inst/scripts/93.biomass_index_carstm_2022_variation3.r
In jae0/snowcrab: Snow crab assessment suite for aegis* and associated projects.
# -------------------------------------------------
# Snow crab --- Areal unit modelling Hurdle / Delta model
# combination of three models via posterior simulation
# 1. Poisson on positive valued numbers offset by swept are
# 2. Meansize in space and time
# 3 Presence-absence
# the convolution of all three after simulation is called a Hurdle or Delta model
# -------------------------------------------------
# this is copied from 03.biomass_index_carstm.r
# but stripped down with modifications for comparisons demanded by 2023 CSAS review
# this variation 3 is about removing spatial and spatiotemporal effects
# -------------------------------------------------
# Part 1 -- construct basic parameter list defining the main characteristics of the study
source( file.path( code_root, "bio_startup.R" ) )
require(bio.snowcrab) # loadfunctions("bio.snowcrab")
year.assessment = 2022
yrs = 1999:year.assessment
spec_bio = bio.taxonomy::taxonomy.recode( from="spec", to="parsimonious", tolookup=2526 )
snowcrab_filter_class = "fb" # fishable biomass (including soft-shelled ) "m.mat" "f.mat" "imm"
# key name
runlabel= paste( "1999_2022_variation3", snowcrab_filter_class, sep="_" )
# params for number
pN = snowcrab_parameters(
project_class="carstm",
yrs=yrs,
areal_units_type="tesselation",
family = "nbinomial",
carstm_modelengine = "inla.reduced3",
carstm_model_label= runlabel,
selection = list(
type = "number",
biologicals=list( spec_bio=spec_bio ),
biologicals_using_snowcrab_filter_class=snowcrab_filter_class
)
)
# params for mean size .. mostly the same as pN
pW = snowcrab_parameters(
project_class="carstm",
yrs=yrs,
areal_units_type="tesselation",
family = "gaussian",
carstm_modelengine = "inla.reduced3",
carstm_model_label= runlabel,
selection = list(
type = "meansize",
biologicals=list( spec_bio=spec_bio ),
biologicals_using_snowcrab_filter_class=snowcrab_filter_class
)
)
# params for probability of observation
pH = snowcrab_parameters(
project_class="carstm",
yrs=yrs,
areal_units_type="tesselation",
family = "binomial", # "binomial", # "nbinomial", "betabinomial", "zeroinflatedbinomial0" , "zeroinflatednbinomial0"
carstm_modelengine = "inla.reduced3",
carstm_model_label= runlabel,
selection = list(
type = "presence_absence",
biologicals=list( spec_bio=spec_bio ),
biologicals_using_snowcrab_filter_class=snowcrab_filter_class
)
)
# use what was defined in the main script
sppoly=areal_units( p=pN )
additional_features = snowcrab_mapping_features(pN) # for mapping below
tmap_mode("plot")
# ------------------------------------------------
# Part 2 -- spatiotemporal statistical model
if ( spatiotemporal_model ) {
# total numbers
sppoly = areal_units( p=pN )
M = snowcrab.db( p=pN, DS="carstm_inputs", sppoly=sppoly ) # will redo if not found
# can just copy datafile: carstm_inputs_snowcrab~tesselation~1~snowcrab~24~1~none~snowcrab_managementareas.rdata
# into working directory to speed things up
io = which(M$tag=="observations")
ip = which(M$tag=="predictions")
iq = unique( c( which( M$totno > 0), ip ) )
iw = unique( c( which( M$totno > 5), ip ) ) # need a good sample to estimate mean size
# number
fit = NULL; gc()
fit = carstm_model( p=pN, data=M[ iq, ], sppoly=sppoly,
posterior_simulations_to_retain="predictions", improve.hyperparam.estimates=TRUE
)
# mean size
fit = NULL; gc()
fit = carstm_model( p=pW, data=M[ iw, ], sppoly = sppoly,
posterior_simulations_to_retain="predictions", improve.hyperparam.estimates=TRUE,
control.inla = list( strategy="laplace", int.strategy="eb" )
)
# model pa using all data
fit = NULL; gc()
fit = carstm_model( p=pH, data=M, sppoly=sppoly,
posterior_simulations_to_retain="predictions", improve.hyperparam.estimates=TRUE,
# control.family=list(control.link=list(model="logit")), # default
control.inla = list( strategy="laplace", int.strategy="eb" )
)
for ( selection in c("number", "meansize", "presence_absence") ) {
# map all :
if ( selection=="number" ) {
p=pN
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
outputdir = file.path( p$modeldir, p$carstm_model_label, "predicted.numerical.densities" )
ylab = "Number"
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
fn_root_prefix = "Predicted_numerical_abundance"
fn_root = "Predicted_numerical_abundance_persistent_spatial_effect"
