Simulation Study/Code/Simulation_Study_Run_Corrected.R
In pbs-assess/hookCompetition: An R package for estimating relative abundance indices from longline data using a censored likelihood approach
# Simulation study demonstrating the censored hook competition method
library(INLA)
library(ggplot2)
library(tidyverse)
library(mgcv)
nspecies <- 3
bite_funs <- cbind(rep('constant',3),
c('exp_decay','mixed', 'constant'))
soak_time <- 5
n_hooks <- 800
nstation <- 6
nyears <- 30
saturation_level <- c(1,2)
mean_attract <- c('constant', 'linear')
sd_log_bite <- c(0.8, 0.2, 0)
n_sim <- 100
hook_sat_level <- 0.85 # true proportion at which saturation effects begin
cprop=0.85 # assumed proportion at which saturation effects begin
cprop2=0.95 # assumed proportion "" "" second model
# how much does the bite rate of each species (linearly) decrease at 100% saturation
# assume linear decrease from 85% saturation onwards
saturation_effects <- cbind(c(0, 0, 0),
c(0, 0.2, 0.8))
# create saturation function
sat_fun <- function(sat_effect, sat_level, hook_sat_level=0.85)
{
val <- rep(1, length(sat_level))
val[which(sat_level>hook_sat_level)] <-
(1 - sat_effect*((sat_level[which(sat_level>hook_sat_level)]-hook_sat_level)/(1-hook_sat_level)))
return(val)
}
# try the hook competition adjusted method
comp_factor_fun <- function(prop_hook, n_hook)
{
prop <- prop_hook
# if all hooks saturated - map to 1 hook
prop[which(prop == 0)] <- 1 / n_hook[which(prop == 0)]
return(-log(prop)/(1-prop))
}
# plot(x=seq(from=0,to=1, length.out=100), y=sat_fun(0.8,seq(from=0,to=1, length.out=100)))
#
# # Plot the bite rates of the two species
# plot(x=seq(from=0, to=5, length.out=100),y=exp(-seq(from=0, to=5, length.out=100))/(1-exp(-5)),
# type = 'l', main='bite rate functions', ylab='bite rate',xlab='time')
# lines(x=seq(from=0, to=5, length.out=100),y=rep(0.2, times=100), col='red')
# sample the unadjusted bite times for each of the 'attracted' fish for each fishing event
bite_samp <- function(bite_fun, n)
{
if(bite_fun=='exp_decay')
{
val <- rexp(n)
}
if(bite_fun=='constant')
{
val <- runif(n, min = 0, max=soak_time)
}
if(bite_fun=='mixed')
{
val <- c(rexp(n),
runif(n, min = 0, max=soak_time))[
rbinom(n=n, size = 1, prob=0.5)+1
]
}
return(val)
}
# define function for competition
# competition_fun <-
# function(data, p_sat, p_baseline){
# val <- rep(1, length(p_sat))
#
# preddata=data
# preddata$prop_sat=p_sat
# #preddata$region <- preddata$region_INLA
# preddata2=preddata
# preddata2$prop_sat=p_baseline
# #browser()
# val2 <-
# apply(predict.gam(mod_species1,
# newdata=preddata,
# type = 'terms'),
# 1, FUN = function(x){exp(sum(x))})/
# apply(predict.gam(mod_species1,
# newdata=preddata2,
# type = 'terms'),
# 1, FUN = function(x){exp(sum(x))})
# # predict.gam(mod_species1,
# # newdata=preddata,
# # type = 'response') /
# # predict.gam(mod_species1,
# # newdata=preddata2,
# # type = 'response')
#
# val[which(p_sat > p_baseline)] <-
# val2[which(p_sat > p_baseline)]
# return(val)
# }
Results <- data.frame(
nsim = rep(1:n_sim, each=nstation*2*2*2*2*4),
sat_level = rep(rep(c('low','high'), times=n_sim),each=2*2*2*4*nstation),
mean_attract = rep(rep(mean_attract, times=n_sim*2), each=2*2*4*nstation),
sat_effects = rep(rep(c('no saturation','saturation'),times=n_sim*2*2), each=2*4*nstation),
bite_fun = rep(rep(c('constant','mixed'), times=n_sim*2*2*2), each=4*nstation),
model=rep(rep(c('naive','adjust','censored','censored_95'), times=n_sim*2*2*2), each=nstation),
Bias=rep(0, times=n_sim*2*2*2*2*4*nstation),
RMSE=rep(0, times=n_sim*2*2*2*2*4*nstation),
Coverage=rep(0, times=n_sim*2*2*2*2*4*nstation),
Rel_Bias=rep(0, times=n_sim*2*2*2*2*4*nstation),
Rel_RMSE=rep(0, times=n_sim*2*2*2*2*4*nstation),
Rel_Coverage=rep(0, times=n_sim*2*2*2*2*4*nstation),
Station=rep(1:nstation, times=n_sim*2*2*2*2*4),
Prop_Sat_85=rep(0, times=n_sim*2*2*2*2*4*nstation),
Prop_Sat_100=rep(0, times=n_sim*2*2*2*2*4*nstation))
results_mapper <- function(n,i,j,k,l,mod)
{
return(
which(Results$nsim == n & Results$sat_level == c('low','high')[i] &
Results$mean_attract == mean_attract[j] &
Results$sat_effects == c('no saturation','saturation')[k] &
Results$bite_fun == c('constant','mixed')[l] &
Results$model == mod)
)
}
for(nsim in 51:n_sim)
{
print(paste0('iteration ',nsim,' out of ',n_sim))
for(i in 1:length(saturation_level))
{
for(j in 1:length(mean_attract))
{
for(k in 1:dim(saturation_effects)[2])
{
if(mean_attract[j] == 'constant')
{
mean_bite =
cbind(c(120, 140, 160, 180, 200, 280)*saturation_level[i],
rep(400,6),
rep(100, 6))
}
if(mean_attract[j] == 'linear')
{
mean_bite =
cbind(c(120, 140, 160, 180, 200, 280)*saturation_level[i],
rep(400,6),
c(120, 140, 160, 180, 200, 220)-100)
}
for(l in 1:dim(bite_funs)[2])
{
saturation_effect <- saturation_effects[,k]
# sample the number of each species that WOULD bite at each station for each year if hooks were available
nbite <- data.frame(bites = rep(0, times=nspecies*nstation*nyears),
attracted = rep(0, times=nspecies*nstation*nyears),
species=rep(1:3, each=nstation*nyears),
station=rep(1:nstation, times=nspecies*nyears),
year=rep(rep(1:nyears, each=nstation), times=nspecies))
nbite$attracted <- rpois(dim(nbite)[1],
lambda = as.numeric(mean_bite[cbind(nbite$station,nbite$species)])*
exp(rnorm(dim(nbite)[1], mean = 0, sd=sd_log_bite[nbite$species])))
for(i2 in 1:nstation)
{
for(j2 in 1:nyears)
{
bite_time_1 <- bite_samp(bite_funs[1,l],sum(nbite$attracted[nbite$species==1 &
nbite$station==i2 &
nbite$year==j2]))
# truncate them to 0-5 interval
while(max(bite_time_1)>soak_time)
{
bite_time_1[bite_time_1>soak_time] <-
bite_samp(bite_funs[1,l],sum(bite_time_1>soak_time))
}
# repeat for species 2 from uniform distribution
bite_time_2 <- bite_samp(bite_funs[2,l],sum(nbite$attracted[nbite$species==2 &
nbite$station==i2 &
nbite$year==j2]))
# truncate them to 0-5 interval
while(max(bite_time_2)>soak_time)
{
bite_time_2[bite_time_2>soak_time] <-
bite_samp(bite_funs[2,l],sum(bite_time_2>soak_time))
