Nothing
#' Clam bioenergetic individual model preprocessor (alternativer version)
#'
#' @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]
#' @export
#'
#' @import matrixStats plotrix rstudioapi
#'
#' @import grDevices graphics utils stats
#'
ClamF_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]]
cat("Data preprocessing")
# Read forcings and parameters from .csv files
Param_matrix=read.csv(paste0(userpath,"/ClamF_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[1:25,3])) # Vector containing all parameters
Dates=Param_matrix[27:28,3] # Vector containing the starting and ending date of teh simulation
IC=as.double(as.matrix(Param_matrix[26,3])) # Initial weight condition
CS=as.double(as.matrix(Param_matrix[29,3])) # 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(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]
Ww=as.vector(matrix(0,nrow=ti)) # Initialize vector weight
Ww[ti]=IC # Wet weight initial value [g]
times<-cbind(ti, tf, timestep) # Vector with integration data
# Initial conditions
a=Param[8] # [cm] Wet weight - length conversion coefficient
k=Param[6] # [-] Wet weight - length conversion exponent
b=Param[9] # [gWW] Dry weight - wet weight conversion coefficient
p=Param[5] # [-] Dry weight - wet weight conversion exponent
Wd=as.vector(matrix(0,nrow=ti)) # Initialize vector dry weight
Wd[ti]=b*Ww[ti]^p # Dry weight initial value [g]
L=as.vector(matrix(0,nrow=ti)) # Initialize vector length
L[ti]=(Ww[ti]/a)^k # Length of the mussel initial value [cm]
# Print to screen inserted parameters
cat(" \n")
cat('The model will be executed with the following parameters:\n');
cat(" \n")
for (i in 1:25){
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,"/ClamF_individual/Inputs/Forcings_plots\n"))
# plot Temperature forcing
Tintsave=Tint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/ClamF_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 Chlorophyll a forcing
Chlaintsave=Chlint[ti:tf]
currentpath=getwd()
filepath=paste0(userpath,"/ClamF_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()
output=list(Param, times, Dates, IC, Tint, Chlint,CS)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.