) ~ normal( log(bmmu[1:MN,j]), bpsd[j] ) ;
}
// could have used lognormal but this parameterization is 10X faster and more stable
target += - log(fabs(Y)); // required due to log transf above
target += - log(fabs(bm));
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
matrix[M,U] TAC;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:3) {
for (i in 1:N) {
F[i,j] = 1.0 - rem[i,j] / bm[i,j] ;
}
}
for (j in 1:U) {
for (i in N1:MN) {
F[i,j] = 1.0 - er * bm[i-1,j] / bm[i,j] ;
}
for (i in 1:MN) {
F[i,j] = -log( fmax( F[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for(j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for(j in 1:U) {
for(i in 1:MN) {
B[i,j] = (bm[i,j] - rem[i,j]) * K[j] ;
C[i,j] = rem[i,j]*K[j] ;
}
for(i in 1:M) {
TAC[i,j] = rem[N+i,j]*K[j] ;
}
}
}
"
)
}
if (DS=="data_aggregated_timeseries" ) {
cfanorth = 1 # column index
cfasouth = 2 # column index
cfa4x = 3 # column index
landings = bio.snowcrab::snowcrab_landings_db()
# NOTE:: message( "Fishing 'yr' for CFA 4X has been set to starting year:: 2001-2002 -> 2001, etc.")
# year is year of capture
# yr is "fishing year" relative to the assessment cycle
landings = landings[ which (landings$cfa %in% c( "cfanorth", "cfasouth", "cfa4x" ) ) , ]
L = tapply( landings$landings, INDEX=landings[,c("yr", "cfa")], FUN=sum, na.rm=T )
nL = nrow(L)
cfaall = tapply( landings$landings, INDEX=landings[,c("yr")], FUN=sum, na.rm=T )
L = cbind( L, cfaall )
L = L / 1000/1000 # convert to kt pN$fishery_model_label = "stan_surplus_production_2022_model_qc_cauchy"
L[ !is.finite(L)] = 0
L = as.data.frame( L[ match( p$yrs, rownames(L) ), areas ] )
# biomass data: post-fishery biomass are determined by survey B)
B = aggregate_simulations( fn=carstm_filenames( p, returnvalue="filename", fn="aggregated_timeseries" ) )$RES
rownames(B) = B$yrs
B = as.data.frame( B[ match( p$yrs, B$yrs ), areas ] )
# cfa4x have had no estimates prior to 2004
cfanorth.baddata = which( p$yrs <= 2004 )
# B[ cfanorth.baddata, cfanorth ] = NA
cfasouth.baddata = which( p$yrs <= 2004 )
# B[ cfasouth.baddata, cfasouth ] = NA
cfa.nodata = which( p$yrs <= 2004 )
B[ cfa.nodata , cfa4x ] = NA
sb = list(
IOA = as.matrix(B), # observed index of abundance
CAT = as.matrix(L) # catches , assume 20% handling mortality and illegal landings
)
return(sb)
}
if (DS=="logistic_model" ) {
message( "Output location is: ", p$fishery_model$outdir )
dir.create( p$fishery_model$outdir, recursive=T, showWarnings=F )
if (is.null(fit)) {
p$fishery_model$stancode$compile()
fit = p$fishery_model$stancode$sample( ... )
}
if (0) {
# Posterior summary statistics .. the $sample() method creates R6 CmdStanMCMC objects,
fit$summary() # summarise_draws() from posterior package
fit$summary("K", "r", "q")
# this is a draws_array object from the posterior package
# str(fit$sampler_diagnostics())
diagnostics_df = as_draws_df(fit$sampler_diagnostics())
print(diagnostics_df)
fit$cmdstan_diagnose()
fit$cmdstan_summary()
# Posterior draws .. $draws() a 3-D array (iteration x chain x variable)
draws_array = fit$draws()
str(draws_array)
draws_df = as_draws_df(draws_array) # as_draws_matrix() for matrix
print(draws_df)
}
fit$save_object( file = p$fishery_model$fnfit ) # save this way due to R-lazy loading; RDS file
res = list( mcmc=stan_extract( as_draws_df(fit$draws() ) ), p=p )
saveRDS(res, file=p$fishery_model$fnres, compress=TRUE)
return(res)
}
if (DS=="samples" ) {
res = NULL
if (file.exists(p$fishery_model$fnres)) res = readRDS(p$fishery_model$fnres)
return(res)
}
if (DS=="fit" ) {
fit = NULL
if (file.exists(p$fishery_model$fnfit)) fit = readRDS(p$fishery_model$fnfit)
return(fit)
}
if (DS=="plot") {
y = res$mcmc
sb= res$p$fishery_model$fmdata
if (is.null(fn)) {
outdir = pN$fishery_model$outdir
} else{
outdir = dirname(fn)
}
ntacs = sb$nProj
yrs0 = res$p$yrs
yrs = c( yrs0, (max(yrs0)+c(1:sb$M) ) )
yrs.last = max(yrs0) + 0.5
ndata = length(yrs0)
hdat = 1:ndata
if (vname =="r.ts") {
# catch this first as the layout is different
if (is.null(fn)) fn=file.path(outdir, "r.ts.density.png" )
br = 75
plot.new()
layout( matrix(c(1:(sb$N*3)), ncol=3, nrow=sb$N ))
par(mar = c(1., 1., 0.65, 0.75))
u = apply( y[["r"]], c(2, 3), median, na.rm=T )
for (i in 1:3) {
for (yr in 1:sb$N) {
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
pdat = u[ yr,i ]
xrange = range( pdat, na.rm=T )
postdat = hist( pdat, breaks=br, plot=FALSE )
yrange = range( 0, postdat$density, na.rm=T ) * 1.02
hist( pdat, freq=FALSE, breaks=br, xlim=xrange, ylim=yrange, main="", xlab="", ylab="Density", col="lightgray", border="gray")
YR = rownames(sb$IOA) [yr]
legend( "topright", bty="n", legend=paste( aulabels[i], YR, "r", " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" ), cex=0.9 )
}}
if (save.plot) savePlot( filename=fn, type="png" )
return( fn)
}
plot.new()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(4.4, 4.4, 0.65, 0.75))
prr = NULL
prr$class ="none" # no priors by default
if ( type=="density" ) { # default
if ( vname=="K" ) {
if (is.null(fn)) fn=file.path(outdir, "K.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="normal"
# E(X) = exp(mu + 1/2 sigma^2)
# med(X) = exp(mu)
# Var(X) = exp(2*mu + sigma^2)*(exp(sigma^2) - 1)
# CV = sqrt( Var(X) ) / E(X) = sqrt(exp(sigma^2) - 1) ~ sigma; sigma < 1/2
# SD(X) = sqrt( exp(2*mu + sigma^2)*(exp(sigma^2) - 1) )
# or = CV * E(X)
prr$mean= sb$Kmu[i]
prr$sd = sb$Ksd[i]
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" ))
}
}
if ( vname=="r" ) {
if (is.null(fn)) fn=file.path(outdir, "r.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) { prr=NULL
prr=NULL
prr$class='normal'
prr$mean=sb$rmu[i]
prr$sd= sb$rsd[i]
pdat = u[,i]
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" ) )
}}
if ( vname=="q" ) {
if (is.null(fn)) fn=file.path(outdir, "q.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="normal"
prr$mean=sb$qmu[i]
prr$sd=sb$qsd[i]
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" )
)}}
if ( vname=="qc" ) {
if (is.null(fn)) fn=file.path(outdir, "qc.density.png" )
u = y[[vname]]
qc = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="cauchy"
prr$a = 0
prr$b = 0.1
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qc[2,i], " {", qc[1,i], ", ", qc[3,i], "} ", sep="" )
)}}
if ( vname=="qs" ) {
if (is.null(fn)) fn=file.path(outdir, "qs.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
for (i in 1:3) {
pdat = u[,i]
# prr=NULL
# prr$class="normal"
# prr$mean=sb$q0x[i]
# prr$sd=sb$q0x[i]*sb$cv
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" )
)}}
if ( vname=="BMSY" ) {
if (is.null(fn)) fn=file.path(outdir, "BMSY.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="none"
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
if ( vname=="FMSY" ) {
if (is.null(fn)) fn=file.path(outdir, "FMSY.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="none"