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
title= paste( snowcrab_filter_class, "Number; no./m^2" )
}
if ( selection=="meansize") {
p=pW
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
ylab = "Mean weight"
outputdir = file.path( p$modeldir, p$carstm_model_label, "predicted.meansize" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
fn_root_prefix = "Predicted_meansize"
fn_root = "Predicted_meansize_persistent_spatial_effect"
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
title= paste( snowcrab_filter_class, "Mean weight; kg" )
}
if ( selection=="presence_absence" ) {
p=pH
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
ylab = "Probability"
outputdir = file.path( p$modeldir, p$carstm_model_label, "predicted.presence_absence" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
fn_root_prefix = "Predicted_presence_absence"
fn_root = "Predicted_presence_absence_persistent_spatial_effect"
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
title= paste( snowcrab_filter_class, "Probability")
}
if (0) {
# choose:
# p = pN
# p = pW
# p = pH
# extract results
fit = carstm_model( p=p, DS="carstm_modelled_fit", sppoly = sppoly ) # extract currently saved model fit
fit$summary$dic$dic
fit$summary$dic$p.eff
plot(fit)
plot(fit, plot.prior=TRUE, plot.hyperparameters=TRUE, plot.fixed.effects=FALSE )
plot( fit, plot.prior=TRUE, plot.hyperparameters=TRUE, plot.fixed.effects=FALSE )
plot( fit$marginals.hyperpar$"Phi for space_time", type="l") # posterior distribution of phi nonspatial dominates
plot( fit$marginals.hyperpar$"Precision for space_time", type="l")
plot( fit$marginals.hyperpar$"Precision for setno", type="l")
fit = NULL
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
# quick plots
vn=c( "random", "space", "combined" )
vn=c( "random", "spacetime", "combined" )
vn="predictions" # numerical density (km^-2)
tmatch= as.character(year.assessment)
carstm_map( res=res, vn=vn, tmatch=tmatch,
sppoly = sppoly,
palette="-RdYlBu",
plot_elements=c( "compass", "scale_bar", "legend" ),
additional_features=additional_features,
title =paste( vn, paste0(tmatch, collapse="-"), "no/m^2" )
)
}
vn="predictions"
toplot = carstm_results_unpack( res, vn )
brks = pretty( quantile(toplot[,,"mean"], probs=c(0,0.975), na.rm=TRUE ) )
for (y in res$time ){
tmatch = as.character(y)
fn_root = paste(fn_root_prefix, paste0(tmatch, collapse="-"), sep="_")
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
plt = carstm_map( res=res, vn=vn, tmatch=tmatch,
sppoly = sppoly,
breaks =brks,
palette="-RdYlBu",
plot_elements="",
# plot_elements=c( "compass", "scale_bar", "legend" ),
additional_features=additional_features,
title = tmatch,
# title=paste(fn_root_prefix, snowcrab_filter_class, paste0(tmatch, collapse="-") )
outfilename=outfilename
)
plt
print(outfilename)
}
# plots with 95% PI
oeffdir = file.path( outputdir, fn_root_prefix, "effects" )
if ( !file.exists(oeffdir)) dir.create( oeffdir, recursive=TRUE, showWarnings=FALSE )
(fn = file.path( oeffdir, "time.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "time" ),
type="b", xlab="Year", ylab=ylab, h=0, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "cyclic.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "cyclic" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5,
xlab="Season", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "temperature.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(t, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="Bottom temperature (degrees Celsius)", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "pca1.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(pca1, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="PCA1", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "pca2.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(pca2, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="PCA2", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "depth.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(z, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="Depth (m)", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
# (fn = file.path( outputdir, "substrate.png"))
# png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
# carstm_plotxy( res, vn=c( "res", "random", "inla.group(substrate.grainsize, method = \"quantile\", n = 11)" ),
# type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
# xlab="Substrate grain size (mm)", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
# dev.off()
if (0) {