}
# repeat for species 3 from uniform distribution
bite_time_3 <- bite_samp(bite_funs[3,l],sum(nbite$attracted[nbite$species==3 &
nbite$station==i2 &
nbite$year==j2]))
# truncate them to 0-5 interval
while(max(bite_time_3)>soak_time)
{
bite_time_3[bite_time_3>soak_time] <-
bite_samp(bite_funs[3,l],sum(bite_time_3>soak_time))
}
# Now we sample the first n_hooks*n_hook_sat_level unadjusted
if((length(bite_time_1) + length(bite_time_2) + length(bite_time_3)) <= n_hooks*hook_sat_level)
{
nbite$bites[nbite$species==1 &
nbite$station==i2 &
nbite$year==j2] <- length(bite_time_1)
nbite$bites[nbite$species==2 &
nbite$station==i2 &
nbite$year==j2] <- length(bite_time_2)
nbite$bites[nbite$species==3 &
nbite$station==i2 &
nbite$year==j2] <- length(bite_time_3)
}
if((length(bite_time_1) + length(bite_time_2) + length(bite_time_3)) > n_hooks*hook_sat_level)
{
species_ind <- c(rep(1, length(bite_time_1)),rep(2,length(bite_time_2)),rep(3,length(bite_time_3)))
# Now we sample the first n_hooks*n_hook_sat_level unadjusted
all_times <- c(bite_time_1,bite_time_2,bite_time_3)
time_ind <- sort.int(all_times, index.return = T, decreasing = F)$ix
# for the remaining hooks we sample/thin according to the sat_fun
current_sat_level <- hook_sat_level
counter <- round(n_hooks*hook_sat_level)
for(k2 in (round(n_hooks*hook_sat_level)+1):(length(all_times)))
{
flag <- T
if(species_ind[time_ind[k2]]==1)
{
time_ind[k2] <- ifelse(rbinom(n=1,size=1,
prob=sat_fun(sat_effect = saturation_effect[1],
sat_level = current_sat_level,
hook_sat_level = hook_sat_level))==1,
time_ind[k2], NA)
flag <- F
}
if(species_ind[time_ind[k2]]==2 & flag)
{
time_ind[k2] <- ifelse(rbinom(n=1,size=1,
prob=sat_fun(sat_effect = saturation_effect[2],
sat_level = current_sat_level,
hook_sat_level = hook_sat_level))==1,
time_ind[k2], NA)
flag <- F
}
if(species_ind[time_ind[k2]]==3 & flag)
{
time_ind[k2] <- ifelse(rbinom(n=1,size=1,
prob=sat_fun(sat_effect = saturation_effect[3],
sat_level = current_sat_level,
hook_sat_level = hook_sat_level))==1,
time_ind[k2], NA)
}
if(!is.na(time_ind[k2]))
{
counter <- counter + 1
current_sat_level <- counter/n_hooks
}
if(counter==n_hooks)
{
time_ind <- time_ind[1:k2]
break
}
}
time_ind <- time_ind[!is.na(time_ind)]
nbite$bites[nbite$species==1 &
nbite$station==i2 &
nbite$year==j2] <- sum(species_ind[time_ind]==1)
nbite$bites[nbite$species==2 &
nbite$station==i2 &
nbite$year==j2] <- sum(species_ind[time_ind]==2)
nbite$bites[nbite$species==3 &
nbite$station==i2 &
nbite$year==j2] <- sum(species_ind[time_ind]==3)
}
}
}
nbite <-
nbite %>%
group_by(station, year) %>%
mutate(prop_sat=sum(bites/n_hooks),
composition=bites/(sum(bites)))
# ggplot(nbite, aes(x=station, y=bites, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth() + geom_hline(yintercept = mean_bite[1,2:3]*exp(0.5*sd_log_bite[c(2,3)]^2))
#
# ggplot(nbite, aes(x=prop_sat, y=composition, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth()
#
# ggplot(nbite[nbite$species!=2,], aes(x=prop_sat, y=composition, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth()
#
# ggplot(nbite[nbite$species!=2,], aes(x=prop_sat, y=composition, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth() + facet_wrap(~factor(station))
Results[results_mapper(nsim,i,j,k,l,'naive'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
Results[results_mapper(nsim,i,j,k,l,'censored'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
Results[results_mapper(nsim,i,j,k,l,'naive'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'censored'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
# fit a naive model that ignores competition
dat <- nbite[nbite$species == 3,]
dat$event_ID <- 1:dim(dat)[1]
mod <- inla(bites ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod)
parameters <- t(sapply(mod$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'naive'),'Bias'] <-
(sapply(mod$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'naive'),'RMSE'] <-
(sapply(mod$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'naive'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Station Abundance') + ggtitle('The true abundance shown in red')
mod2 <- inla(bites ~ factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod2)
parameters <- t(sapply(mod2$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'naive'),'Rel_Bias'][-1] <-
(sapply(mod2$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'naive'),'Rel_RMSE'][-1] <-
(sapply(mod2$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'naive'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=2:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=2:nstation, y2=mean_bite[-1,3]/mean_bite[1,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Relative Abundance') + ggtitle('The true relative abundance shown in red')
dat$bites <- round(dat$bites*comp_factor_fun(1-dat$prop_sat, rep(n_hooks,length(dat$prop_sat))))
mod3 <- inla(bites ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod3)
parameters <- t(sapply(mod3$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Bias'] <-
(sapply(mod3$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'adjust'),'RMSE'] <-
(sapply(mod3$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Adjusted Station Abundance') + ggtitle('The true abundance shown in red')
mod4 <- inla(bites ~ factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod4)
parameters <- t(sapply(mod4$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Rel_Bias'][-1] <-
(sapply(mod4$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Rel_RMSE'][-1] <-
(sapply(mod4$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=2:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=2:nstation, y2=mean_bite[-1,3]/mean_bite[1,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Adjusted Relative Abundance') + ggtitle('The true relative abundance shown in red')