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
if ( vname=="bosd" ) {
if (is.null(fn)) fn=file.path(outdir, "bosd.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class='uniform'
prr$max=3
prr$min=0
#prr$class="lognormal"
#prr$meanlog=sb$bomup
#prr$sdlog=sqrt(sb$bosdp)
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
if ( vname=="bpsd" ) {
if (is.null(fn)) fn=file.path(outdir, "bpsd.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class='uniform'
prr$max=3
prr$min=0
#prr$class="lognormal"
#prr$meanlog=sb$bpmup
#prr$sdlog=sqrt(sb$bpsdp)
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
}
# --------------
if ( type=="timeseries" ) {
plot.new()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(4.4, 4.4, 0.65, 0.75))
if (vname=="biomass") {
if (is.null(fn)) fn=file.path(outdir, "biomass.timeseries.png" )
u = y[["B"]]
for (i in 1:3) {
meanval = apply( u[,1:sb$N,i], 2, mean, na.rm=T )
prs = seq( from=0.025, to=0.975, length.out=600)
Bq = apply( u[,1:sb$N,i], 2, quantile, probs=prs, na.rm=T )
#yran = range(c(0, Bq, sb$IOA[,i] ), na.rm=T )*1.01
yran = range(c(0, Bq ), na.rm=T )*1.01
plot( yrs0, Bq[1,], type="n", ylim=yran, xlim=range(yrs0), xlab="", ylab="" ) #change xlim to yrs0 to remove 3 yr projection
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
for ( j in 1:length(prs) ) {
lines ( yrs0, Bq[j,], lwd=4, col=cols2[j] )
}
# lines( yrs0, B, lwd=3, col="darkgreen" )
#abline (v=yrs.last , lwd=2, lty="dashed" ) #can comment out this line if not providing forward projection
if (i==2) title( ylab="Fishable biomass (kt)" )
if (i==3) title( xlab="Year" )
#points( yrs0, qIOA, pch=20, col="darkgreen" )
#lines ( yrs0, qIOA, lwd=3, col="darkgreen", lty="dashed" )
lines ( yrs0, meanval, lwd=2, col="blue", lty="dotted" )
#points( yrs0, IOA, pch=20, col="darkred" )
#lines( yrs0, IOA, lwd=3, lty="dotdash", col="red" )
# legend( "topright", bty="n", legend=aulabels[i])
}
}
if (vname=="rem") {
if (is.null(fn)) fn=file.path(outdir, "rem.timeseries.png" )
u = y[[vname]]
for (i in 1:3) {
meanval = apply( u[,,i], 2, mean, na.rm=T )
prs = seq( from=0.025, to=0.975, length.out=600)
Bq = apply( u[,,i], 2, quantile, probs=prs, na.rm=T )
#yran = range(c(0, Bq, sb$IOA[,i] ), na.rm=T )*1.01
yran = range(c(0, Bq ), na.rm=T )*1.01
plot( yrs, Bq[1,], type="n", ylim=yran, xlim=range(yrs0), xlab="", ylab="" ) #change xlim to yrs0 to remove 3 yr projection
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
for ( j in 1:length(prs) ) {
lines ( yrs, Bq[j,], lwd=4, col=cols2[j] )
}
# lines( yrs, rem, lwd=3, col="darkgreen" )
#abline (v=yrs.last , lwd=2, lty="dashed" ) #can comment out this line if not providing forward projection
if (i==2) title( ylab="Fishable biomass (kt)" )
if (i==3) title( xlab="Year" )
#points( yrs0, qIOA, pch=20, col="darkgreen" )
#lines ( yrs0, qIOA, lwd=3, col="darkgreen", lty="dashed" )
lines ( yrs, meanval, lwd=2, col="blue", lty="dotted" )
#points( yrs0, IOA, pch=20, col="darkred" )
#lines( yrs0, IOA, lwd=3, lty="dotdash", col="red" )
legend( "topright", bty="n", legend=aulabels[i])
}
}
if (vname=="fishingmortality") {
if (is.null(fn)) fn=file.path(outdir, "fishingmortality.timeseries.png" )
Fmsy = apply( y[["FMSY"]], 2, mean, na.rm=T )
prs = seq( from=0.025, to=0.975, length.out=600)
F = y[["F"]]
Fi = apply( F[, 1:sb$N, ] , c(2,3), quantile, probs=prs, na.rm=T )
for (i in 1:3) {
yran = range(c(0, max(c(Fi,Fmsy))), na.rm=T )*1.05
yran = pmin( yran, 1.2 )
plot( yrs0, Fi[1,,i], type="n", ylim=yran, xlab="", ylab="" )
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
if (i %in% c(1,2)){
for ( j in 1:length(prs) ) {
lines ( yrs0, Fi[j,,i], lwd=4, col=cols2[j] )
}}
if (i==3){
for ( j in 1:length(prs) ) {
lines ( yrs0-0.2, Fi[j,,i], lwd=4, col=cols2[j] )
}}
if (i==2) title( ylab="Fishing mortality" )
if (i==3) title( xlab="Year" )
# legend( "topright", bty="n", legend=aulabels[i])
abline (h=-log(1-0.2), lwd=2, lty="dashed" )
abline (h=Fmsy[i], lwd=2, lty="solid", col="red" )
}
}
}
if (type=="hcr") {
if (vname=="default") {
if (is.null(fn)) fn=file.path(outdir, "hcr.default.png" )
B = apply( y[["B"]], c(2,3), median, na.rm=T )
F = apply( y[["F"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
for (i in 1:3 ) {
ylims = c(0, min( 1, max( FMSY[i] * 1.25, F[hdat,i] ) ) )
plot( B[hdat,i], F[hdat,i], type="b", xlim=c(0, K[i] * 1.1 ),
ylim=ylims, col="darkorange", cex=0.8, lwd=2, xlab="", ylab="", pch=20 )
# nn = as.matrix( cbind( Bx=as.vector( y$B[,ndata,i] ), Fx = as.vector( y$F[,ndata,i] ) ))
# ellipse.2d(nn[,1], nn[,2], pv=0.05, sc=30)
if (i==3) title( xlab="Fishable biomass (kt)" )
if (i==2) title( ylab="Fishing mortality" )
F30 = -log(1-0.3)
F10 = -log(1-0.1)
Fref = 0.22
Bmsy = K[i] * 0.5
Bref = K[i] * 0.2
BK = K[i]
BK25 = K[i] * .25
Fhistorical = mean( F[hdat,i], na.rm=T )
Bhistorical = mean( B[hdat,i], na.rm=T )
yl = 0.05
polygon(x=c(Bmsy,Bmsy*2,Bmsy*2, Bmsy),y=c(-0.08,-0.1,FMSY[i],FMSY[i]),col='lightgreen',border=NA)
polygon(x=c(Bmsy/2,Bmsy,Bmsy, Bmsy/2),y=c(-0.08,-0.1,FMSY[i],FMSY[i]),col='lightgoldenrod',border=NA)
polygon(x=c(0,Bmsy/2,Bmsy/2, 0),y=c(-0.08,-0.1,FMSY[i],FMSY[i]),col='darksalmon',border=NA)
#might need adjustment below to offset F vs B. Need to plot F against PREfishery biomass
lines( B[hdat,i], F[hdat,i], type="b", xlim=c(0, K[i] * 1.1 ),
ylim=ylims, col='blue', cex=0.8, lwd=2, xlab="", ylab="", pch=20 )
abline (h=Fref, lty="solid", col="gray", lwd=2 )
abline (h=F10, lty="dotted", col="gray")
# text( 0.05*K[i], F10, "10% HR", pos=1 )
abline (h=F30, lty="dotted", col="gray")
# text( 0.05*K[i], F30, "30% HR", pos=1 )
abline (h=FMSY[i], lty="dashed", col="red" )
# abline (h=Fhistorical, lty="dashed")
# text( 0.05*K[i], Fhistorical, "Mean", pos=1, lwd=2 )
# abline (v=Bref, lty="dotted")
# text( Bref-0.2, 0.25, "Lower biomass reference point\n (LBRP = 0.2 * BMSY)" , srt=90, pos=3)
abline (v=Bmsy, lty="dotted")
abline (v=BK, lty="dotted")
abline (v=BK25, lty="dotted")
text( Bmsy-0.01*K[i], yl, "K/2" , srt=90, pos=3)
text( BK-0.01*K[i], yl, "K" , srt=90, pos=3)
text( BK25-0.01*K[i], yl, "K/4" , srt=90, pos=3)
text( 0.05*K[i], Fref, "20% HR", pos=1 )
text( 0.05*K[i], FMSY[i], "FMSY", pos=3, lwd=2, col="red" )
if (i %in% c(1,2)){
text( B[1:(ndata-1),i], F[1:(ndata-1),i], labels=yrs0[-ndata], pos=3, cex= 0.8 )
points( B[ndata,i], F[ndata,i], pch=21, bg='darkorange', cex= 1.4 )
text( B[ndata,i], F[ndata,i], labels=yrs0[ndata], pos=3, cex= 1.4, font=2 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
}
if (i==3){
text( B[1:(ndata-1),i], F[1:(ndata-1),i], labels=(yrs0[-ndata]), pos=3, cex= 0.8 )
points( B[ndata,i], F[ndata,i], pch=21, bg='darkorange', cex= 1.4 )
text( B[ndata,i], F[ndata,i], labels=yrs0[ndata], pos=3, cex= 1.4, font=2 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