fit = carstm_model( p=pW, DS="carstm_modelled_fit", sppoly = sppoly ) # to load currently saved results
plot( fit, plot.prior=TRUE, plot.hyperparameters=TRUE, plot.fixed.effects=FALSE )
plot( fit$marginals.hyperpar$"Phi for space_time", type="l") # posterior distribution of phi nonspatial dominates
plot( fit$marginals.hyperpar$"Precision for space_time", type="l")
plot( fit$marginals.hyperpar$"Precision for setno", type="l")
}
}
} #end each seletion
} # end spatiotemporal model
# ----------------------
# Part 3: assimilation of models
assimilate_numbers_and_size = TRUE
if (assimilate_numbers_and_size ) {
# wgts_max = 1.1 # kg, hard upper limit
# N_max = NULL
# # quantile( M$totno[ipositive]/M$data_offset[ipositive], probs=0.95, na.rm=TRUE )
# posterior sims
sims = carstm_posterior_simulations( pN=pN, pW=pW, pH=pH, pa_threshold=0.05, qmax=0.99 )
sims = sims / 10^6 # 10^6 kg -> kt;; kt/km^2
SM = aggregate_simulations(
sims=sims,
sppoly=sppoly,
fn=carstm_filenames( pN, returnvalue="filename", fn="aggregated_timeseries" ),
yrs=pN$yrs,
method="sum",
redo=TRUE
)
if (0) {
# to compute habitat prob
sims = carstm_posterior_simulations( pH=pH, pa_threshold=0.05, qmax=0.99 )
SM = aggregate_simulations(
sims=sims,
sppoly=sppoly,
fn=carstm_filenames( pN, returnvalue="filename", fn="aggregated_timeseries" ),
yrs=pN$yrs,
method="mean",
redo=TRUE
)
outputdir = file.path( carstm_filenames( pN, returnvalue="output_directory"), "aggregated_habitat_timeseries" )
RES= SM$RES
}
RES= SM$RES
# RES = aggregate_simulations( fn=carstm_filenames( pN, returnvalue="filename", fn="aggregated_timeseries" ) )$RES
# note: using pN, even though this is biomass
outputdir = file.path( carstm_filenames( pN, returnvalue="output_directory"), "aggregated_biomass_timeseries" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
( fn = file.path( outputdir, "cfa_all.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfaall ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfaall_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfaall_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
( fn = file.path( outputdir, "cfa_south.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfasouth ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfasouth_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfasouth_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
( fn = file.path( outputdir, "cfa_north.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfanorth ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfanorth_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfanorth_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
( fn = file.path( outputdir, "cfa_4x.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfa4x ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfa4x_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfa4x_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
regions = c("cfanorth", "cfasouth", "cfa4x" )
region_label = c("N-ENS", "S-ENS", "4X")
a= cbind( "cfanorth", RES[,c("yrs", "cfanorth", "cfanorth_lb", "cfanorth_ub")] )
b= cbind( "cfasouth", RES[,c("yrs", "cfasouth", "cfasouth_lb", "cfasouth_ub")] )
c= cbind( "cfa4x", RES[,c("yrs", "cfa4x", "cfa4x_lb", "cfa4x_ub")] )
names(a) = names(b) = names(c) = c("region", "year", "mean", "lb", "ub")
tdb = rbind(a, b, c)
tdb$region = factor(tdb$region, levels=regions, labels =region_label)
tdb = tdb[(which(!is.na(tdb$region))), ]
fn = file.path( outputdir, "biomass_M0.png" )
require(ggplot2)
library(ggbreak)
color_map = c("#E69F00", "#56B4E9", "#CC79A7" )
out = ggplot(tdb, aes(x=year, y=mean, fill=region, colour=region)) +
geom_line( alpha=0.9, linewidth=1.2 ) +
geom_point(aes(shape=region), size=3, alpha=0.7 ) +
geom_errorbar(aes(ymin=lb,ymax=ub), linewidth=0.8, alpha=0.8, width=0.3) +
labs(x=NULL, y=NULL) +
# labs(x="Year", y="Biomass index (kt)", size = rel(1.5)) +
scale_colour_manual(values=color_map) +
scale_fill_manual(values=color_map) +
scale_shape_manual(values = c(15, 17, 19)) +
theme_light( base_size = 22) +
theme( legend.position=c(0.75, 0.9), legend.title=element_blank()) +
scale_y_break(c(14, 28), scales = 1)
# scale_y_continuous( limits=c(0, 300) )
ggsave(filename=fn, plot=out, device="png", width=12, height = 8)
# map it ..mean density
sppoly = areal_units( p=pN ) # to reload
vn = paste("biomass", "predicted", sep=".")