#
# Try the censored approach
# derive the competition function
# fit model
# mod_species1 <- gam(formula=
# composition ~ factor(station) + s(prop_sat, bs='cs') ,
# method.args=list(family='quasibinomial'),
# weights = nbite[nbite$species==1,]$prop_sat*800,
# family='quasibinomial',
# data = nbite[nbite$species==1,])
# mod_species1 <- gam(formula=
# bites ~ factor(station) + s(prop_sat, bs='cs') + offset(I(log(prop_sat))),
# #method.args=list(family='quasibinomial'),
# #weights = nbite[nbite$species==1,]$prop_sat*800,
# family='quasipoisson',
# data = nbite[nbite$species==1,])
# define function for distributing excess hooks across species
# mod_dist <- gam(bites ~ factor(station)*factor(species) + I(log(prop_sat)) + s(prop_sat, by=factor(species)),
# family='quasipoisson', data=nbite)
# nbite_fac <- nbite
# nbite_fac$species=factor(nbite_fac$species)
# nbite_fac$station=factor(nbite_fac$station)
# #plot(mod_dist)
# pred <- #exp(mod_dist$coefficients['factor(species)3'])/(exp(mod_dist$coefficients['factor(species)2'])+exp(mod_dist$coefficients['factor(species)3']))
# predict.gam(mod_dist, newdata = nbite_fac,#data.frame(
# #prop_sat = rep(0.8 ,nspecies*nstation*nyears), species=rep(1:nspecies, times=nstation*nyears),station=rep(1:nstation, each=nspecies*nyears)#species=c(2,3),station=c(1,1)
# type = 'response') #exclude=c('factor(station)','factor(station):factor(species)','I(log(prop_sat))','s(prop_sat):factor(species)1'))
# #pred <- apply(pred, 1, FUN = function(x){return(exp(sum(x)))})
# #pred <- pred[3]/sum(pred)
# pred <-
# cbind(nbite,pred) %>%
# group_by(station, year) %>%
# mutate(prop_bite = ...8/sum(...8)) %>%
# filter(species==3)
# censorship interval
upper_bound <- rep(0, length(nbite[nbite$species==3,]$prop_sat))
species_1_uncensoredprop <- 0.5
if(cprop < 1)
{
# use the competition_fun to derive the scale factor
#scale_fac <- competition_fun(nbite[nbite$species==3,],nbite[nbite$species==3,]$prop_sat,species_1_uncensoredprop)
# divide the number of spiny dogfish observations by the scale factor to obtain 'excess hooks'
#upper_bound <- nbite[nbite$species==1,]$bites - (nbite[nbite$species==1,]$bites / scale_fac)
# assuming each 'non-spiny dogfish' species is equally affected by competition calculate
# proportion of hooks to be allocated to target species
# target_prop <- nbite[nbite$species==3,]$bites /
# (nbite[nbite$species==2,]$bites + nbite[nbite$species==3,]$bites)
# Use the Baranov Catch equation to (starting at 85% saturation) to derive scale factor
dat <- nbite[nbite$species==3,]
scale_fac <- rep(0, length(dat$bites))
scale_fac[dat$prop_sat>cprop] <-
comp_factor_fun(1-signif((dat[dat$prop_sat>cprop,]$prop_sat-cprop)/(1-cprop),5),
rep(round((1-cprop)*n_hooks),sum(dat$prop_sat>cprop)))
upper_bound[dat$prop_sat>cprop] <- round(
(dat$prop_sat[dat$prop_sat>cprop]-cprop)*n_hooks*
scale_fac[dat$prop_sat>cprop])
#target_prop <- pred$prop_bite#rep(pred$prop_bite,length(dat$bites))#dat$bites/(dat$prop_sat*n_hooks) #rep(pred,length(dat$bites))
# How many excess hooks should go to the target species?
upper_bound <- round(upper_bound)
# Use the quantile of binomial distribution to get a probabalistic upper bound
#upper_bound <- qbinom(size=round(upper_bound), prob = target_prop, p=1)
#upper_bound <- rep(Inf, length(nbite[nbite$species==3,]$prop_sat))
#hist(dat$bites + upper_bound - dat$attracted)
}
dat <- nbite[nbite$species==3,]
dat$low <- rep(Inf,dim(dat)[1])
dat$high <- rep(Inf,dim(dat)[1])
dat$low[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))] <-
as.matrix(dat[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1)),
c('bites')])[,1]
dat$high[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))] <-
dat$bites[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))] +
upper_bound[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))]
ind_resp <- which(names(dat) %in% c('bites', 'low', 'high'))
dat$event_ID <- 1:dim(dat)[1]
mod5 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod5)
parameters <- t(sapply(mod5$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored'),'Bias'] <-
(sapply(mod5$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'censored'),'RMSE'] <-
(sapply(mod5$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# ylab('Censored Station Abundance') + ggtitle('The true abundance shown in red')
#
mod6 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod6)
parameters <- t(sapply(mod6$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored'),'Rel_Bias'][-1] <-
(sapply(mod6$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'censored'),'Rel_RMSE'][-1] <-
(sapply(mod6$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
### Repeat for second censored model
# censorship interval
upper_bound2 <- rep(0, length(nbite[nbite$species==3,]$prop_sat))
species_1_uncensoredprop <- 0.5
if(cprop2 < 1)
{
# use the competition_fun to derive the scale factor
#scale_fac <- competition_fun(nbite[nbite$species==3,],nbite[nbite$species==3,]$prop_sat,species_1_uncensoredprop)
# divide the number of spiny dogfish observations by the scale factor to obtain 'excess hooks'
#upper_bound <- nbite[nbite$species==1,]$bites - (nbite[nbite$species==1,]$bites / scale_fac)
# assuming each 'non-spiny dogfish' species is equally affected by competition calculate
# proportion of hooks to be allocated to target species
# target_prop <- nbite[nbite$species==3,]$bites /
# (nbite[nbite$species==2,]$bites + nbite[nbite$species==3,]$bites)
# Use the Baranov Catch equation to (starting at 85% saturation) to derive scale factor
dat <- nbite[nbite$species==3,]
scale_fac2 <- rep(0, length(dat$bites))
scale_fac2[dat$prop_sat>cprop2] <-
comp_factor_fun(1-signif((dat[dat$prop_sat>cprop2,]$prop_sat-cprop2)/(1-cprop2),5),
rep(round((1-cprop2)*n_hooks),sum(dat$prop_sat>cprop2)))
upper_bound2[dat$prop_sat>cprop2] <- round(
(dat$prop_sat[dat$prop_sat>cprop2]-cprop2)*n_hooks*
scale_fac[dat$prop_sat>cprop2])
#target_prop <- pred$prop_bite#rep(pred$prop_bite,length(dat$bites))#dat$bites/(dat$prop_sat*n_hooks) #rep(pred,length(dat$bites))