}
# abline (v=Bhistorical, lty="dashed")
# text( Bhistorical-0.01*K[i], yl, "Mean" , srt=90, pos=3, lwd=2)
}
#Enable below to see the annual F estimates for inclusion in the document
print("F for N-ENS" )
print(F[hdat,1] )
print("F for S-ENS" )
print(F[hdat,2] )
print("F for 4X" )
print(F[hdat,3] )
}
if (vname=="default.unmodelled") {
if (is.null(fn)) fn=file.path(outdir, "hcr.default.unmodelled.png" )
B = sb$IOA
F = apply( y[["F"]], c(2,3), median, na.rm=T )
areas = c("cfa4x", "cfasouth", "cfanorth" )
regions = c("4X", "S-ENS", "N-ENS")
td = exploitationrates(p=p, areas=areas, labels=regions, CFA4X.exclude.year.assessment=FALSE )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
for (i in 1:3 ) {
ylims = c(0, FMSY[i] * 1.25)
plot( B[hdat,i], F[hdat,i], type="b", xlim=c(0, K[i] * 1.1 ),
ylim=ylims, col="darkorange", cex=0.8, lwd=2, xlab="", ylab="", pch=20 )
# nn = as.matrix( cbind( Bx=as.vector( y$B[,ndata,i] ), Fx = as.vector( y$F[,ndata,i] ) ))
# ellipse.2d(nn[,1], nn[,2], pv=0.05, sc=30)
if (i==3) title( xlab="Fishable biomass (kt)" )
if (i==2) title( ylab="Fishing mortality" )
F30 = -log(1-0.3)
F10 = -log(1-0.1)
Fref = 0.22
Bmsy = BMSY[i]
Bref = K[i] * 0.2
BK = K[i]
BK25 = K[i] * .25
Fhistorical = mean( F[hdat,i], na.rm=T )
Bhistorical = mean( B[hdat,i], na.rm=T )
yl = 0.05
abline (h=Fref, lty="solid", col="gray", lwd=2 )
abline (h=F10, lty="dotted", col="gray")
# text( 0.05*K[i], F10, "10% HR", pos=1 )
abline (h=F30, lty="dotted", col="gray")
# text( 0.05*K[i], F30, "30% HR", pos=1 )
abline (h=FMSY[i], lty="dashed", col="red" )
# abline (h=Fhistorical, lty="dashed")
# text( 0.05*K[i], Fhistorical, "Mean", pos=1, lwd=2 )
# abline (v=Bref, lty="dotted")
# text( Bref-0.2, 0.25, "Lower biomass reference point\n (LBRP = 0.2 * BMSY)" , srt=90, pos=3)
abline (v=Bmsy, lty="dotted")
abline (v=BK, lty="dotted")
abline (v=BK25, lty="dotted")
text( 0.05*K[i], Fref, "20% HR", pos=1 )
text( 0.05*K[i], FMSY[i], "FMSY", pos=3, lwd=2, col="red" )
text( BK-0.01*K[i], yl, "K" , srt=90, pos=3)
text( Bmsy-0.01*K[i], yl, "K/2" , srt=90, pos=3)
text( BK25-0.01*K[i], yl, "K/4" , srt=90, pos=3)
text( B[hdat,i], F[hdat,i], labels=yrs0, pos=3, cex= 0.8 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
# abline (v=Bhistorical, lty="dashed")
# text( Bhistorical-0.01*K[i], yl, "Mean" , srt=90, pos=3, lwd=2)
}
}
if (vname=="simple") {
if (is.null(fn)) fn=file.path(outdir, "hcr.simple.png" )
require(car)
B = apply( y[["B"]], c(2,3), median, na.rm=T )
F = apply( y[["F"]], c(2,3), median, na.rm=T )
C = apply( y[["C"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
aulabels = c("N-ENS", "S-ENS", "4X")
for (i in 1:3 ) {
ylims = max(C[,i] )* c(0, 1.1)
plot( B[hdat,i], C[hdat,i], type="l", xlim=c(0, K[i]*1.05 ),
ylim=ylims, xlab="", ylab="", lwd=2, col="darkorange" )
abline(0,0.1, lty="dotted", lwd=2, col="gray" )
abline(0,0.2, lwd=3, col="gray" )
abline(0,0.3, lty="dotted", lwd=2, col="gray" )
points( B[hdat,i], C[hdat,i], col="orange", cex=0.8, pch=20 )
text( B[hdat,i], C[hdat,i], labels=yrs0, pos=3, cex= 0.85 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
# nn = as.matrix( cbind( Bx=as.vector( y$B[,ndata,i] ), Fx = as.vector( y$F[,ndata,i] ) ))
# ellipse.2d(nn[,1], nn[,2], pv=0.05, sc=30)
if (i==3) title( xlab="Fishable biomass (kt)" )
if (i==2) title( ylab="Catch (kt)" )
Cmsy = ( exp( FMSY[i] ) - 1)
Cref = ( exp( FMSY[i] * 0.2 ) - 1) * K[i]
Bmsy = BMSY[i]
Bref = K[i] * 0.2
BK = K[i]
BK25 = K[i] * .25
# Chistorical = mean( C[hdat,i], na.rm=T )
# Bhistorical = mean( B[hdat,i], na.rm=T )
yl = 0.1 * max(C[hdat,i])
# abline (h=Fref, lty="dotted")
# text( 0.25, Fref, "Target\n (0.2 * FMSY) ", pos=1 )
abline (0, Cmsy, lty="dotted", col="red")
# text( 0.1*K[i], Cmsy, "FMSY", pos=1 )
# abline (h=Chistorical, lty="dashed")
# text( 0.1*K[i], Chistorical, "Mean", pos=3, lwd=2 )
# abline (v=Bref, lty="dotted")
# text( Bref-0.2, 0.25, "Lower biomass reference point\n (LBRP = 0.2 * BMSY)" , srt=90, pos=3)
abline (v=BK, lty="dotted")
text( BK-0.01*K[i], yl, "K" , srt=90, pos=3)
abline (v=BK/2, lty="dotted")
text( BK/2-0.01*K[i], yl, "K/2" , srt=90, pos=3)
abline (v=BK25, lty="dotted")
text( BK25-0.01*K[i], yl, "K/4" , srt=90, pos=3)
}
}
}
if (type=="diagnostic.catch") {
}
if (type=="diagnostic.phase") {
if (is.null(fn)) fn=file.path(outdir, "diagnostic.phase.png" )
B = apply( y[["B"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
for (i in 1:3 ) {
plot( B[1:ndata-1,i], B[2:ndata,i], type="b", xlab="t", ylab="t+1",
xlim=c(0, K[i] * 1.25 ), ylim=max(K[i] )* c(0, 1.25), lwd=2, col="darkorange" )
# abline(0,0.1, lty="dotted", lwd=2, col="gray" )
abline( coef=c(0,1) )
#text( B[1:ndata-1,], B[2:ndata,], labels=yrs4 , pos=4, cex=0.8 )
}
}
if (type=="diagnostic.errors") {
if (is.null(fn)) fn=file.path(outdir, "diagnostic.errors.png" )
# observation vs process error
graphics.off()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(5, 4, 0, 2))
require(car)
eP = y[["bpsd"]]
eO = y[["bosd"]]
for (i in 1:3 ) {
plot( eP[,,i], eO[,,i], type="p", pch=22 )
if (i==2) title( ylab="Process error (SD)" )
if (i==3) title( xlab="Observation error (SD)" )
}
}
if (type=="diagnostic.production") {
B = apply( y[["B"]], c(2,3), median, na.rm=T )
P = apply( y[["P"]], c(2,3), median, na.rm=T )
C = apply( y[["C"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
MSY = apply( y[["MSY"]], c(2), median, na.rm=T )
# production vs biomass
plot.new()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(5, 4, 0, 2))
for (i in 1:3) {
plot( B[,i], P[,i], type="n", pch=20, ylim=c(0, max( c(P[,i], MSY[i]))*1.1), xlim=c(0,K[i]*1.05), xlab="Biomass; kt", ylab="Yield; kt" )
a = MSY[i] / (BMSY[i])^2
curve( -a*(x-BMSY[i])^2 + MSY[i], from=0, to=K[i], add=TRUE, lwd=3, col="gray" )
abline(v=BMSY[i], lty="dotted", lwd=3, col="gray")
points( B[,i], P[,i], type="p", pch=20 )
text( B[,i], P[,i], yrs0, pos=3, cex=0.8 )
# abline(h=0)
}
}
if (is.null(fn)) fn=file.path(outdir, "diagnostic.production.png" )
if(save.plot) savePlot( filename=fn, type="png" )
return( fn)
}
}
jae0/snowcrab documentation built on Feb. 27, 2024, 2:42 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions fishery_model
fishery_model = function( p=NULL, DS="plot",
plotresults=TRUE, tag="default", areas=c("cfanorth", "cfasouth", "cfa4x"),
vname="", type="density", res=NULL, fit=NULL, fn=NULL, aulabels=c("N-ENS","S-ENS","4X"), save.plot=TRUE, ... ) {
# sb = bio.snowcrab::fishery_model( DS="data_aggregated_timeseries", p=p )
if (tag=="default") {
if (!is.null(p)) if (exists("tag", p)) tag = p$tag
}
if (DS=="logistic_parameters") {
p = parameters_add(p, list(...)) # add passed args to parameter list, priority to args
out = list()
if (!exists("method", out)) out$method = "stan" # "jags", etc.
