## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(echo = TRUE)
library(ZooScatR)
library(reshape2)
library(ggplot2)
## ----settings-----------------------------------------------------------------
fname <- paste0(system.file(package="ZooScatR"),"/extdata/configs/config_0.dat") #Loacation of the parameters file
para = read_para(fname) #Read parameters file
para$simu$var0 = 18 #simulate from 10
para$simu$var1 = 300 #...to 300 kHz
para$simu$ni = 200 #resudce the number of elements and frequencies to improve speed
para$simu$n = 283
#Create list with soundspeed info
misc <- list(cw=1500)
#change to the more realistic krill shape
profname <- paste0(system.file(package="ZooScatR"),"/extdata/profiles/euphaus1.dat") #krill example
para$shape$prof_name <- profname
#make a length simulation
para$shape$ave_flag = 1
#make an orientation simulation
para$orient$ave_flag = 1
## ----simulation---------------------------------------------------------------
#Run DWBA based on config file
res <- bscat(para=para, misc=misc, simOut = TRUE, nang=100, nl=100) #Target strength vs Frequency
## ----plots_osim---------------------------------------------------------------
o_sim = melt(res$ysim)
o_sim$theta = res$ang[o_sim$Var2]
o_sim$Frequency = res$var[o_sim$Var1]
o_sim=o_sim[,3:ncol(o_sim)]
names(o_sim)[1] <- 'TS'
mTS = data.frame(Frequency=res$var,TS=res$y)
ggplot()+geom_line(data=o_sim, aes(x = Frequency, y=TS, group=theta),lty=2, lwd=0.5, alpha=0.4)+
geom_line(data=mTS, aes(x=Frequency, y=TS), lty=1, lwd=2)+theme_classic()+theme(text=element_text(size=14))
ggplot(data=o_sim, aes(x=Frequency, y=theta, fill=TS))+
geom_raster()+
scale_fill_viridis_c()+
scale_y_continuous(expand=c(0,0))+
scale_x_continuous(expand=c(0,0))+
theme_classic()+theme(text=element_text(size=14))
## ----plots_L------------------------------------------------------------------
l_sim = melt(res$ysimL)
l_sim$Length = res$L[l_sim$Var2]
l_sim$Frequency = res$var[l_sim$Var1]
l_sim=l_sim[,3:ncol(l_sim)]
names(l_sim)[1] <- 'TS'
ggplot()+geom_line(data=l_sim, aes(x = Frequency, y=TS, group=Length),lty=2, lwd=0.5, alpha=0.4)+
geom_line(data=mTS, aes(x=Frequency, y=TS), lty=1, lwd=2)+theme_classic()+theme(text=element_text(size=14))
ggplot(data=l_sim, aes(x=Frequency, y=Length, fill=TS))+
geom_raster()+
scale_fill_viridis_c()+
scale_y_continuous(expand=c(0,0))+
scale_x_continuous(expand=c(0,0))+
theme_classic()+theme(text=element_text(size=14))
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