# How many excess hooks should go to the target species?
upper_bound2 <- round(upper_bound2)
# Use the quantile of binomial distribution to get a probabalistic upper bound
#upper_bound <- qbinom(size=round(upper_bound), prob = target_prop, p=1)
#upper_bound <- rep(Inf, length(nbite[nbite$species==3,]$prop_sat))
#hist(dat$bites + upper_bound - dat$attracted)
}
dat <- nbite[nbite$species==3,]
dat$low <- rep(Inf,dim(dat)[1])
dat$high <- rep(Inf,dim(dat)[1])
dat$low[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))] <-
as.matrix(dat[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1)),
c('bites')])[,1]
dat$high[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))] <-
dat$bites[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))] +
upper_bound2[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))]
ind_resp <- which(names(dat) %in% c('bites', 'low', 'high'))
dat$event_ID <- 1:dim(dat)[1]
mod7 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod5)
parameters <- t(sapply(mod7$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Bias'] <-
(sapply(mod7$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'RMSE'] <-
(sapply(mod7$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# ylab('Censored Station Abundance') + ggtitle('The true abundance shown in red')
#
mod8 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod6)
parameters <- t(sapply(mod8$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Rel_Bias'][-1] <-
(sapply(mod8$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Rel_RMSE'][-1] <-
(sapply(mod8$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
print(Results[results_mapper(nsim,i,j,k,l,'naive'),])
print(Results[results_mapper(nsim,i,j,k,l,'adjust'),])
print(Results[results_mapper(nsim,i,j,k,l,'censored'),])
print(Results[results_mapper(nsim,i,j,k,l,'censored_95'),])
}
}
}
}
}
#saveRDS(Results, 'Simulation_Results_Corrected.rds')
Results <- readRDS('Simulation_Results_Corrected.rds')
library(inlabru)
# Change the factors to ordered factors to improve plotting
Results$sat_level <- factor(Results$sat_level, levels=c('low','high'), ordered = T)
Results$mean_attract <- factor(Results$mean_attract, levels=c('constant','linear'), ordered = T)
Results$model <- factor(Results$model, levels=c('naive','adjust','censored','censored_95'), ordered = T)
# Create artificial 'relative abundance' of target and aggressive species plots
rel_abund_dat <- data.frame(expand.grid(
species=c('target species','aggressive species'),
sat_level=factor(c('low','high'), levels=c('low','high'), ordered = T),
mean_attract=factor(c('constant','constant','linear','linear')),
Year=c(1,2,3,4,5,6)))
rel_abund_dat$Abundance <- 1
rel_abund_dat$Abundance[rel_abund_dat$species=='target species'&
rel_abund_dat$mean_attract=='linear'] <-
rel_abund_dat$Year[rel_abund_dat$species=='target species'&
rel_abund_dat$mean_attract=='linear']
rel_abund_dat$Abundance[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='low'] <-
(c(120,140, 160, 180, 200, 280)/120)[rel_abund_dat$Year[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='low']]
rel_abund_dat$Abundance[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='high'] <-
2*(c(120,140, 160, 180, 200, 280)/120)[rel_abund_dat$Year[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='high']]
rel_abund_plot <-
ggplot(rel_abund_dat,
aes(x=Year, y=Abundance, linetype=species) ) +
geom_rect(data= ~.x[.x$Year==1,],
aes(x=Year, y=Abundance, linetype=species, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_line() +
facet_grid(mean_attract+sat_level~.,
labeller = labeller(
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
))) +
ylab('') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank()) +
guides(fill='none') +
theme(strip.background = element_blank(),strip.text = element_blank(),
legend.position = c(0.43,0.94),legend.box.background=element_blank(),
legend.background=element_blank(),
axis.title.y = element_blank()) +
guides(linetype=guide_legend('')) +
ylim(c(0,6))
# THESE ARE DESIGNED FOR A4 LANDSCAPE or 5.83 x 11.3
# NOTICE THE HACK IN MULTIPLOT'S LAYOUT ARGUMENT
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_Bias),
UCL = quantile(Rel_Bias, prob=0.975),
LCL = quantile(Rel_Bias, prob=0.025)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('Bias in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Bias') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'),
shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_Bias),
UCL = median(Rel_Bias)+(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias),
LCL = median(Rel_Bias)-(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
#geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('Bias in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Bias') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'),
shape=guide_legend(title='Method')),
rel_abund_plot,
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1, !(model %in% c('naive','adjust'))) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_Bias),
UCL = median(Rel_Bias)+(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias),
LCL = median(Rel_Bias)-(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('Bias in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Bias') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('Censored 0.85','Censored 0.95'),
values=c('circle','triangle')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
rel_abund_plot,
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Coverage_Mean = mean(Rel_Coverage),
UCL=mean(Rel_Coverage)+(2/sqrt(100))*sqrt(mean(Rel_Coverage)*(1-mean(Rel_Coverage))),
LCL=mean(Rel_Coverage)-(2/sqrt(100))*sqrt(mean(Rel_Coverage)*(1-mean(Rel_Coverage)))) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Coverage_Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Coverage_Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0.95) +
ggtitle('Coverage of intervals of relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Coverage') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_RMSE),
UCL = median(Rel_RMSE)+(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE),
LCL = median(Rel_RMSE)-(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_RMSE)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('MSE in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('MSE') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1, model!='naive') %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_RMSE),
UCL = median(Rel_RMSE)+(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE),
LCL = median(Rel_RMSE)-(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_RMSE)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('MSE in relative abundance for each method') +#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('MSE') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('ICR','Censored 0.85','Censored 0.95'),
values=c('triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Sat85_Mean = mean(Prop_Sat_85),
Sat100_Mean = mean(Prop_Sat_100)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Sat85_Mean, colour='85% Saturation')) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Sat85_Mean, colour='85% Saturation', fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 1) +
#geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
geom_point(aes(x=Station, y=Sat100_Mean, colour='100% Saturation'),position = position_dodge(width=0.8), size=2) +
ylim(c(0,1)) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
ggtitle('Proportion of Fishing Events with Specified Level of Hook Saturation')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Proportion of fishing events') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('100%','>85%')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')) +