if (!exists("carstm_model_label", p)) p$carstm_model_label = "default"
if (!exists("outdir", out)) out$outdir = file.path( p$modeldir, p$carstm_model_label, "fishery_model_results", tag )
if (!exists("fnres", out)) out$fnres = file.path( out$outdir, paste( "logistics_model_results", p$year.assessment, out$method, tag, "RDS", sep=".") )
if (!exists("fnfit", out)) out$fnfit = file.path( out$outdir, paste( "logistics_model_fit", p$year.assessment, out$method, tag, "RDS", sep=".") )
dir.create( out$outdir, showWarnings = FALSE, recursive = TRUE )
message( "Results will be saved to:", out$outdir)
# observations
if (!exists("fmdata", out)) {
out$fmdata = fishery_model( DS="data_aggregated_timeseries", p=p )
oo = apply( out$fmdata$IOA, 2, range, na.rm=TRUE )
for (i in 1:ncol(oo)) {
out$fmdata$IOA[,i] = (out$fmdata$IOA[,i] - oo[1,i] )/ diff(oo[,i]) # force median 0.5 with most data inside 0,1
}
# out$fmdata$IOA_min = apply( out$fmdata$IOA, 2, min, na.rm=TRUE )
}
if (!exists("er", out$fmdata)) out$fmdata$er = 0.2 # target exploitation rate
if (!exists("U", out$fmdata)) out$fmdata$U = ncol( out$fmdata$IOA) # number of regions
if (!exists("N", out$fmdata)) out$fmdata$N = nrow( out$fmdata$IOA) # no years with data
if (!exists("M", out$fmdata)) out$fmdata$M = 3 # no years for projections
if (!exists("ty", out$fmdata)) out$fmdata$ty = which(p$yrs == 2004) # index of the transition year (2004) between spring and fall surveys
if (!exists("cfa4x", out$fmdata)) out$fmdata$cfa4x = 3 # column index of cfa4x
if (!exists("eps", out$fmdata)) out$fmdata$eps = 1e-9 # small non-zero number
out$fmdata$missing = ifelse( is.finite(out$fmdata$IOA), 0, 1)
out$fmdata$missing_n = colSums(out$fmdata$missing)
out$fmdata$missing_ntot = sum(out$fmdata$missing_n)
# this must be done last
out$fmdata$IOA[ which(!is.finite(out$fmdata$IOA)) ] = 0 # reset NAs to 0 as stan does not take NAs
out$fmdata$CAT[ which(!is.finite(out$fmdata$CAT)) ] = out$fmdata$eps # remove NA's
# priors
if (!exists("Kmu", out$fmdata)) out$fmdata$Kmu = c( 5.5, 65.0, 2.0 ) ## based upon prior historical analyses (when stmv and kriging were attempted)
if (!exists("rmu", out$fmdata)) out$fmdata$rmu = c( 1.0, 1.0, 1.0 ) ## biological constraint
if (!exists("qmu", out$fmdata)) out$fmdata$qmu = c( 1.0, 1.0, 1.0 ) ## based upon video observations q is close to 1 .. but sampling locations can of course cause bias (avoiding rocks and bedrock)
if (!exists("Ksd", out$fmdata)) out$fmdata$Ksd = c( 0.25, 0.25, 0.25 ) * out$fmdata$Kmu
if (!exists("rsd", out$fmdata)) out$fmdata$rsd = c( 0.1, 0.1, 0.1 ) * out$fmdata$rmu # smaller SD's to encourage solutions closer to prior means
if (!exists("qsd", out$fmdata)) out$fmdata$qsd = c( 0.1, 0.1, 0.1 ) * out$fmdata$qmu
return(out)
}
if (DS=="stan_surplus_production_2019_model") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.0> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=eps, upper=1.0> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps, upper=1.0> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps, upper=1.25> [M+N,U] bm; // permit overshoot bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ beta( 8, 2 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ beta( 1, 100000 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] / K[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] /K[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3]/K[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j]/K[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3]/ K[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] / K[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( fmax(fmin(b0,0.99),eps), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_variation1_wider_qc_uniform") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ uniform( -0.5, 0.5 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 2 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_uniform") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=0, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.25> [U] bosd; // observation error
vector <lower=eps, upper=0.25> [U] bpsd; // process error
// vector <lower=eps, upper=0.25> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coefficient
qc ~ uniform( 0, 1 ) ; // i.e., Y:b offset constant ;
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_variation1_wider_qc_normal") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ normal( 0, 0.25 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_variation1_wider_qc_normal_0") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1, upper=1> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ normal( 0, 0.000001 ) ; // i.e.,force to be 0
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_beta") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=0, upper=0.5> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ beta( 1, 2 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_cauchy") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=0, upper=1.0> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ cauchy( 0, 0.1 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_2022_model_qc_cauchy_wider") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
int NU;
int Ndata;
MN = M+N ;
N1 = N+1;
NU = N*U;
Ndata = NU - missing_ntot;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=-1.0, upper=1.0> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] rem_sd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ cauchy( 0, 0.1 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - CAT[1,j]/K[j] , eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i-1,j]/K[j] , eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - CAT[i,3]/K[3] , eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:2) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - (CAT[ty-1,j]/K[j] + CAT[ty,j]/K[j] ) / 2.0 , eps) ) ) , bosd[j] ) ; //NENS and SENS
}
( Y[ty,3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[ty,3] - CAT[ty,3]/K[3] , eps) ) ) , bosd[3] ) ; //SENS
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - CAT[i,j]/K[j] , eps) ) ) , bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - CAT[i-1,j]/K[j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
vector[Ndata] log_lik;
int n;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
// for loo calcs (pointwise loglikelihoods)
n=0;
for (j in 1:U) {
for (i in 1:N) {
if ( missing[i,j] == 0 ) {
n += 1;
log_lik[n] = normal_lpdf( Y[i,j] | B[i,j], bosd[j] );
}
}
}
}
"
)
}
if (DS=="stan_surplus_production_catch_observation") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
vector[U] qsd ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
MN = M+N ;
N1 = N+1;
}
parameters {
vector <lower=eps> [U] K;
vector <lower=0.25, upper=2.0> [U] r; // biologically should be ~ 1
vector <lower=eps, upper=2.5> [U] q; // multiplicative factor, unlikely to be >200%
vector <lower=eps, upper=0.5> [U] qc; // offset .. unlikely to be off by > 50%
vector <lower=eps, upper=0.5> [U] bosd; // observation error
vector <lower=eps, upper=0.5> [U] bpsd; // process error
vector <lower=eps, upper=0.5> [U] catsd; // catch error
vector <lower=eps> [U] b0;
vector <lower=eps> [missing_ntot] IOAmissing;
matrix <lower=eps> [M+N,U] bm; // force bm max 1
matrix <lower=eps> [N,U] cat; // estimated catch
vector <lower=eps, upper=0.5> [U] catQ; // multiplicative factor .. fraction misreported
}
transformed parameters {
matrix[N,U] Y; // index of abundance
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j] ; // translation of a zscore to a positive internal scale
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
b0 ~ normal( 0.5, 0.1 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
catsd ~ cauchy( 0, 0.1 ) ;