outputdir = file.path( carstm_filenames( pN, returnvalue="output_directory"), "predicted_biomass_densitites" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
B = apply( sims, c(1,2), mean )
B[ which(!is.finite(B)) ] = NA
brks = pretty( log10( quantile( B[], probs=c(0.05, 0.95), na.rm=TRUE )* 10^6) )
additional_features = snowcrab_mapping_features(pN) # for mapping below
for (i in 1:length(pN$yrs) ) {
y = as.character( pN$yrs[i] )
sppoly[,vn] = log10( B[,y]* 10^6 )
outfilename = file.path( outputdir , paste( "biomass", y, "png", sep=".") )
plt = carstm_map( sppoly=sppoly, vn=vn,
breaks=brks,
additional_features=additional_features,
title=y,
# title=paste( "log_10( Predicted biomass density; kg/km^2 )", y ),
palette="-RdYlBu",
plot_elements=c( "compass", "scale_bar", "legend" ),
outfilename=outfilename
)
plt
}
} # end assimilate size and numbers
# prep data for discrete version
# Rdata files are ready load them through julia and model
# fishery_model_data_inputs( year.assessment=year.assessment, type="biomass_dynamics", for_julia=TRUE )
## Plot maps of residuals of numbers per set obs vs pred
#To add a title to any carstm_map, please see below example
#carstm_map( res=res, vn=vn, main=list(label="my plot title", cex=2) )
# -------------------------------------------------
# Part 1 -- construct basic parameter list defining the main characteristics of the study
# require(aegis)
p = pN # bio.snowcrab::snowcrab_parameters( project_class="carstm", yrs=1999:year.assessment )
outputdir = file.path( p$modeldir, p$carstm_model_label, "residuals" )
# extract results and examine
fit = carstm_model( p=p, DS="carstm_modelled_fit" ) # extract currently saved model fit
summary(fit)
res = carstm_model( p=p, DS="carstm_modelled_summary" )
# prediction surface
crs_lonlat = st_crs(projection_proj4string("lonlat_wgs84"))
sppoly = areal_units( p=p ) # will redo if not found
sppoly = st_transform(sppoly, crs=crs_lonlat )
# do this immediately to reduce storage for sppoly (before adding other variables)
M = snowcrab.db( p=p, DS="biological_data" ) # will redo if not found .. not used here but used for data matching/lookup in other aegis projects that use bathymetry
M$tiyr=lubridate::decimal_date(M$timestamp)
# M$totno = M$totno_adjusted / M$cf_set_no # convert density to counts
# M$totwgt = M$totwgt_adjusted / M$cf_set_mass # convert density to total wgt
# M$data_offset = 1 / M$cf_set_no ## offset only used in poisson model
# reduce size
M = M[ which( M$lon > p$corners$lon[1] & M$lon < p$corners$lon[2] & M$lat > p$corners$lat[1] & M$lat < p$corners$lat[2] ), ]
# levelplot(z.mean~plon+plat, data=M, aspect="iso")
M$AUID = st_points_in_polygons(
pts = st_as_sf( M, coords=c("lon","lat"), crs=crs_lonlat ),
polys = sppoly[, "AUID"],
varname="AUID"
)
M = M[!is.na(M$AUID),]
names(M)[which(names(M)=="yr") ] = "year"
# M = M[ which(M$year %in% p$yrs), ]
# M$tiyr = lubridate::decimal_date ( M$timestamp )
# M$dyear = M$tiyr - M$year
MM = res$M
obsMM = MM[MM$tag=="observations",]
plocs = MM[MM$tag=="predictions",]
obs = M
if (p$variabletomodel=="totno") {
obs$density = obs$totno / obs$data_offset
rr = as.data.frame.table(res$totno.predicted)
}
if (p$variabletomodel=="totwgt") {
obs$density = obs$totwgt / obs$data_offset
rr = as.data.frame.table(res$totwgt.predicted)
}
rr$AUID = as.character( rr$AUID)
region.id = slot(sppoly, "region.id" )
rr$space = match( rr$AUID, region.id )
rr$AUID = rr$space
rr$year = as.numeric( as.character( rr$year) )
obs = merge( obs, rr, by=c("year", "AUID"), all.x=TRUE, all.y=FALSE )
obs$Freq[ !is.finite(obs$Freq) ] = 0
obs$resid = obs$Freq - obs$density
obs$resid_per_set = obs$resid * obs$data_offset
obs$yr = obs$year
vn = "resid"
vn = "resid_per_set"
#er = range( obs[,vn], na.rm=T) * c(0.95, 1.05)
er = c(-100, 100)
resol = p$pres
B = bathymetry_db(p=p, DS="baseline") # 1 km (p$pres )
for ( y in 2000:2018 ) {
ii = which( obs$yr==y & is.finite(obs[,vn] ))
if ( length(ii) > 3 ) {
dir.create( file.path( outputdir, "residuals", p$carstm_model_label), recursive=TRUE, showWarnings =FALSE)
fn = file.path( outputdir, "residuals", p$carstm_model_label, paste( "residuals", y, "png", sep=".") )
png( filename=fn, width=3072, height=2304, pointsize=40, res=300 )
lp = map_simple( toplot=obs[ ii, c("plon","plat", vn) ], plotarea=B, resol=1, theta=15, filterdistances=7.5, vn=vn, annot=paste("Residuals", y), er=er )
print(lp)
dev.off()
print(fn)
}
}
# end
jae0/snowcrab documentation built on Feb. 27, 2024, 2:42 p.m.
