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#' Clam bioenergetic individual model preprocessor
#'
#' @param userpath the path where folder containing model inputs and outputs is located
#' @param forcings a list containing model forcings
#' @return a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
#' @export
#'
#' @import matrixStats plotrix rstudioapi
#'
#' @import grDevices graphics utils stats
#'
Clam_ind_pre<-function(userpath,forcings){
rm(list=ls()) # Clean workspace
# Extracts forcings values from the list
timeT=forcings[[1]]
Tint=forcings[[2]]
timeChl=forcings[[3]]
Chlint=forcings[[4]]
timePOC=forcings[[5]]
POCint=forcings[[6]]
timePOM=forcings[[7]]
POMint=forcings[[8]]
timeTSS=forcings[[9]]
TSSint=forcings[[10]]
cat("Data preprocessing")
# Read forcings and parameters from .csv files
Param_matrix=read.csv(paste0(userpath,"/Clam_individual/Inputs/Parameters//Parameters.csv"),sep=",") # Reading the matrix containing parameters and their description
# Extract parameters and forcing values from parameters matrix and convert to type 'double' the vector contents
Param=as.double(as.matrix(Param_matrix[1:22,3])) # Vector containing all parameters
Dates=Param_matrix[24:25,3] # Vector containing the starting and ending date of teh simulation
IC=as.double(as.matrix(Param_matrix[23,3])) # Initial weight condition
CS=as.double(as.matrix(Param_matrix[26,3])) # Commercial size
# Prepare data for ODE solution
t0=min(as.numeric(as.Date(timeT[1], "%d/%m/%Y")), as.numeric(as.Date(timeChl[1], "%d/%m/%Y")), as.numeric(as.Date(timePOC[1], "%d/%m/%Y")), as.numeric(as.Date(timePOM[1], "%d/%m/%Y")), as.numeric(as.Date(timeTSS[1], "%d/%m/%Y")), as.numeric(as.Date(Dates[1], "%d/%m/%Y"))) # starting minimum starting date for forcings and observations
timestep=1 # Time step for integration [day]
ti=as.numeric(as.Date(Dates[1], "%d/%m/%Y"))-t0 # Start of integration [day]
tf=as.numeric(as.Date(Dates[2], "%d/%m/%Y"))-t0 # End of integration [day]
weight=as.vector(matrix(0,nrow=ti)) # Initialize vector weight
weight[ti]=IC # Weight initial value [g]
times<-cbind(ti, tf, timestep) # Vector with integration data
# Initial conditions
aF=Param[18] # [gWW] Dry weight - wet weight conversion coefficient
bF=Param[19] # [-] Dry weight - wet weight exponent
a=Param[20] # [m] Dry weight - length conversion coefficient
b=Param[21] # [-] Weight to length exponent
Wd=as.vector(matrix(0,nrow=ti)) # Initialize vector dry weight
Wd[ti]=IC # dry weight initial value [g]
Ww=as.vector(matrix(0,nrow=ti)) # Initialize vector wet weight
Ww[ti]=(Wd[ti]/aF)^(1/bF) # Wet weight initial value [g]
L=as.vector(matrix(0,nrow=ti)) # Initialize vector length
L[ti]=(Ww[ti]/a)^b #Length of the clam initial value [mm]
# Detritus
lambda=Param[22] # Chla-C proportionality coefficient: relates Chlorophyll-a to phytoplankton concentration
Phyint=as.vector(matrix(0,nrow=ti-1)) # Initialize vector Phyint
DTint=as.vector(matrix(0,nrow=ti-1)) # Initialize vector DTint
for (i in ti:tf) {
Phyint[i]=lambda*Chlint[i]/1000 # Phytoplankton concentration [mgC/l]
DTint[i]=POCint[i]-Phyint[i] # Detritus concentration [mgC/l]
if (DTint[i] < 0) { # Adjusts "wrong" detritus values
DTint[i]=0
} # end if
} # end for
# Print to screen inserted parameters
cat(" \n")
cat('The model will be executed with the following parameters:\n');
cat(" \n")
for (i in 1:22){
cat(paste0(toString(Param_matrix[i,2]), ": ", toString(Param_matrix[i,3]), " " ,toString(Param_matrix[i,4])),"\n")
}
cat(" \n")
cat('Weight initial condition is: ', toString(IC)," g\n")
cat(" \n")
cat("Integration is performed between ", toString(Dates[1]), " and ", toString(Dates[2]),"\n")
cat(" \n")
cat('Commercial size is ', toString(CS)," mm")
cat(" \n")
# Plot to screen inserted forcing functions
cat(" \n")
cat("Forcings are represented in graphs available at the following folder\n")
cat(paste0(userpath,"/Clam_individual/Inputs/Forcings_plots\n"))
# Plot Temperature forcing
Tintsave=Tint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/Clam_individual/Inputs/Forcings_plots//Water_temperature.jpeg")
jpeg(filepath,800,600)
days <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), by = "days", length = tf-ti+1)
plot(days, Tintsave, ylab="Water temperature (Celsius degrees)", xlab="",xaxt = "n",type="l",cex.lab=1.4)
labDates <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), tail(days, 1), by = "months")
axis.Date(side = 1, days, at = labDates, format = "%d %b %y", las = 2)
dev.off()
# Plot Chla forcing
Chlaintsave=Chlint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/Clam_individual/Inputs/Forcings_plots//Chlorophyll_a.jpeg")
jpeg(filepath,800,600)
days <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), by = "days", length = tf-ti+1)
plot(days, Chlaintsave, ylab="Chlorophyll_a (mg/m^3)", xlab="", xaxt = "n",type="l",cex.lab=1.4)
labDates <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), tail(days, 1), by = "months")
axis.Date(side = 1, days, at = labDates, format = "%d %b %y", las = 2)
dev.off()
# plot POC forcing
POCintsave=POCint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/Clam_individual/Inputs/Forcings_plots//POC.jpeg")
jpeg(filepath,800,600)
days <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), by = "days", length = tf-ti+1)
plot(days, POCintsave, ylab="POC (mgC/l)", xlab="", xaxt = "n",type="l",cex.lab=1.4)
labDates <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), tail(days, 1), by = "months")
axis.Date(side = 1, days, at = labDates, format = "%d %b %y", las = 2)
dev.off()
# Plot POM forcing
POMintsave=POMint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/Clam_individual/Inputs/Forcings_plots//POM.jpeg")
jpeg(filepath,800,600)
days <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), by = "days", length = tf-ti+1)
plot(days, POMintsave, ylab="POM (mg/l)", xlab="", xaxt = "n",type="l",cex.lab=1.4)
labDates <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), tail(days, 1), by = "months")
axis.Date(side = 1, days, at = labDates, format = "%d %b %y", las = 2)
dev.off()
# Plot TSS forcing
TSSintsave=TSSint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/Clam_individual/Inputs/Forcings_plots//TSM.jpeg")
jpeg(filepath,800,600)
days <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), by = "days", length = tf-ti+1)
plot(days, TSSintsave, ylab="TSM (mg/l)", xlab="", xaxt = "n",type="l",cex.lab=1.4)
labDates <- seq(as.Date(Dates[1], format = "%d/%m/%Y"), tail(days, 1), by = "months")
axis.Date(side = 1, days, at = labDates, format = "%d %b %y", las = 2)
dev.off()
output=list(Param, times, Dates, IC, Tint, Phyint, DTint, POCint, POMint, TSSint, CS)
}
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