catQ ~ beta( 1, 5 ) ;
q ~ normal( qmu, qsd ) ; // i.e., Y:b scaling coeeficient
qc ~ beta( 1, 5 ) ; // i.e., Y:b offset constant ; plot(dbeta(seq(0,1,by=0.1), 1, 10 ) )
// -------------------
// biomass observation model
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
// catch observation model -- cat = CAT/K *catQ
// spring surveys
for (j in 1:2) {
( CAT[1,j]/K[j] ) * (1.0 + catQ[j]) ~ normal( cat[1,j], catsd[j] );
for (i in 2:(ty-1) ){
( CAT[i-1,j]/K[j] ) * (1.0 + catQ[j]) ~ normal( cat[i-1,j], catsd[j] );
}
}
for (i in 1:(ty-1) ){
( CAT[i,3]/K[3] ) * (1.0 + catQ[3]) ~ normal( cat[i,3], catsd[3] );
}
// transition year (ty)
for (j in 1:2) {
( CAT[ty-1,j] + CAT[ty,j] ) / ( 2.0* K[j] ) * (1.0 + catQ[j]) ~ normal( cat[ty,j], catsd[j] );
}
( CAT[ty,3] / K[3] ) * (1.0 + catQ[3]) ~ normal( cat[ty,3], catsd[3] );
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( CAT[i,j]/K[j] ) * (1.0 + catQ[j]) ~ normal( cat[i,j], catsd[j] );
}
}
// biomass observation model
// spring surveys
for (j in 1:2) {
( Y[1, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[1,j] - cat[1,j], eps) )) , bosd[j] ) ;
for (i in 2:(ty-1) ){
( Y[i, j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - cat[i-1,j], eps) )), bosd[j] ) ;
}
}
for (i in 1:(ty-1) ){
( Y[i, 3] / q[3] ) + qc[3] ~ normal( ( ( fmax( bm[i,3] - cat[i,3], eps) )) , bosd[3] ) ;
}
// transition year (ty)
for (j in 1:3) {
( Y[ty,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[ty,j] - cat[ty,j], eps) ) ) , bosd[j] ) ;
}
// fall surveys
for (j in 1:3) {
for (i in (ty+1):N) {
( Y[i,j] / q[j] ) + qc[j] ~ normal( ( ( fmax( bm[i,j] - cat[i,j], eps) ) ), bosd[j] ) ; // fall surveys
}
}
// -------------------
// biomass process model
// fmax .. force positive value .. initial conditions
bm[1,] ~ normal( (b0), bpsd ) ;
for (j in 1:U) {
real o;
for (i in 2:N) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - cat[i-1,j] )), bpsd[j] ) ;
}
for (i in N1:MN) {
o = r[j] * fmax( 1.0 - bm[i-1,j], eps ) ;
bm[i,j] ~ normal( ( ( bm[i-1,j] * ( 1.0 + o ) - er*bm[(i-1),j] )), bpsd[j] ) ;
}
}
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:U) {
for (i in 1:N) {
F[i,j] = -log( fmax( 1.0 - CAT[i,j]/K[j] / bm[i,j], eps) ) ;
}
for (i in N1:MN) {
F[i,j] = -log( fmax( 1.0 - er * bm[i-1,j] / bm[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for (j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for (j in 1:U) {
for(i in 1:N) {
B[i,j] = bm[i,j] * K[j] - CAT[i,j] ;
C[i,j] = CAT[i,j] ;
}
for (i in N1:MN) {
B[i,j] = (bm[i,j] - er*bm[(i-1),j]) * K[j] ;
C[i,j] = er*bm[(i-1),j] * K[j] ;
}
}
}
"
)
}
if (DS=="stan_surplus_production_2020") {
return( "
data {
int<lower=0> N; // no. years
int<lower=0> U; // no. regions
int<lower=0> M; // no. years to project
int ty;
real er ;
real eps ;
vector[U] Ksd;
vector[U] rsd;
vector[U] qsd;
vector[U] Kmu ;
vector[U] rmu ;
vector[U] qmu ;
matrix[N,U] CAT;
matrix[N,U] IOA;
matrix[N,U] missing;
array[U] int missing_n;
int missing_ntot;
}
transformed data {
int MN;
int N1;
MN = M+N ;
N1 = N+1;
}
parameters {
vector <lower=eps>[U] K;
vector <lower=eps>[U] r;
vector <lower=eps>[U] q;
vector <lower=eps>[U] qs;
vector <lower=eps,upper=(1-eps)>[U] bosd; // observation error
vector <lower=eps,upper=(1-eps)>[U] bpsd; // process error
vector <lower=eps,upper=(1-eps)>[U] b0;
vector <lower=eps>[missing_ntot] IOAmissing;
matrix <lower=eps>[M+N,U] bm;
}
transformed parameters {
matrix[N,U] Y; // index of abundance
matrix[N,U] Ymu; // collator used to force positive values for lognormal
matrix[MN,U] bmmu; // collator used to force positive values for lognormal
matrix[MN,U] rem; // observed catch
// copy parameters to a new variable (Y) with imputed missing values
{
int ii;
ii = 0;
for (j in 1:U) {
for (i in 1:N) {
Y[i,j] = IOA[i,j];
if ( missing[i,j] == 1 ) {
ii = ii+1;
Y[i,j] = IOAmissing[ii];
}
}
}
}
// -------------------
// removals (catch) observation model, standardized to K (assuming no errors in observation of catch!)
for (j in 1:U) {
rem[1:N,j] = CAT[1:N,j]/K[j] ;
rem[(N+1):MN,j] = er*bm[ N:(MN-1),j] ; // forecasts
}
// -------------------
// observation model calcs and contraints:
// Ymu = 'surveyed/observed' residual biomass at time of survey (Bsurveyed)
// cfanorth(1) and cfasouth(2)
// This is slightly complicated because a fall / spring survey correction is required:
// B represents the total fishable biomass available in fishing year y
// in fall surveys: Btot(t) = Bsurveyed(t) + removals(t)
// in spring surveys: Btot(t) = Bsurveyed(t) + removals(t-1)
// spring surveys from 1998 to 2003
// this is conceptualized in the following time line:
// '|' == start/end of each new fishing year
// Sf = Survey in fall
// Ss = Survey in spring
// |...(t-2)...|.Ss..(t-1)...|...(t=2004)..Sf.|...(t+1).Sf..|...(t+2)..Sf.|...
// Cfa 4X -- fall/winter fishery
// Btot(t) = Bsurveyed(t) + removals(t) ## .. 2018-2019 -> 2018
for (j in 1:2) {
Ymu[1,j] = qs[j] * bm[1,j] - rem[1,j] ; // starting year approximation
Ymu[2:(ty-1),j] = qs[j] * bm[2:(ty-1),j] - rem[1:(ty-2),j] ; //spring surveys
Ymu[ty,j] = q[j] * bm[ty,j] - (rem[(ty-1),j] + rem[ty,j] )/2.0 ; // transition year .. approximation
Ymu[(ty+1):N,j] = q[j] * bm[(ty+1):N,j] - rem[(ty+1):N,j] ; // fall surveys
}
{
int k;
k=3;
Ymu[1,k] = q[k] * bm[1,k] - rem[1,k] ; // starting year approximation ymu[1991] = bm[1991]-rem[1991]
Ymu[2:(ty-1),k] = q[k] * bm[2:(ty-1),k] - rem[2:(ty-1),k];
Ymu[ty:N,k] = q[k] * bm[ty:N,k] - rem[ty:N,k];
}
for (j in 1:U) {
for (i in 1:N) {
Ymu[i,j] = K[j] * fmax( Ymu[i,j], eps); // force positive value
}
}
// -------------------
// process model calcs and constraints
for (j in 1:U) {
bmmu[1,j] = b0[j] ; // biomass at first year
for (i in 2:MN) {
bmmu[i,j] = bm[i-1,j] * ( 1.0 + r[j]*(1-bm[i-1,j]) ) - rem[i-1,j] ;
}
}
for (j in 1:U) {
for (i in 1:MN) {
bmmu[i,j] = fmax(bmmu[i,j], eps); // force positive value
}
}
}
model {
// -------------------
// priors for parameters
K ~ normal( Kmu, Ksd ) ;
r ~ normal( rmu, rsd ) ;
q ~ normal( qmu, qsd ) ;
qs ~ normal( qmu, qsd ) ;
b0 ~ beta( 8, 2 ) ; // starting b prior to first catch event
bosd ~ cauchy( 0, 0.1 ) ; // slightly informative .. center of mass between (0,1)
bpsd ~ cauchy( 0, 0.1 ) ;
// -------------------
// biomass observation model
for (j in 1:U) {
log(Y[1:N,j]) ~ normal( log(Ymu[1:N,j]), bosd[j] ) ; // stan thinks Y is being transformed due to attempt to impute missing values .. ignore
}
// -------------------
// biomass process model
for (j in 1:U) {
log(bm[1:MN,j]) ~ normal( log(bmmu[1:MN,j]), bpsd[j] ) ;
}
// could have used lognormal but this parameterization is 10X faster and more stable
target += - log(fabs(Y)); // required due to log transf above
target += - log(fabs(bm));
}
generated quantities {
vector[U] MSY;
vector[U] BMSY;
vector[U] FMSY;
matrix[MN,U] B;
matrix[MN,U] C;
matrix[MN,U] F;
matrix[M,U] TAC;
// -------------------
// fishing mortality
// fall fisheries
for (j in 1:3) {
for (i in 1:N) {
F[i,j] = 1.0 - rem[i,j] / bm[i,j] ;
}
}
for (j in 1:U) {
for (i in N1:MN) {
F[i,j] = 1.0 - er * bm[i-1,j] / bm[i,j] ;
}
for (i in 1:MN) {
F[i,j] = -log( fmax( F[i,j], eps) ) ;
}
}
// -------------------
// parameter estimates for output
for(j in 1:U) {
MSY[j] = r[j]* exp(K[j]) / 4 ; // maximum height of of the latent productivity (yield)
BMSY[j] = exp(K[j])/2 ; // biomass at MSY
FMSY[j] = 2.0 * MSY[j] / exp(K[j]) ; // fishing mortality at MSY
}
// recaled estimates
for(j in 1:U) {
for(i in 1:MN) {
B[i,j] = (bm[i,j] - rem[i,j]) * K[j] ;
C[i,j] = rem[i,j]*K[j] ;
}
for(i in 1:M) {
TAC[i,j] = rem[N+i,j]*K[j] ;
}
}
}
"
)
}
if (DS=="data_aggregated_timeseries" ) {
cfanorth = 1 # column index
cfasouth = 2 # column index
cfa4x = 3 # column index
landings = bio.snowcrab::snowcrab_landings_db()