labs(colour='Baits Removed'),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
pbs-assess/hookCompetition documentation built on April 27, 2023, 12:47 p.m.
R Package Documentation
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# Simulation study demonstrating the censored hook competition method
library(INLA)
library(ggplot2)
library(tidyverse)
library(mgcv)
nspecies <- 3
bite_funs <- cbind(rep('constant',3),
c('exp_decay','mixed', 'constant'))
soak_time <- 5
n_hooks <- 800
nstation <- 6
nyears <- 30
saturation_level <- c(1,2)
mean_attract <- c('constant', 'linear')
sd_log_bite <- c(0.8, 0.2, 0)
n_sim <- 100
hook_sat_level <- 0.85 # true proportion at which saturation effects begin
cprop=0.85 # assumed proportion at which saturation effects begin
cprop2=0.95 # assumed proportion "" "" second model
# how much does the bite rate of each species (linearly) decrease at 100% saturation
# assume linear decrease from 85% saturation onwards
saturation_effects <- cbind(c(0, 0, 0),
c(0, 0.2, 0.8))
# create saturation function
sat_fun <- function(sat_effect, sat_level, hook_sat_level=0.85)
{
val <- rep(1, length(sat_level))
val[which(sat_level>hook_sat_level)] <-
(1 - sat_effect*((sat_level[which(sat_level>hook_sat_level)]-hook_sat_level)/(1-hook_sat_level)))
return(val)
}
# try the hook competition adjusted method
comp_factor_fun <- function(prop_hook, n_hook)
{
prop <- prop_hook
# if all hooks saturated - map to 1 hook
prop[which(prop == 0)] <- 1 / n_hook[which(prop == 0)]
return(-log(prop)/(1-prop))
}
# plot(x=seq(from=0,to=1, length.out=100), y=sat_fun(0.8,seq(from=0,to=1, length.out=100)))
#
# # Plot the bite rates of the two species
# plot(x=seq(from=0, to=5, length.out=100),y=exp(-seq(from=0, to=5, length.out=100))/(1-exp(-5)),
# type = 'l', main='bite rate functions', ylab='bite rate',xlab='time')
# lines(x=seq(from=0, to=5, length.out=100),y=rep(0.2, times=100), col='red')
# sample the unadjusted bite times for each of the 'attracted' fish for each fishing event
bite_samp <- function(bite_fun, n)
{
if(bite_fun=='exp_decay')
{
val <- rexp(n)
}
if(bite_fun=='constant')
{
val <- runif(n, min = 0, max=soak_time)
}
if(bite_fun=='mixed')
{
val <- c(rexp(n),
runif(n, min = 0, max=soak_time))[
rbinom(n=n, size = 1, prob=0.5)+1
]
}
return(val)
}
# define function for competition
# competition_fun <-
# function(data, p_sat, p_baseline){
# val <- rep(1, length(p_sat))
#
# preddata=data
# preddata$prop_sat=p_sat
# #preddata$region <- preddata$region_INLA
# preddata2=preddata
# preddata2$prop_sat=p_baseline
# #browser()
# val2 <-
# apply(predict.gam(mod_species1,
# newdata=preddata,
# type = 'terms'),
# 1, FUN = function(x){exp(sum(x))})/
# apply(predict.gam(mod_species1,
# newdata=preddata2,
# type = 'terms'),
# 1, FUN = function(x){exp(sum(x))})
# # predict.gam(mod_species1,
# # newdata=preddata,
# # type = 'response') /
# # predict.gam(mod_species1,
# # newdata=preddata2,
# # type = 'response')
#
# val[which(p_sat > p_baseline)] <-
# val2[which(p_sat > p_baseline)]
# return(val)
# }
Results <- data.frame(
nsim = rep(1:n_sim, each=nstation*2*2*2*2*4),
sat_level = rep(rep(c('low','high'), times=n_sim),each=2*2*2*4*nstation),
mean_attract = rep(rep(mean_attract, times=n_sim*2), each=2*2*4*nstation),
sat_effects = rep(rep(c('no saturation','saturation'),times=n_sim*2*2), each=2*4*nstation),
bite_fun = rep(rep(c('constant','mixed'), times=n_sim*2*2*2), each=4*nstation),
model=rep(rep(c('naive','adjust','censored','censored_95'), times=n_sim*2*2*2), each=nstation),
Bias=rep(0, times=n_sim*2*2*2*2*4*nstation),
RMSE=rep(0, times=n_sim*2*2*2*2*4*nstation),
Coverage=rep(0, times=n_sim*2*2*2*2*4*nstation),
Rel_Bias=rep(0, times=n_sim*2*2*2*2*4*nstation),
Rel_RMSE=rep(0, times=n_sim*2*2*2*2*4*nstation),
Rel_Coverage=rep(0, times=n_sim*2*2*2*2*4*nstation),
Station=rep(1:nstation, times=n_sim*2*2*2*2*4),
Prop_Sat_85=rep(0, times=n_sim*2*2*2*2*4*nstation),
Prop_Sat_100=rep(0, times=n_sim*2*2*2*2*4*nstation))
results_mapper <- function(n,i,j,k,l,mod)
{
return(
which(Results$nsim == n & Results$sat_level == c('low','high')[i] &
Results$mean_attract == mean_attract[j] &
Results$sat_effects == c('no saturation','saturation')[k] &
Results$bite_fun == c('constant','mixed')[l] &
Results$model == mod)
)
}
for(nsim in 51:n_sim)
{
print(paste0('iteration ',nsim,' out of ',n_sim))
for(i in 1:length(saturation_level))
{
for(j in 1:length(mean_attract))
{
for(k in 1:dim(saturation_effects)[2])
{
if(mean_attract[j] == 'constant')
{
mean_bite =
cbind(c(120, 140, 160, 180, 200, 280)*saturation_level[i],
rep(400,6),
rep(100, 6))
}
if(mean_attract[j] == 'linear')
{
mean_bite =
cbind(c(120, 140, 160, 180, 200, 280)*saturation_level[i],
rep(400,6),
c(120, 140, 160, 180, 200, 220)-100)
}
for(l in 1:dim(bite_funs)[2])
{
saturation_effect <- saturation_effects[,k]
# sample the number of each species that WOULD bite at each station for each year if hooks were available
nbite <- data.frame(bites = rep(0, times=nspecies*nstation*nyears),
attracted = rep(0, times=nspecies*nstation*nyears),
species=rep(1:3, each=nstation*nyears),
station=rep(1:nstation, times=nspecies*nyears),
year=rep(rep(1:nyears, each=nstation), times=nspecies))
nbite$attracted <- rpois(dim(nbite)[1],
lambda = as.numeric(mean_bite[cbind(nbite$station,nbite$species)])*
exp(rnorm(dim(nbite)[1], mean = 0, sd=sd_log_bite[nbite$species])))
for(i2 in 1:nstation)
{
for(j2 in 1:nyears)
{
bite_time_1 <- bite_samp(bite_funs[1,l],sum(nbite$attracted[nbite$species==1 &
nbite$station==i2 &
nbite$year==j2]))
# truncate them to 0-5 interval
while(max(bite_time_1)>soak_time)
{
bite_time_1[bite_time_1>soak_time] <-
bite_samp(bite_funs[1,l],sum(bite_time_1>soak_time))
}
# repeat for species 2 from uniform distribution
bite_time_2 <- bite_samp(bite_funs[2,l],sum(nbite$attracted[nbite$species==2 &
nbite$station==i2 &
nbite$year==j2]))
# truncate them to 0-5 interval
while(max(bite_time_2)>soak_time)
{
bite_time_2[bite_time_2>soak_time] <-
bite_samp(bite_funs[2,l],sum(bite_time_2>soak_time))
}
# repeat for species 3 from uniform distribution
bite_time_3 <- bite_samp(bite_funs[3,l],sum(nbite$attracted[nbite$species==3 &
nbite$station==i2 &
nbite$year==j2]))
# truncate them to 0-5 interval
while(max(bite_time_3)>soak_time)
{
bite_time_3[bite_time_3>soak_time] <-
bite_samp(bite_funs[3,l],sum(bite_time_3>soak_time))
}
# Now we sample the first n_hooks*n_hook_sat_level unadjusted
if((length(bite_time_1) + length(bite_time_2) + length(bite_time_3)) <= n_hooks*hook_sat_level)
{
nbite$bites[nbite$species==1 &
nbite$station==i2 &
nbite$year==j2] <- length(bite_time_1)
nbite$bites[nbite$species==2 &
nbite$station==i2 &
nbite$year==j2] <- length(bite_time_2)
nbite$bites[nbite$species==3 &
nbite$station==i2 &
nbite$year==j2] <- length(bite_time_3)
}
if((length(bite_time_1) + length(bite_time_2) + length(bite_time_3)) > n_hooks*hook_sat_level)
{
species_ind <- c(rep(1, length(bite_time_1)),rep(2,length(bite_time_2)),rep(3,length(bite_time_3)))
# Now we sample the first n_hooks*n_hook_sat_level unadjusted
all_times <- c(bite_time_1,bite_time_2,bite_time_3)
time_ind <- sort.int(all_times, index.return = T, decreasing = F)$ix
# for the remaining hooks we sample/thin according to the sat_fun
current_sat_level <- hook_sat_level
counter <- round(n_hooks*hook_sat_level)
for(k2 in (round(n_hooks*hook_sat_level)+1):(length(all_times)))
{
flag <- T
if(species_ind[time_ind[k2]]==1)
{
time_ind[k2] <- ifelse(rbinom(n=1,size=1,
prob=sat_fun(sat_effect = saturation_effect[1],
sat_level = current_sat_level,
hook_sat_level = hook_sat_level))==1,
