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#' Mussel bioenergetic spatialized model - spatialization loop
#'
#' Solves the bioenergetic balance for Mussel
#'
#' @param userpath the path where the working folder is located
#' @param forcings 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] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
#' @return A list containing model outputs that main script saves to .nc; .csv and .asc files
#'
#' @import matrixStats plotrix rstudioapi
#'
Mussel_spatial_loop<-function(userpath,forcings){
# rm(list=ls()) # Clean workspace
out_pre<-Mussel_spatial_pre_int(userpath,forcings)
# Extract preprocessor outputs
Param=out_pre[[1]]
times=out_pre[[2]]
Dates=out_pre[[3]]
IC=out_pre[[4]]
Tint=out_pre[[5]]
Phyint=out_pre[[6]]
DTint=out_pre[[7]]
POCint=out_pre[[8]]
Ccont=out_pre[[9]]
Ncont=out_pre[[10]]
Pcont=out_pre[[11]]
POMint=out_pre[[12]]
TSSint=out_pre[[13]]
CS=out_pre[[14]]
# Solves ODE
out_RKsolver<-Mussel_spatial_RKsolver(Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint)
# Post-process data
out_post<-Mussel_spatial_post(userpath, out_RKsolver, times, Dates,CS)
return(out_post)
}
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