# NOTE:: message( "Fishing 'yr' for CFA 4X has been set to starting year:: 2001-2002 -> 2001, etc.")
# year is year of capture
# yr is "fishing year" relative to the assessment cycle
landings = landings[ which (landings$cfa %in% c( "cfanorth", "cfasouth", "cfa4x" ) ) , ]
L = tapply( landings$landings, INDEX=landings[,c("yr", "cfa")], FUN=sum, na.rm=T )
nL = nrow(L)
cfaall = tapply( landings$landings, INDEX=landings[,c("yr")], FUN=sum, na.rm=T )
L = cbind( L, cfaall )
L = L / 1000/1000 # convert to kt pN$fishery_model_label = "stan_surplus_production_2022_model_qc_cauchy"
L[ !is.finite(L)] = 0
L = as.data.frame( L[ match( p$yrs, rownames(L) ), areas ] )
# biomass data: post-fishery biomass are determined by survey B)
B = aggregate_simulations( fn=carstm_filenames( p, returnvalue="filename", fn="aggregated_timeseries" ) )$RES
rownames(B) = B$yrs
B = as.data.frame( B[ match( p$yrs, B$yrs ), areas ] )
# cfa4x have had no estimates prior to 2004
cfanorth.baddata = which( p$yrs <= 2004 )
# B[ cfanorth.baddata, cfanorth ] = NA
cfasouth.baddata = which( p$yrs <= 2004 )
# B[ cfasouth.baddata, cfasouth ] = NA
cfa.nodata = which( p$yrs <= 2004 )
B[ cfa.nodata , cfa4x ] = NA
sb = list(
IOA = as.matrix(B), # observed index of abundance
CAT = as.matrix(L) # catches , assume 20% handling mortality and illegal landings
)
return(sb)
}
if (DS=="logistic_model" ) {
message( "Output location is: ", p$fishery_model$outdir )
dir.create( p$fishery_model$outdir, recursive=T, showWarnings=F )
if (is.null(fit)) {
p$fishery_model$stancode$compile()
fit = p$fishery_model$stancode$sample( ... )
}
if (0) {
# Posterior summary statistics .. the $sample() method creates R6 CmdStanMCMC objects,
fit$summary() # summarise_draws() from posterior package
fit$summary("K", "r", "q")
# this is a draws_array object from the posterior package
# str(fit$sampler_diagnostics())
diagnostics_df = as_draws_df(fit$sampler_diagnostics())
print(diagnostics_df)
fit$cmdstan_diagnose()
fit$cmdstan_summary()
# Posterior draws .. $draws() a 3-D array (iteration x chain x variable)
draws_array = fit$draws()
str(draws_array)
draws_df = as_draws_df(draws_array) # as_draws_matrix() for matrix
print(draws_df)
}
fit$save_object( file = p$fishery_model$fnfit ) # save this way due to R-lazy loading; RDS file
res = list( mcmc=stan_extract( as_draws_df(fit$draws() ) ), p=p )
saveRDS(res, file=p$fishery_model$fnres, compress=TRUE)
return(res)
}
if (DS=="samples" ) {
res = NULL
if (file.exists(p$fishery_model$fnres)) res = readRDS(p$fishery_model$fnres)
return(res)
}
if (DS=="fit" ) {
fit = NULL
if (file.exists(p$fishery_model$fnfit)) fit = readRDS(p$fishery_model$fnfit)
return(fit)
}
if (DS=="plot") {
y = res$mcmc
sb= res$p$fishery_model$fmdata
if (is.null(fn)) {
outdir = pN$fishery_model$outdir
} else{
outdir = dirname(fn)
}
ntacs = sb$nProj
yrs0 = res$p$yrs
yrs = c( yrs0, (max(yrs0)+c(1:sb$M) ) )
yrs.last = max(yrs0) + 0.5
ndata = length(yrs0)
hdat = 1:ndata
if (vname =="r.ts") {
# catch this first as the layout is different
if (is.null(fn)) fn=file.path(outdir, "r.ts.density.png" )
br = 75
plot.new()
layout( matrix(c(1:(sb$N*3)), ncol=3, nrow=sb$N ))
par(mar = c(1., 1., 0.65, 0.75))
u = apply( y[["r"]], c(2, 3), median, na.rm=T )
for (i in 1:3) {
for (yr in 1:sb$N) {
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
pdat = u[ yr,i ]
xrange = range( pdat, na.rm=T )
postdat = hist( pdat, breaks=br, plot=FALSE )
yrange = range( 0, postdat$density, na.rm=T ) * 1.02
hist( pdat, freq=FALSE, breaks=br, xlim=xrange, ylim=yrange, main="", xlab="", ylab="Density", col="lightgray", border="gray")
YR = rownames(sb$IOA) [yr]
legend( "topright", bty="n", legend=paste( aulabels[i], YR, "r", " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" ), cex=0.9 )
}}
if (save.plot) savePlot( filename=fn, type="png" )
return( fn)
}
plot.new()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(4.4, 4.4, 0.65, 0.75))
prr = NULL
prr$class ="none" # no priors by default
if ( type=="density" ) { # default
if ( vname=="K" ) {
if (is.null(fn)) fn=file.path(outdir, "K.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="normal"
# E(X) = exp(mu + 1/2 sigma^2)
# med(X) = exp(mu)
# Var(X) = exp(2*mu + sigma^2)*(exp(sigma^2) - 1)
# CV = sqrt( Var(X) ) / E(X) = sqrt(exp(sigma^2) - 1) ~ sigma; sigma < 1/2
# SD(X) = sqrt( exp(2*mu + sigma^2)*(exp(sigma^2) - 1) )
# or = CV * E(X)
prr$mean= sb$Kmu[i]
prr$sd = sb$Ksd[i]
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" ))
}
}
if ( vname=="r" ) {
if (is.null(fn)) fn=file.path(outdir, "r.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) { prr=NULL
prr=NULL
prr$class='normal'
prr$mean=sb$rmu[i]
prr$sd= sb$rsd[i]
pdat = u[,i]
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" ) )
}}
if ( vname=="q" ) {
if (is.null(fn)) fn=file.path(outdir, "q.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="normal"
prr$mean=sb$qmu[i]
prr$sd=sb$qsd[i]
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" )
)}}
if ( vname=="qc" ) {
if (is.null(fn)) fn=file.path(outdir, "qc.density.png" )
u = y[[vname]]
qc = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="cauchy"
prr$a = 0
prr$b = 0.1
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qc[2,i], " {", qc[1,i], ", ", qc[3,i], "} ", sep="" )
)}}
if ( vname=="qs" ) {
if (is.null(fn)) fn=file.path(outdir, "qs.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
for (i in 1:3) {
pdat = u[,i]
# prr=NULL
# prr$class="normal"
# prr$mean=sb$q0x[i]
# prr$sd=sb$q0x[i]*sb$cv
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n", legend=paste( aulabels[i], "\n", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "} ", sep="" )
)}}
if ( vname=="BMSY" ) {
if (is.null(fn)) fn=file.path(outdir, "BMSY.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="none"
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
if ( vname=="FMSY" ) {
if (is.null(fn)) fn=file.path(outdir, "FMSY.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class="none"
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
if ( vname=="bosd" ) {
if (is.null(fn)) fn=file.path(outdir, "bosd.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class='uniform'
prr$max=3
prr$min=0
#prr$class="lognormal"
#prr$meanlog=sb$bomup
#prr$sdlog=sqrt(sb$bosdp)
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
if ( vname=="bpsd" ) {
if (is.null(fn)) fn=file.path(outdir, "bpsd.density.png" )
u = y[[vname]]