time_ind[k2], NA)
flag <- F
}
if(species_ind[time_ind[k2]]==2 & flag)
{
time_ind[k2] <- ifelse(rbinom(n=1,size=1,
prob=sat_fun(sat_effect = saturation_effect[2],
sat_level = current_sat_level,
hook_sat_level = hook_sat_level))==1,
time_ind[k2], NA)
flag <- F
}
if(species_ind[time_ind[k2]]==3 & flag)
{
time_ind[k2] <- ifelse(rbinom(n=1,size=1,
prob=sat_fun(sat_effect = saturation_effect[3],
sat_level = current_sat_level,
hook_sat_level = hook_sat_level))==1,
time_ind[k2], NA)
}
if(!is.na(time_ind[k2]))
{
counter <- counter + 1
current_sat_level <- counter/n_hooks
}
if(counter==n_hooks)
{
time_ind <- time_ind[1:k2]
break
}
}
time_ind <- time_ind[!is.na(time_ind)]
nbite$bites[nbite$species==1 &
nbite$station==i2 &
nbite$year==j2] <- sum(species_ind[time_ind]==1)
nbite$bites[nbite$species==2 &
nbite$station==i2 &
nbite$year==j2] <- sum(species_ind[time_ind]==2)
nbite$bites[nbite$species==3 &
nbite$station==i2 &
nbite$year==j2] <- sum(species_ind[time_ind]==3)
}
}
}
nbite <-
nbite %>%
group_by(station, year) %>%
mutate(prop_sat=sum(bites/n_hooks),
composition=bites/(sum(bites)))
# ggplot(nbite, aes(x=station, y=bites, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth() + geom_hline(yintercept = mean_bite[1,2:3]*exp(0.5*sd_log_bite[c(2,3)]^2))
#
# ggplot(nbite, aes(x=prop_sat, y=composition, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth()
#
# ggplot(nbite[nbite$species!=2,], aes(x=prop_sat, y=composition, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth()
#
# ggplot(nbite[nbite$species!=2,], aes(x=prop_sat, y=composition, group=factor(species), colour=factor(species))) +
# geom_point() + geom_smooth() + facet_wrap(~factor(station))
Results[results_mapper(nsim,i,j,k,l,'naive'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
Results[results_mapper(nsim,i,j,k,l,'censored'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
Results[results_mapper(nsim,i,j,k,l,'naive'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'censored'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Prop_Sat_100'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat==1)}))
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Prop_Sat_85'] <- as.numeric(by(nbite, nbite$station, FUN=function(x){mean(x$prop_sat>cprop)}))
# fit a naive model that ignores competition
dat <- nbite[nbite$species == 3,]
dat$event_ID <- 1:dim(dat)[1]
mod <- inla(bites ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod)
parameters <- t(sapply(mod$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'naive'),'Bias'] <-
(sapply(mod$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'naive'),'RMSE'] <-
(sapply(mod$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'naive'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Station Abundance') + ggtitle('The true abundance shown in red')
mod2 <- inla(bites ~ factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod2)
parameters <- t(sapply(mod2$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'naive'),'Rel_Bias'][-1] <-
(sapply(mod2$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'naive'),'Rel_RMSE'][-1] <-
(sapply(mod2$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'naive'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=2:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=2:nstation, y2=mean_bite[-1,3]/mean_bite[1,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Relative Abundance') + ggtitle('The true relative abundance shown in red')
dat$bites <- round(dat$bites*comp_factor_fun(1-dat$prop_sat, rep(n_hooks,length(dat$prop_sat))))
mod3 <- inla(bites ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod3)
parameters <- t(sapply(mod3$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Bias'] <-
(sapply(mod3$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'adjust'),'RMSE'] <-
(sapply(mod3$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Adjusted Station Abundance') + ggtitle('The true abundance shown in red')
mod4 <- inla(bites ~ factor(station) + f(event_ID, constr=T, model='iid'),
data = dat, family = 'poisson')
#summary(mod4)
parameters <- t(sapply(mod4$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Rel_Bias'][-1] <-
(sapply(mod4$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Rel_RMSE'][-1] <-
(sapply(mod4$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'adjust'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=2:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=2:nstation, y2=mean_bite[-1,3]/mean_bite[1,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# xlab('Station') +
# ylab('Adjusted Relative Abundance') + ggtitle('The true relative abundance shown in red')
#
# Try the censored approach
# derive the competition function
# fit model
# mod_species1 <- gam(formula=
# composition ~ factor(station) + s(prop_sat, bs='cs') ,
# method.args=list(family='quasibinomial'),
# weights = nbite[nbite$species==1,]$prop_sat*800,
# family='quasibinomial',
# data = nbite[nbite$species==1,])
# mod_species1 <- gam(formula=
# bites ~ factor(station) + s(prop_sat, bs='cs') + offset(I(log(prop_sat))),
# #method.args=list(family='quasibinomial'),
# #weights = nbite[nbite$species==1,]$prop_sat*800,
# family='quasipoisson',
# data = nbite[nbite$species==1,])
# define function for distributing excess hooks across species
# mod_dist <- gam(bites ~ factor(station)*factor(species) + I(log(prop_sat)) + s(prop_sat, by=factor(species)),
# family='quasipoisson', data=nbite)
# nbite_fac <- nbite
# nbite_fac$species=factor(nbite_fac$species)
# nbite_fac$station=factor(nbite_fac$station)
# #plot(mod_dist)
# pred <- #exp(mod_dist$coefficients['factor(species)3'])/(exp(mod_dist$coefficients['factor(species)2'])+exp(mod_dist$coefficients['factor(species)3']))
# predict.gam(mod_dist, newdata = nbite_fac,#data.frame(
# #prop_sat = rep(0.8 ,nspecies*nstation*nyears), species=rep(1:nspecies, times=nstation*nyears),station=rep(1:nstation, each=nspecies*nyears)#species=c(2,3),station=c(1,1)
# type = 'response') #exclude=c('factor(station)','factor(station):factor(species)','I(log(prop_sat))','s(prop_sat):factor(species)1'))
# #pred <- apply(pred, 1, FUN = function(x){return(exp(sum(x)))})
# #pred <- pred[3]/sum(pred)
# pred <-
# cbind(nbite,pred) %>%
# group_by(station, year) %>%
# mutate(prop_bite = ...8/sum(...8)) %>%
# filter(species==3)
# censorship interval
upper_bound <- rep(0, length(nbite[nbite$species==3,]$prop_sat))
species_1_uncensoredprop <- 0.5
if(cprop < 1)
{
# use the competition_fun to derive the scale factor
#scale_fac <- competition_fun(nbite[nbite$species==3,],nbite[nbite$species==3,]$prop_sat,species_1_uncensoredprop)
# divide the number of spiny dogfish observations by the scale factor to obtain 'excess hooks'
#upper_bound <- nbite[nbite$species==1,]$bites - (nbite[nbite$species==1,]$bites / scale_fac)
# assuming each 'non-spiny dogfish' species is equally affected by competition calculate
# proportion of hooks to be allocated to target species
# target_prop <- nbite[nbite$species==3,]$bites /
# (nbite[nbite$species==2,]$bites + nbite[nbite$species==3,]$bites)
# Use the Baranov Catch equation to (starting at 85% saturation) to derive scale factor
dat <- nbite[nbite$species==3,]
scale_fac <- rep(0, length(dat$bites))
scale_fac[dat$prop_sat>cprop] <-
comp_factor_fun(1-signif((dat[dat$prop_sat>cprop,]$prop_sat-cprop)/(1-cprop),5),
rep(round((1-cprop)*n_hooks),sum(dat$prop_sat>cprop)))
upper_bound[dat$prop_sat>cprop] <- round(
(dat$prop_sat[dat$prop_sat>cprop]-cprop)*n_hooks*
scale_fac[dat$prop_sat>cprop])
#target_prop <- pred$prop_bite#rep(pred$prop_bite,length(dat$bites))#dat$bites/(dat$prop_sat*n_hooks) #rep(pred,length(dat$bites))