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# -------------------------------------------------
# Snow crab --- Areal unit modelling Hurdle / Delta model
# combination of three models via posterior simulation
# 1. Poisson on positive valued numbers offset by swept are
# 2. Meansize in space and time
# 3 Presence-absence
# the convolution of all three after simulation is called a Hurdle or Delta model
# -------------------------------------------------
# this is copied from 03.biomass_index_carstm.r
# but stripped down with modifications for comparisons demanded by 2023 CSAS review
# this variation 3 is about removing spatial and spatiotemporal effects
# -------------------------------------------------
# Part 1 -- construct basic parameter list defining the main characteristics of the study
source( file.path( code_root, "bio_startup.R" ) )
require(bio.snowcrab) # loadfunctions("bio.snowcrab")
year.assessment = 2022
yrs = 1999:year.assessment
spec_bio = bio.taxonomy::taxonomy.recode( from="spec", to="parsimonious", tolookup=2526 )
snowcrab_filter_class = "fb" # fishable biomass (including soft-shelled ) "m.mat" "f.mat" "imm"
# key name
runlabel= paste( "1999_2022_variation3", snowcrab_filter_class, sep="_" )
# params for number
pN = snowcrab_parameters(
project_class="carstm",
yrs=yrs,
areal_units_type="tesselation",
family = "nbinomial",
carstm_modelengine = "inla.reduced3",
carstm_model_label= runlabel,
selection = list(
type = "number",
biologicals=list( spec_bio=spec_bio ),
biologicals_using_snowcrab_filter_class=snowcrab_filter_class
)
)
# params for mean size .. mostly the same as pN
pW = snowcrab_parameters(
project_class="carstm",
yrs=yrs,
areal_units_type="tesselation",
family = "gaussian",
carstm_modelengine = "inla.reduced3",
carstm_model_label= runlabel,
selection = list(
type = "meansize",
biologicals=list( spec_bio=spec_bio ),
biologicals_using_snowcrab_filter_class=snowcrab_filter_class
)
)
# params for probability of observation
pH = snowcrab_parameters(
project_class="carstm",
yrs=yrs,
areal_units_type="tesselation",
family = "binomial", # "binomial", # "nbinomial", "betabinomial", "zeroinflatedbinomial0" , "zeroinflatednbinomial0"
carstm_modelengine = "inla.reduced3",
carstm_model_label= runlabel,
selection = list(
type = "presence_absence",
biologicals=list( spec_bio=spec_bio ),
biologicals_using_snowcrab_filter_class=snowcrab_filter_class
)
)
# use what was defined in the main script
sppoly=areal_units( p=pN )
additional_features = snowcrab_mapping_features(pN) # for mapping below
tmap_mode("plot")
# ------------------------------------------------
# Part 2 -- spatiotemporal statistical model
if ( spatiotemporal_model ) {
# total numbers
sppoly = areal_units( p=pN )
M = snowcrab.db( p=pN, DS="carstm_inputs", sppoly=sppoly ) # will redo if not found
# can just copy datafile: carstm_inputs_snowcrab~tesselation~1~snowcrab~24~1~none~snowcrab_managementareas.rdata
# into working directory to speed things up
io = which(M$tag=="observations")
ip = which(M$tag=="predictions")
iq = unique( c( which( M$totno > 0), ip ) )
iw = unique( c( which( M$totno > 5), ip ) ) # need a good sample to estimate mean size
# number
fit = NULL; gc()
fit = carstm_model( p=pN, data=M[ iq, ], sppoly=sppoly,
posterior_simulations_to_retain="predictions", improve.hyperparam.estimates=TRUE
)
# mean size
fit = NULL; gc()
fit = carstm_model( p=pW, data=M[ iw, ], sppoly = sppoly,
posterior_simulations_to_retain="predictions", improve.hyperparam.estimates=TRUE,
control.inla = list( strategy="laplace", int.strategy="eb" )
)
# model pa using all data
fit = NULL; gc()
fit = carstm_model( p=pH, data=M, sppoly=sppoly,
posterior_simulations_to_retain="predictions", improve.hyperparam.estimates=TRUE,
# control.family=list(control.link=list(model="logit")), # default
control.inla = list( strategy="laplace", int.strategy="eb" )
)
for ( selection in c("number", "meansize", "presence_absence") ) {
# map all :
if ( selection=="number" ) {
p=pN
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
outputdir = file.path( p$modeldir, p$carstm_model_label, "predicted.numerical.densities" )
ylab = "Number"
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
fn_root_prefix = "Predicted_numerical_abundance"
fn_root = "Predicted_numerical_abundance_persistent_spatial_effect"
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
title= paste( snowcrab_filter_class, "Number; no./m^2" )
}
if ( selection=="meansize") {
p=pW
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