qs = apply( u, 2, quantile, probs=c(0.025, 0.5, 0.975) )
qs = signif( qs, 3 )
for (i in 1:3) {
pdat = u[,i]
prr=NULL
prr$class='uniform'
prr$max=3
prr$min=0
#prr$class="lognormal"
#prr$meanlog=sb$bpmup
#prr$sdlog=sqrt(sb$bpsdp)
plot.freq.distribution.prior.posterior( prior=prr, posterior=pdat, ... )
legend( "topright", bty="n",
legend=paste( aulabels[i], " ", vname, " = ", qs[2,i], " {", qs[1,i], ", ", qs[3,i], "}", sep="" )
)}}
}
# --------------
if ( type=="timeseries" ) {
plot.new()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(4.4, 4.4, 0.65, 0.75))
if (vname=="biomass") {
if (is.null(fn)) fn=file.path(outdir, "biomass.timeseries.png" )
u = y[["B"]]
for (i in 1:3) {
meanval = apply( u[,1:sb$N,i], 2, mean, na.rm=T )
prs = seq( from=0.025, to=0.975, length.out=600)
Bq = apply( u[,1:sb$N,i], 2, quantile, probs=prs, na.rm=T )
#yran = range(c(0, Bq, sb$IOA[,i] ), na.rm=T )*1.01
yran = range(c(0, Bq ), na.rm=T )*1.01
plot( yrs0, Bq[1,], type="n", ylim=yran, xlim=range(yrs0), xlab="", ylab="" ) #change xlim to yrs0 to remove 3 yr projection
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
for ( j in 1:length(prs) ) {
lines ( yrs0, Bq[j,], lwd=4, col=cols2[j] )
}
# lines( yrs0, B, lwd=3, col="darkgreen" )
#abline (v=yrs.last , lwd=2, lty="dashed" ) #can comment out this line if not providing forward projection
if (i==2) title( ylab="Fishable biomass (kt)" )
if (i==3) title( xlab="Year" )
#points( yrs0, qIOA, pch=20, col="darkgreen" )
#lines ( yrs0, qIOA, lwd=3, col="darkgreen", lty="dashed" )
lines ( yrs0, meanval, lwd=2, col="blue", lty="dotted" )
#points( yrs0, IOA, pch=20, col="darkred" )
#lines( yrs0, IOA, lwd=3, lty="dotdash", col="red" )
# legend( "topright", bty="n", legend=aulabels[i])
}
}
if (vname=="rem") {
if (is.null(fn)) fn=file.path(outdir, "rem.timeseries.png" )
u = y[[vname]]
for (i in 1:3) {
meanval = apply( u[,,i], 2, mean, na.rm=T )
prs = seq( from=0.025, to=0.975, length.out=600)
Bq = apply( u[,,i], 2, quantile, probs=prs, na.rm=T )
#yran = range(c(0, Bq, sb$IOA[,i] ), na.rm=T )*1.01
yran = range(c(0, Bq ), na.rm=T )*1.01
plot( yrs, Bq[1,], type="n", ylim=yran, xlim=range(yrs0), xlab="", ylab="" ) #change xlim to yrs0 to remove 3 yr projection
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
for ( j in 1:length(prs) ) {
lines ( yrs, Bq[j,], lwd=4, col=cols2[j] )
}
# lines( yrs, rem, lwd=3, col="darkgreen" )
#abline (v=yrs.last , lwd=2, lty="dashed" ) #can comment out this line if not providing forward projection
if (i==2) title( ylab="Fishable biomass (kt)" )
if (i==3) title( xlab="Year" )
#points( yrs0, qIOA, pch=20, col="darkgreen" )
#lines ( yrs0, qIOA, lwd=3, col="darkgreen", lty="dashed" )
lines ( yrs, meanval, lwd=2, col="blue", lty="dotted" )
#points( yrs0, IOA, pch=20, col="darkred" )
#lines( yrs0, IOA, lwd=3, lty="dotdash", col="red" )
legend( "topright", bty="n", legend=aulabels[i])
}
}
if (vname=="fishingmortality") {
if (is.null(fn)) fn=file.path(outdir, "fishingmortality.timeseries.png" )
Fmsy = apply( y[["FMSY"]], 2, mean, na.rm=T )
prs = seq( from=0.025, to=0.975, length.out=600)
F = y[["F"]]
Fi = apply( F[, 1:sb$N, ] , c(2,3), quantile, probs=prs, na.rm=T )
for (i in 1:3) {
yran = range(c(0, max(c(Fi,Fmsy))), na.rm=T )*1.05
yran = pmin( yran, 1.2 )
plot( yrs0, Fi[1,,i], type="n", ylim=yran, xlab="", ylab="" )
cols = gray.colors( floor(length( prs)/2) )
cols2 = c(cols[length(cols):1], cols )
if (i %in% c(1,2)){
for ( j in 1:length(prs) ) {
lines ( yrs0, Fi[j,,i], lwd=4, col=cols2[j] )
}}
if (i==3){
for ( j in 1:length(prs) ) {
lines ( yrs0-0.2, Fi[j,,i], lwd=4, col=cols2[j] )
}}
if (i==2) title( ylab="Fishing mortality" )
if (i==3) title( xlab="Year" )
# legend( "topright", bty="n", legend=aulabels[i])
abline (h=-log(1-0.2), lwd=2, lty="dashed" )
abline (h=Fmsy[i], lwd=2, lty="solid", col="red" )
}
}
}
if (type=="hcr") {
if (vname=="default") {
if (is.null(fn)) fn=file.path(outdir, "hcr.default.png" )
B = apply( y[["B"]], c(2,3), median, na.rm=T )
F = apply( y[["F"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
for (i in 1:3 ) {
ylims = c(0, min( 1, max( FMSY[i] * 1.25, F[hdat,i] ) ) )
plot( B[hdat,i], F[hdat,i], type="b", xlim=c(0, K[i] * 1.1 ),
ylim=ylims, col="darkorange", cex=0.8, lwd=2, xlab="", ylab="", pch=20 )
# nn = as.matrix( cbind( Bx=as.vector( y$B[,ndata,i] ), Fx = as.vector( y$F[,ndata,i] ) ))
# ellipse.2d(nn[,1], nn[,2], pv=0.05, sc=30)
if (i==3) title( xlab="Fishable biomass (kt)" )
if (i==2) title( ylab="Fishing mortality" )
F30 = -log(1-0.3)
F10 = -log(1-0.1)
Fref = 0.22
Bmsy = K[i] * 0.5
Bref = K[i] * 0.2
BK = K[i]
BK25 = K[i] * .25
Fhistorical = mean( F[hdat,i], na.rm=T )
Bhistorical = mean( B[hdat,i], na.rm=T )
yl = 0.05
polygon(x=c(Bmsy,Bmsy*2,Bmsy*2, Bmsy),y=c(-0.08,-0.1,FMSY[i],FMSY[i]),col='lightgreen',border=NA)
polygon(x=c(Bmsy/2,Bmsy,Bmsy, Bmsy/2),y=c(-0.08,-0.1,FMSY[i],FMSY[i]),col='lightgoldenrod',border=NA)
polygon(x=c(0,Bmsy/2,Bmsy/2, 0),y=c(-0.08,-0.1,FMSY[i],FMSY[i]),col='darksalmon',border=NA)
#might need adjustment below to offset F vs B. Need to plot F against PREfishery biomass
lines( B[hdat,i], F[hdat,i], type="b", xlim=c(0, K[i] * 1.1 ),
ylim=ylims, col='blue', cex=0.8, lwd=2, xlab="", ylab="", pch=20 )
abline (h=Fref, lty="solid", col="gray", lwd=2 )
abline (h=F10, lty="dotted", col="gray")
# text( 0.05*K[i], F10, "10% HR", pos=1 )
abline (h=F30, lty="dotted", col="gray")
# text( 0.05*K[i], F30, "30% HR", pos=1 )
abline (h=FMSY[i], lty="dashed", col="red" )
# abline (h=Fhistorical, lty="dashed")
# text( 0.05*K[i], Fhistorical, "Mean", pos=1, lwd=2 )
# abline (v=Bref, lty="dotted")
# text( Bref-0.2, 0.25, "Lower biomass reference point\n (LBRP = 0.2 * BMSY)" , srt=90, pos=3)
abline (v=Bmsy, lty="dotted")
abline (v=BK, lty="dotted")
abline (v=BK25, lty="dotted")
text( Bmsy-0.01*K[i], yl, "K/2" , srt=90, pos=3)
text( BK-0.01*K[i], yl, "K" , srt=90, pos=3)
text( BK25-0.01*K[i], yl, "K/4" , srt=90, pos=3)
text( 0.05*K[i], Fref, "20% HR", pos=1 )
text( 0.05*K[i], FMSY[i], "FMSY", pos=3, lwd=2, col="red" )
if (i %in% c(1,2)){
text( B[1:(ndata-1),i], F[1:(ndata-1),i], labels=yrs0[-ndata], pos=3, cex= 0.8 )
points( B[ndata,i], F[ndata,i], pch=21, bg='darkorange', cex= 1.4 )
text( B[ndata,i], F[ndata,i], labels=yrs0[ndata], pos=3, cex= 1.4, font=2 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
}
if (i==3){
text( B[1:(ndata-1),i], F[1:(ndata-1),i], labels=(yrs0[-ndata]), pos=3, cex= 0.8 )