# How many excess hooks should go to the target species?
upper_bound <- round(upper_bound)
# Use the quantile of binomial distribution to get a probabalistic upper bound
#upper_bound <- qbinom(size=round(upper_bound), prob = target_prop, p=1)
#upper_bound <- rep(Inf, length(nbite[nbite$species==3,]$prop_sat))
#hist(dat$bites + upper_bound - dat$attracted)
}
dat <- nbite[nbite$species==3,]
dat$low <- rep(Inf,dim(dat)[1])
dat$high <- rep(Inf,dim(dat)[1])
dat$low[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))] <-
as.matrix(dat[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1)),
c('bites')])[,1]
dat$high[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))] <-
dat$bites[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))] +
upper_bound[which(dat$prop_sat >= cprop &
0 < upper_bound &
dat$bites < quantile(dat$bites,1))]
ind_resp <- which(names(dat) %in% c('bites', 'low', 'high'))
dat$event_ID <- 1:dim(dat)[1]
mod5 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod5)
parameters <- t(sapply(mod5$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored'),'Bias'] <-
(sapply(mod5$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'censored'),'RMSE'] <-
(sapply(mod5$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# ylab('Censored Station Abundance') + ggtitle('The true abundance shown in red')
#
mod6 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod6)
parameters <- t(sapply(mod6$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored'),'Rel_Bias'][-1] <-
(sapply(mod6$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'censored'),'Rel_RMSE'][-1] <-
(sapply(mod6$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
### Repeat for second censored model
# censorship interval
upper_bound2 <- rep(0, length(nbite[nbite$species==3,]$prop_sat))
species_1_uncensoredprop <- 0.5
if(cprop2 < 1)
{
# use the competition_fun to derive the scale factor
#scale_fac <- competition_fun(nbite[nbite$species==3,],nbite[nbite$species==3,]$prop_sat,species_1_uncensoredprop)
# divide the number of spiny dogfish observations by the scale factor to obtain 'excess hooks'
#upper_bound <- nbite[nbite$species==1,]$bites - (nbite[nbite$species==1,]$bites / scale_fac)
# assuming each 'non-spiny dogfish' species is equally affected by competition calculate
# proportion of hooks to be allocated to target species
# target_prop <- nbite[nbite$species==3,]$bites /
# (nbite[nbite$species==2,]$bites + nbite[nbite$species==3,]$bites)
# Use the Baranov Catch equation to (starting at 85% saturation) to derive scale factor
dat <- nbite[nbite$species==3,]
scale_fac2 <- rep(0, length(dat$bites))
scale_fac2[dat$prop_sat>cprop2] <-
comp_factor_fun(1-signif((dat[dat$prop_sat>cprop2,]$prop_sat-cprop2)/(1-cprop2),5),
rep(round((1-cprop2)*n_hooks),sum(dat$prop_sat>cprop2)))
upper_bound2[dat$prop_sat>cprop2] <- round(
(dat$prop_sat[dat$prop_sat>cprop2]-cprop2)*n_hooks*
scale_fac[dat$prop_sat>cprop2])
#target_prop <- pred$prop_bite#rep(pred$prop_bite,length(dat$bites))#dat$bites/(dat$prop_sat*n_hooks) #rep(pred,length(dat$bites))
# How many excess hooks should go to the target species?
upper_bound2 <- round(upper_bound2)
# Use the quantile of binomial distribution to get a probabalistic upper bound
#upper_bound <- qbinom(size=round(upper_bound), prob = target_prop, p=1)
#upper_bound <- rep(Inf, length(nbite[nbite$species==3,]$prop_sat))
#hist(dat$bites + upper_bound - dat$attracted)
}
dat <- nbite[nbite$species==3,]
dat$low <- rep(Inf,dim(dat)[1])
dat$high <- rep(Inf,dim(dat)[1])
dat$low[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))] <-
as.matrix(dat[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1)),
c('bites')])[,1]
dat$high[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))] <-
dat$bites[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))] +
upper_bound2[which(dat$prop_sat >= cprop2 &
0 < upper_bound2 &
dat$bites < quantile(dat$bites,1))]
ind_resp <- which(names(dat) %in% c('bites', 'low', 'high'))
dat$event_ID <- 1:dim(dat)[1]
mod7 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ -1 + factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod5)
parameters <- t(sapply(mod7$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Bias'] <-
(sapply(mod7$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'RMSE'] <-
(sapply(mod7$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))}) -
mean_bite[,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Coverage'] <-
ifelse(parameters[,1] <= mean_bite[,3] & parameters[,3] >= mean_bite[,3],
1,0)
# ggplot(data.frame(parameters), aes(y=Median, ymax=UCL, ymin=LCL, x=1:6)) +
# geom_errorbar() +
# geom_line(data = data.frame(x2=1:nstation, y2=mean_bite[,3], UCL=0, LCL=0), aes(x=x2,y=y2), colour='red') +
# ylab('Censored Station Abundance') + ggtitle('The true abundance shown in red')
#
mod8 <- inla(formula = inla.mdata(cbind(bites,low,high)) ~ factor(station) + f(event_ID, constr=T, model='iid'),
family="cenpoisson2",verbose=F,
data= dat)
#summary(mod6)
parameters <- t(sapply(mod8$marginals.fixed, FUN = function(x){
inla.qmarginal(p=c(0.025, 0.5, 0.975),
marginal=inla.tmarginal(fun=exp,marginal=x))}))[-1,]
colnames(parameters)=c('LCL', 'Median','UCL')
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Rel_Bias'][-1] <-
(sapply(mod8$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Rel_RMSE'][-1] <-
(sapply(mod8$marginals.fixed, FUN = function(x){
inla.emarginal(fun=function(x){return(x)},marginal=inla.tmarginal(fun=exp,marginal=x))})[-1] -
mean_bite[-1,3]/mean_bite[1,3])^2
Results[results_mapper(nsim,i,j,k,l,'censored_95'),'Rel_Coverage'][-1] <-
ifelse(parameters[,1] <= mean_bite[-1,3]/mean_bite[1,3] & parameters[,3] >= mean_bite[-1,3]/mean_bite[1,3],
1,0)
print(Results[results_mapper(nsim,i,j,k,l,'naive'),])
print(Results[results_mapper(nsim,i,j,k,l,'adjust'),])
print(Results[results_mapper(nsim,i,j,k,l,'censored'),])
print(Results[results_mapper(nsim,i,j,k,l,'censored_95'),])
}
}
}
}
}
#saveRDS(Results, 'Simulation_Results_Corrected.rds')
Results <- readRDS('Simulation_Results_Corrected.rds')
library(inlabru)
# Change the factors to ordered factors to improve plotting
Results$sat_level <- factor(Results$sat_level, levels=c('low','high'), ordered = T)
Results$mean_attract <- factor(Results$mean_attract, levels=c('constant','linear'), ordered = T)
Results$model <- factor(Results$model, levels=c('naive','adjust','censored','censored_95'), ordered = T)
# Create artificial 'relative abundance' of target and aggressive species plots
rel_abund_dat <- data.frame(expand.grid(
species=c('target species','aggressive species'),
sat_level=factor(c('low','high'), levels=c('low','high'), ordered = T),
mean_attract=factor(c('constant','constant','linear','linear')),
Year=c(1,2,3,4,5,6)))
rel_abund_dat$Abundance <- 1
rel_abund_dat$Abundance[rel_abund_dat$species=='target species'&
rel_abund_dat$mean_attract=='linear'] <-
rel_abund_dat$Year[rel_abund_dat$species=='target species'&