ylab = "Mean weight"
outputdir = file.path( p$modeldir, p$carstm_model_label, "predicted.meansize" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
fn_root_prefix = "Predicted_meansize"
fn_root = "Predicted_meansize_persistent_spatial_effect"
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
title= paste( snowcrab_filter_class, "Mean weight; kg" )
}
if ( selection=="presence_absence" ) {
p=pH
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
ylab = "Probability"
outputdir = file.path( p$modeldir, p$carstm_model_label, "predicted.presence_absence" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
fn_root_prefix = "Predicted_presence_absence"
fn_root = "Predicted_presence_absence_persistent_spatial_effect"
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
title= paste( snowcrab_filter_class, "Probability")
}
if (0) {
# choose:
# p = pN
# p = pW
# p = pH
# extract results
fit = carstm_model( p=p, DS="carstm_modelled_fit", sppoly = sppoly ) # extract currently saved model fit
fit$summary$dic$dic
fit$summary$dic$p.eff
plot(fit)
plot(fit, plot.prior=TRUE, plot.hyperparameters=TRUE, plot.fixed.effects=FALSE )
plot( fit, plot.prior=TRUE, plot.hyperparameters=TRUE, plot.fixed.effects=FALSE )
plot( fit$marginals.hyperpar$"Phi for space_time", type="l") # posterior distribution of phi nonspatial dominates
plot( fit$marginals.hyperpar$"Precision for space_time", type="l")
plot( fit$marginals.hyperpar$"Precision for setno", type="l")
fit = NULL
res = carstm_model( p=p, DS="carstm_modelled_summary", sppoly = sppoly ) # to load currently saved results
# quick plots
vn=c( "random", "space", "combined" )
vn=c( "random", "spacetime", "combined" )
vn="predictions" # numerical density (km^-2)
tmatch= as.character(year.assessment)
carstm_map( res=res, vn=vn, tmatch=tmatch,
sppoly = sppoly,
palette="-RdYlBu",
plot_elements=c( "compass", "scale_bar", "legend" ),
additional_features=additional_features,
title =paste( vn, paste0(tmatch, collapse="-"), "no/m^2" )
)
}
vn="predictions"
toplot = carstm_results_unpack( res, vn )
brks = pretty( quantile(toplot[,,"mean"], probs=c(0,0.975), na.rm=TRUE ) )
for (y in res$time ){
tmatch = as.character(y)
fn_root = paste(fn_root_prefix, paste0(tmatch, collapse="-"), sep="_")
outfilename = file.path( outputdir, paste(fn_root, "png", sep=".") )
plt = carstm_map( res=res, vn=vn, tmatch=tmatch,
sppoly = sppoly,
breaks =brks,
palette="-RdYlBu",
plot_elements="",
# plot_elements=c( "compass", "scale_bar", "legend" ),
additional_features=additional_features,
title = tmatch,
# title=paste(fn_root_prefix, snowcrab_filter_class, paste0(tmatch, collapse="-") )
outfilename=outfilename
)
plt
print(outfilename)
}
# plots with 95% PI
oeffdir = file.path( outputdir, fn_root_prefix, "effects" )
if ( !file.exists(oeffdir)) dir.create( oeffdir, recursive=TRUE, showWarnings=FALSE )
(fn = file.path( oeffdir, "time.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "time" ),
type="b", xlab="Year", ylab=ylab, h=0, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "cyclic.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "cyclic" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5,
xlab="Season", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "temperature.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(t, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="Bottom temperature (degrees Celsius)", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "pca1.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(pca1, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="PCA1", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "pca2.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(pca2, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="PCA2", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
(fn = file.path( oeffdir, "depth.png"))
png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
carstm_plotxy( res, vn=c( "res", "random", "inla.group(z, method = \"quantile\", n = 11)" ),
type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
xlab="Depth (m)", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
dev.off()
# (fn = file.path( outputdir, "substrate.png"))
# png( filename=fn, width=1024, height=1024, pointsize=12, res=196 )
# carstm_plotxy( res, vn=c( "res", "random", "inla.group(substrate.grainsize, method = \"quantile\", n = 11)" ),
# type="b", col="slategray", pch=19, lty=1, lwd=2.5 ,
# xlab="Substrate grain size (mm)", ylab=ylab, cex=1.25, cex.axis=1.25, cex.lab=1.25 )
# dev.off()
if (0) {