points( B[ndata,i], F[ndata,i], pch=21, bg='darkorange', cex= 1.4 )
text( B[ndata,i], F[ndata,i], labels=yrs0[ndata], pos=3, cex= 1.4, font=2 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
}
# abline (v=Bhistorical, lty="dashed")
# text( Bhistorical-0.01*K[i], yl, "Mean" , srt=90, pos=3, lwd=2)
}
#Enable below to see the annual F estimates for inclusion in the document
print("F for N-ENS" )
print(F[hdat,1] )
print("F for S-ENS" )
print(F[hdat,2] )
print("F for 4X" )
print(F[hdat,3] )
}
if (vname=="default.unmodelled") {
if (is.null(fn)) fn=file.path(outdir, "hcr.default.unmodelled.png" )
B = sb$IOA
F = apply( y[["F"]], c(2,3), median, na.rm=T )
areas = c("cfa4x", "cfasouth", "cfanorth" )
regions = c("4X", "S-ENS", "N-ENS")
td = exploitationrates(p=p, areas=areas, labels=regions, CFA4X.exclude.year.assessment=FALSE )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
for (i in 1:3 ) {
ylims = c(0, FMSY[i] * 1.25)
plot( B[hdat,i], F[hdat,i], type="b", xlim=c(0, K[i] * 1.1 ),
ylim=ylims, col="darkorange", cex=0.8, lwd=2, xlab="", ylab="", pch=20 )
# nn = as.matrix( cbind( Bx=as.vector( y$B[,ndata,i] ), Fx = as.vector( y$F[,ndata,i] ) ))
# ellipse.2d(nn[,1], nn[,2], pv=0.05, sc=30)
if (i==3) title( xlab="Fishable biomass (kt)" )
if (i==2) title( ylab="Fishing mortality" )
F30 = -log(1-0.3)
F10 = -log(1-0.1)
Fref = 0.22
Bmsy = BMSY[i]
Bref = K[i] * 0.2
BK = K[i]
BK25 = K[i] * .25
Fhistorical = mean( F[hdat,i], na.rm=T )
Bhistorical = mean( B[hdat,i], na.rm=T )
yl = 0.05
abline (h=Fref, lty="solid", col="gray", lwd=2 )
abline (h=F10, lty="dotted", col="gray")
# text( 0.05*K[i], F10, "10% HR", pos=1 )
abline (h=F30, lty="dotted", col="gray")
# text( 0.05*K[i], F30, "30% HR", pos=1 )
abline (h=FMSY[i], lty="dashed", col="red" )
# abline (h=Fhistorical, lty="dashed")
# text( 0.05*K[i], Fhistorical, "Mean", pos=1, lwd=2 )
# abline (v=Bref, lty="dotted")
# text( Bref-0.2, 0.25, "Lower biomass reference point\n (LBRP = 0.2 * BMSY)" , srt=90, pos=3)
abline (v=Bmsy, lty="dotted")
abline (v=BK, lty="dotted")
abline (v=BK25, lty="dotted")
text( 0.05*K[i], Fref, "20% HR", pos=1 )
text( 0.05*K[i], FMSY[i], "FMSY", pos=3, lwd=2, col="red" )
text( BK-0.01*K[i], yl, "K" , srt=90, pos=3)
text( Bmsy-0.01*K[i], yl, "K/2" , srt=90, pos=3)
text( BK25-0.01*K[i], yl, "K/4" , srt=90, pos=3)
text( B[hdat,i], F[hdat,i], labels=yrs0, pos=3, cex= 0.8 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
# abline (v=Bhistorical, lty="dashed")
# text( Bhistorical-0.01*K[i], yl, "Mean" , srt=90, pos=3, lwd=2)
}
}
if (vname=="simple") {
if (is.null(fn)) fn=file.path(outdir, "hcr.simple.png" )
require(car)
B = apply( y[["B"]], c(2,3), median, na.rm=T )
F = apply( y[["F"]], c(2,3), median, na.rm=T )
C = apply( y[["C"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
aulabels = c("N-ENS", "S-ENS", "4X")
for (i in 1:3 ) {
ylims = max(C[,i] )* c(0, 1.1)
plot( B[hdat,i], C[hdat,i], type="l", xlim=c(0, K[i]*1.05 ),
ylim=ylims, xlab="", ylab="", lwd=2, col="darkorange" )
abline(0,0.1, lty="dotted", lwd=2, col="gray" )
abline(0,0.2, lwd=3, col="gray" )
abline(0,0.3, lty="dotted", lwd=2, col="gray" )
points( B[hdat,i], C[hdat,i], col="orange", cex=0.8, pch=20 )
text( B[hdat,i], C[hdat,i], labels=yrs0, pos=3, cex= 0.85 )
text( 0, ylims[2]*0.9, labels=aulabels[i], pos=3, cex= 0.85 )
# nn = as.matrix( cbind( Bx=as.vector( y$B[,ndata,i] ), Fx = as.vector( y$F[,ndata,i] ) ))
# ellipse.2d(nn[,1], nn[,2], pv=0.05, sc=30)
if (i==3) title( xlab="Fishable biomass (kt)" )
if (i==2) title( ylab="Catch (kt)" )
Cmsy = ( exp( FMSY[i] ) - 1)
Cref = ( exp( FMSY[i] * 0.2 ) - 1) * K[i]
Bmsy = BMSY[i]
Bref = K[i] * 0.2
BK = K[i]
BK25 = K[i] * .25
# Chistorical = mean( C[hdat,i], na.rm=T )
# Bhistorical = mean( B[hdat,i], na.rm=T )
yl = 0.1 * max(C[hdat,i])
# abline (h=Fref, lty="dotted")
# text( 0.25, Fref, "Target\n (0.2 * FMSY) ", pos=1 )
abline (0, Cmsy, lty="dotted", col="red")
# text( 0.1*K[i], Cmsy, "FMSY", pos=1 )
# abline (h=Chistorical, lty="dashed")
# text( 0.1*K[i], Chistorical, "Mean", pos=3, lwd=2 )
# abline (v=Bref, lty="dotted")
# text( Bref-0.2, 0.25, "Lower biomass reference point\n (LBRP = 0.2 * BMSY)" , srt=90, pos=3)
abline (v=BK, lty="dotted")
text( BK-0.01*K[i], yl, "K" , srt=90, pos=3)
abline (v=BK/2, lty="dotted")
text( BK/2-0.01*K[i], yl, "K/2" , srt=90, pos=3)
abline (v=BK25, lty="dotted")
text( BK25-0.01*K[i], yl, "K/4" , srt=90, pos=3)
}
}
}
if (type=="diagnostic.catch") {
}
if (type=="diagnostic.phase") {
if (is.null(fn)) fn=file.path(outdir, "diagnostic.phase.png" )
B = apply( y[["B"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
for (i in 1:3 ) {
plot( B[1:ndata-1,i], B[2:ndata,i], type="b", xlab="t", ylab="t+1",
xlim=c(0, K[i] * 1.25 ), ylim=max(K[i] )* c(0, 1.25), lwd=2, col="darkorange" )
# abline(0,0.1, lty="dotted", lwd=2, col="gray" )
abline( coef=c(0,1) )
#text( B[1:ndata-1,], B[2:ndata,], labels=yrs4 , pos=4, cex=0.8 )
}
}
if (type=="diagnostic.errors") {
if (is.null(fn)) fn=file.path(outdir, "diagnostic.errors.png" )
# observation vs process error
graphics.off()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(5, 4, 0, 2))
require(car)
eP = y[["bpsd"]]
eO = y[["bosd"]]
for (i in 1:3 ) {
plot( eP[,,i], eO[,,i], type="p", pch=22 )
if (i==2) title( ylab="Process error (SD)" )
if (i==3) title( xlab="Observation error (SD)" )
}
}
if (type=="diagnostic.production") {
B = apply( y[["B"]], c(2,3), median, na.rm=T )
P = apply( y[["P"]], c(2,3), median, na.rm=T )
C = apply( y[["C"]], c(2,3), median, na.rm=T )
K = apply( y[["K"]], c(2), median, na.rm=T )
FMSY = apply( y[["FMSY"]], c(2), median, na.rm=T )
BMSY = apply( y[["BMSY"]], c(2), median, na.rm=T )
MSY = apply( y[["MSY"]], c(2), median, na.rm=T )
# production vs biomass
plot.new()
layout( matrix(c(1,2,3), 3, 1 ))
par(mar = c(5, 4, 0, 2))
for (i in 1:3) {
plot( B[,i], P[,i], type="n", pch=20, ylim=c(0, max( c(P[,i], MSY[i]))*1.1), xlim=c(0,K[i]*1.05), xlab="Biomass; kt", ylab="Yield; kt" )
a = MSY[i] / (BMSY[i])^2
curve( -a*(x-BMSY[i])^2 + MSY[i], from=0, to=K[i], add=TRUE, lwd=3, col="gray" )
abline(v=BMSY[i], lty="dotted", lwd=3, col="gray")
points( B[,i], P[,i], type="p", pch=20 )
text( B[,i], P[,i], yrs0, pos=3, cex=0.8 )
# abline(h=0)
}
}
if (is.null(fn)) fn=file.path(outdir, "diagnostic.production.png" )
if(save.plot) savePlot( filename=fn, type="png" )
return( fn)
}
}
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