rel_abund_dat$mean_attract=='linear']
rel_abund_dat$Abundance[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='low'] <-
(c(120,140, 160, 180, 200, 280)/120)[rel_abund_dat$Year[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='low']]
rel_abund_dat$Abundance[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='high'] <-
2*(c(120,140, 160, 180, 200, 280)/120)[rel_abund_dat$Year[rel_abund_dat$species=='aggressive species'&
rel_abund_dat$sat_level=='high']]
rel_abund_plot <-
ggplot(rel_abund_dat,
aes(x=Year, y=Abundance, linetype=species) ) +
geom_rect(data= ~.x[.x$Year==1,],
aes(x=Year, y=Abundance, linetype=species, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_line() +
facet_grid(mean_attract+sat_level~.,
labeller = labeller(
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
))) +
ylab('') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank()) +
guides(fill='none') +
theme(strip.background = element_blank(),strip.text = element_blank(),
legend.position = c(0.43,0.94),legend.box.background=element_blank(),
legend.background=element_blank(),
axis.title.y = element_blank()) +
guides(linetype=guide_legend('')) +
ylim(c(0,6))
# THESE ARE DESIGNED FOR A4 LANDSCAPE or 5.83 x 11.3
# NOTICE THE HACK IN MULTIPLOT'S LAYOUT ARGUMENT
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_Bias),
UCL = quantile(Rel_Bias, prob=0.975),
LCL = quantile(Rel_Bias, prob=0.025)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('Bias in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Bias') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'),
shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_Bias),
UCL = median(Rel_Bias)+(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias),
LCL = median(Rel_Bias)-(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
#geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('Bias in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Bias') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'),
shape=guide_legend(title='Method')),
rel_abund_plot,
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1, !(model %in% c('naive','adjust'))) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_Bias),
UCL = median(Rel_Bias)+(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias),
LCL = median(Rel_Bias)-(2/sqrt(length(Rel_Bias)))*mad(Rel_Bias)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('Bias in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Bias') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('Censored 0.85','Censored 0.95'),
values=c('circle','triangle')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
rel_abund_plot,
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Coverage_Mean = mean(Rel_Coverage),
UCL=mean(Rel_Coverage)+(2/sqrt(100))*sqrt(mean(Rel_Coverage)*(1-mean(Rel_Coverage))),
LCL=mean(Rel_Coverage)-(2/sqrt(100))*sqrt(mean(Rel_Coverage)*(1-mean(Rel_Coverage)))) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Coverage_Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Coverage_Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0.95) +
ggtitle('Coverage of intervals of relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Coverage') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_RMSE),
UCL = median(Rel_RMSE)+(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE),
LCL = median(Rel_RMSE)-(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_RMSE)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('MSE in relative abundance for each method')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('MSE') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('CPUE','ICR','Censored 0.85','Censored 0.95'),
values=c('circle','triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1, model!='naive') %>%
group_by(model, Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Mean = median(Rel_RMSE),
UCL = median(Rel_RMSE)+(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE),
LCL = median(Rel_RMSE)-(2/sqrt(length(Rel_RMSE)))*mad(Rel_RMSE)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_RMSE)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, shape=model)) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Mean, ymin=LCL, ymax=UCL, colour=model, group=model, fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 0.3) +
geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
geom_hline(yintercept=0) +
ggtitle('MSE in relative abundance for each method') +#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('MSE') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('ICR','Censored 0.85','Censored 0.95')) +
scale_shape_manual(labels=c('ICR','Censored 0.85','Censored 0.95'),
values=c('triangle','square','square')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
multiplot(
rel_abund_plot + ggtitle('Simulated abundance'),
Results %>%
filter(Station>1) %>%
group_by(Station, bite_fun, sat_level, sat_effects, mean_attract) %>%
mutate(Sat85_Mean = mean(Prop_Sat_85),
Sat100_Mean = mean(Prop_Sat_100)) %>%
ungroup(Station) %>%
mutate(random_samp = c(T, rep(F, length(Rel_Bias)-1))) %>%
group_by(Station) %>%
ggplot(aes(x=Station, y=Sat85_Mean, colour='85% Saturation')) +
geom_rect(data= ~.x[.x$random_samp==T,],
aes(x=Station, y=Sat85_Mean, colour='85% Saturation', fill = mean_attract),
xmin = -Inf,xmax = Inf,
ymin = -Inf,ymax = Inf,alpha = 1) +
#geom_errorbar(position = position_dodge(width=0.8)) +
geom_point(position = position_dodge(width=0.8), size=2) +
geom_point(aes(x=Station, y=Sat100_Mean, colour='100% Saturation'),position = position_dodge(width=0.8), size=2) +
ylim(c(0,1)) +
facet_grid(mean_attract + sat_level ~ bite_fun + sat_effects , scales = 'free_y',
labeller = labeller(
sat_effects=c(
`no saturation` = 'p* = 1',
saturation = 'p* = 0.85'
),
bite_fun=c(
constant = 'Uniform Distributions',
mixed = 'Mixture of Distributions'
),
mean_attract = c(
constant = 'constant target species \nabundance',
linear = 'linearly increasing target \nspecies abundance '
),
sat_level = c(
low = 'saturation less "common"',
high = 'saturation "common"'
)
)) +
ggtitle('Proportion of Fishing Events with Specified Level of Hook Saturation')+#,
#subtitle = 'Rows are trends in relative abundance of target species and the average degree of hook saturation.\nColumns describe arrival time distributions and hook location abilities after 85% of baits removed.') +
ylab('Proportion of fishing events') +
xlab('Year') + guides(fill='none') +
scale_fill_brewer(palette = 'Pastel1') +
theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
panel.background = element_blank(), axis.line = element_blank(),
legend.position = 'left', strip.text.y = element_blank()) +
scale_color_viridis_d(labels=c('100%','>85%')) +
guides(color=guide_legend(override.aes=list(fill=NA),title='Method'), shape=guide_legend(title='Method')) +
labs(colour='Baits Removed'),
layout = matrix(c(rep(NA,55),rep(1,445),rep(2,2000)), nrow = 500, ncol = 5, byrow = F))
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