fit = carstm_model( p=pW, DS="carstm_modelled_fit", sppoly = sppoly ) # to load currently saved results
plot( fit, plot.prior=TRUE, plot.hyperparameters=TRUE, plot.fixed.effects=FALSE )
plot( fit$marginals.hyperpar$"Phi for space_time", type="l") # posterior distribution of phi nonspatial dominates
plot( fit$marginals.hyperpar$"Precision for space_time", type="l")
plot( fit$marginals.hyperpar$"Precision for setno", type="l")
}
}
} #end each seletion
} # end spatiotemporal model
# ----------------------
# Part 3: assimilation of models
assimilate_numbers_and_size = TRUE
if (assimilate_numbers_and_size ) {
# wgts_max = 1.1 # kg, hard upper limit
# N_max = NULL
# # quantile( M$totno[ipositive]/M$data_offset[ipositive], probs=0.95, na.rm=TRUE )
# posterior sims
sims = carstm_posterior_simulations( pN=pN, pW=pW, pH=pH, pa_threshold=0.05, qmax=0.99 )
sims = sims / 10^6 # 10^6 kg -> kt;; kt/km^2
SM = aggregate_simulations(
sims=sims,
sppoly=sppoly,
fn=carstm_filenames( pN, returnvalue="filename", fn="aggregated_timeseries" ),
yrs=pN$yrs,
method="sum",
redo=TRUE
)
if (0) {
# to compute habitat prob
sims = carstm_posterior_simulations( pH=pH, pa_threshold=0.05, qmax=0.99 )
SM = aggregate_simulations(
sims=sims,
sppoly=sppoly,
fn=carstm_filenames( pN, returnvalue="filename", fn="aggregated_timeseries" ),
yrs=pN$yrs,
method="mean",
redo=TRUE
)
outputdir = file.path( carstm_filenames( pN, returnvalue="output_directory"), "aggregated_habitat_timeseries" )
RES= SM$RES
}
RES= SM$RES
# RES = aggregate_simulations( fn=carstm_filenames( pN, returnvalue="filename", fn="aggregated_timeseries" ) )$RES
# note: using pN, even though this is biomass
outputdir = file.path( carstm_filenames( pN, returnvalue="output_directory"), "aggregated_biomass_timeseries" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
( fn = file.path( outputdir, "cfa_all.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfaall ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfaall_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfaall_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
( fn = file.path( outputdir, "cfa_south.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfasouth ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfasouth_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfasouth_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
( fn = file.path( outputdir, "cfa_north.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfanorth ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfanorth_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfanorth_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
( fn = file.path( outputdir, "cfa_4x.png") )
png( filename=fn, width=3072, height=2304, pointsize=12, res=300 )
plot( cfa4x ~ yrs, data=RES, lty="solid", lwd=4, pch=20, col="slateblue", type="b", ylab="Biomass index (kt)", xlab="")
lines( cfa4x_lb ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
lines( cfa4x_ub ~ yrs, data=RES, lty="dotted", lwd=2, col="slategray" )
dev.off()
regions = c("cfanorth", "cfasouth", "cfa4x" )
region_label = c("N-ENS", "S-ENS", "4X")
a= cbind( "cfanorth", RES[,c("yrs", "cfanorth", "cfanorth_lb", "cfanorth_ub")] )
b= cbind( "cfasouth", RES[,c("yrs", "cfasouth", "cfasouth_lb", "cfasouth_ub")] )
c= cbind( "cfa4x", RES[,c("yrs", "cfa4x", "cfa4x_lb", "cfa4x_ub")] )
names(a) = names(b) = names(c) = c("region", "year", "mean", "lb", "ub")
tdb = rbind(a, b, c)
tdb$region = factor(tdb$region, levels=regions, labels =region_label)
tdb = tdb[(which(!is.na(tdb$region))), ]
fn = file.path( outputdir, "biomass_M0.png" )
require(ggplot2)
library(ggbreak)
color_map = c("#E69F00", "#56B4E9", "#CC79A7" )
out = ggplot(tdb, aes(x=year, y=mean, fill=region, colour=region)) +
geom_line( alpha=0.9, linewidth=1.2 ) +
geom_point(aes(shape=region), size=3, alpha=0.7 ) +
geom_errorbar(aes(ymin=lb,ymax=ub), linewidth=0.8, alpha=0.8, width=0.3) +
labs(x=NULL, y=NULL) +
# labs(x="Year", y="Biomass index (kt)", size = rel(1.5)) +
scale_colour_manual(values=color_map) +
scale_fill_manual(values=color_map) +
scale_shape_manual(values = c(15, 17, 19)) +
theme_light( base_size = 22) +
theme( legend.position=c(0.75, 0.9), legend.title=element_blank()) +
scale_y_break(c(14, 28), scales = 1)
# scale_y_continuous( limits=c(0, 300) )
ggsave(filename=fn, plot=out, device="png", width=12, height = 8)
# map it ..mean density
sppoly = areal_units( p=pN ) # to reload
vn = paste("biomass", "predicted", sep=".")
outputdir = file.path( carstm_filenames( pN, returnvalue="output_directory"), "predicted_biomass_densitites" )
if ( !file.exists(outputdir)) dir.create( outputdir, recursive=TRUE, showWarnings=FALSE )
B = apply( sims, c(1,2), mean )
B[ which(!is.finite(B)) ] = NA
brks = pretty( log10( quantile( B[], probs=c(0.05, 0.95), na.rm=TRUE )* 10^6) )
additional_features = snowcrab_mapping_features(pN) # for mapping below
for (i in 1:length(pN$yrs) ) {
y = as.character( pN$yrs[i] )
sppoly[,vn] = log10( B[,y]* 10^6 )
outfilename = file.path( outputdir , paste( "biomass", y, "png", sep=".") )
plt = carstm_map( sppoly=sppoly, vn=vn,
breaks=brks,
additional_features=additional_features,
title=y,
# title=paste( "log_10( Predicted biomass density; kg/km^2 )", y ),
palette="-RdYlBu",
plot_elements=c( "compass", "scale_bar", "legend" ),
outfilename=outfilename
)
plt
}
} # end assimilate size and numbers
# prep data for discrete version
# Rdata files are ready load them through julia and model
# fishery_model_data_inputs( year.assessment=year.assessment, type="biomass_dynamics", for_julia=TRUE )
## Plot maps of residuals of numbers per set obs vs pred
#To add a title to any carstm_map, please see below example
#carstm_map( res=res, vn=vn, main=list(label="my plot title", cex=2) )
# -------------------------------------------------
# Part 1 -- construct basic parameter list defining the main characteristics of the study
# require(aegis)
p = pN # bio.snowcrab::snowcrab_parameters( project_class="carstm", yrs=1999:year.assessment )
outputdir = file.path( p$modeldir, p$carstm_model_label, "residuals" )
# extract results and examine
fit = carstm_model( p=p, DS="carstm_modelled_fit" ) # extract currently saved model fit
summary(fit)
res = carstm_model( p=p, DS="carstm_modelled_summary" )
# prediction surface
crs_lonlat = st_crs(projection_proj4string("lonlat_wgs84"))
sppoly = areal_units( p=p ) # will redo if not found
sppoly = st_transform(sppoly, crs=crs_lonlat )
# do this immediately to reduce storage for sppoly (before adding other variables)
M = snowcrab.db( p=p, DS="biological_data" ) # will redo if not found .. not used here but used for data matching/lookup in other aegis projects that use bathymetry
M$tiyr=lubridate::decimal_date(M$timestamp)
# M$totno = M$totno_adjusted / M$cf_set_no # convert density to counts
# M$totwgt = M$totwgt_adjusted / M$cf_set_mass # convert density to total wgt
# M$data_offset = 1 / M$cf_set_no ## offset only used in poisson model
# reduce size
M = M[ which( M$lon > p$corners$lon[1] & M$lon < p$corners$lon[2] & M$lat > p$corners$lat[1] & M$lat < p$corners$lat[2] ), ]
# levelplot(z.mean~plon+plat, data=M, aspect="iso")
M$AUID = st_points_in_polygons(
pts = st_as_sf( M, coords=c("lon","lat"), crs=crs_lonlat ),
polys = sppoly[, "AUID"],
varname="AUID"
)
M = M[!is.na(M$AUID),]
names(M)[which(names(M)=="yr") ] = "year"
# M = M[ which(M$year %in% p$yrs), ]
# M$tiyr = lubridate::decimal_date ( M$timestamp )
# M$dyear = M$tiyr - M$year
MM = res$M
obsMM = MM[MM$tag=="observations",]
plocs = MM[MM$tag=="predictions",]
obs = M
if (p$variabletomodel=="totno") {
obs$density = obs$totno / obs$data_offset
rr = as.data.frame.table(res$totno.predicted)
}
if (p$variabletomodel=="totwgt") {
obs$density = obs$totwgt / obs$data_offset
rr = as.data.frame.table(res$totwgt.predicted)
}
rr$AUID = as.character( rr$AUID)
region.id = slot(sppoly, "region.id" )
rr$space = match( rr$AUID, region.id )
rr$AUID = rr$space
rr$year = as.numeric( as.character( rr$year) )
obs = merge( obs, rr, by=c("year", "AUID"), all.x=TRUE, all.y=FALSE )
obs$Freq[ !is.finite(obs$Freq) ] = 0
obs$resid = obs$Freq - obs$density
obs$resid_per_set = obs$resid * obs$data_offset
obs$yr = obs$year
vn = "resid"
vn = "resid_per_set"
#er = range( obs[,vn], na.rm=T) * c(0.95, 1.05)
er = c(-100, 100)
resol = p$pres
B = bathymetry_db(p=p, DS="baseline") # 1 km (p$pres )
for ( y in 2000:2018 ) {
ii = which( obs$yr==y & is.finite(obs[,vn] ))
if ( length(ii) > 3 ) {
dir.create( file.path( outputdir, "residuals", p$carstm_model_label), recursive=TRUE, showWarnings =FALSE)
fn = file.path( outputdir, "residuals", p$carstm_model_label, paste( "residuals", y, "png", sep=".") )
png( filename=fn, width=3072, height=2304, pointsize=40, res=300 )
lp = map_simple( toplot=obs[ ii, c("plon","plat", vn) ], plotarea=B, resol=1, theta=15, filterdistances=7.5, vn=vn, annot=paste("Residuals", y), er=er )
print(lp)
dev.off()
print(fn)
}
}
# end
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