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Set up and compile a rodeo model.

model_setup.Rd

This function orchestrates the setup of a rodeo model by reading various definition files (variables, parameters, functions, processes, stoichiometry), applying replacements to process expressions, generating forcing functions, and finally compiling the model.

Usage

model_setup(
  base_path = NULL,
  vars = "vars.tsv",
  pars = "pars.tsv",
  funs = "funs.tsv",
  pros = "pros.tsv",
  stoi = "stoi.tsv",
  repl = "replacements.tsv",
  datafile = paste0(system.file("models", package = "salmoRodeo"), "/inputs.tsv"),
  input_columns = c("stagnation", "VE", "ZMIX", "QIN", "IIN", "TE", "PIN", "NIN",
    "POMIN"),
  sources = "functions_extended.f95",
  phyto_groups = 3
)

Arguments

base_path

Path to the model files. Can be empty, if vars, pars, funs, pros, soi and repl contain full path and file names.

vars

File name of the variables definition TSV file.

pars

File name of the parameters definition TSV file.

funs

File name of the functions definition TSV file.

pros

File name of the processes definition TSV file.

stoi

File name of the stoichiometry definition TSV file.

repl

File name of the replacements definition TSV file.

datafile

Path and file name of the input data TSV file used for forcings.

input_columns

A character vector of column names from datafile to be used as input forcings.

sources

File name to additional Fortran source files to be compiled with the model (e.g., functions_extended.f95).

phyto_groups

An integer (2 or 3) indicating the number of phytoplankton groups, affecting how process and replacement files are read.

Value

A rodeo model object, compiled and ready for simulation.

Examples

if (FALSE) { # \dontrun{
# This example requires dummy files and the 'rodeo' package
# and is skipped in automatic checks.
# Create dummy files
dir.create("model_files", showWarnings = FALSE)
cat("name\tmin\tmax\tunit\tdescription\n",
    "N\t0\tInf\tmmol/m3\tNitrogen\n", file = "model_files/vars.tsv")
cat("name\tdefault\tunit\tdescription\n",
    "KN\t0.1\tmmol/m3\tHalf-saturation constant for N\n", file = "model_files/pars.tsv")
cat("name\texpression\n",
    "f_N\tN/(KN+N)\n", file = "model_files/funs.tsv")
cat("name\texpression\ttwoPhytoGroups\tthreePhytoGroups\n",
    "uptake\tN*f_N\tN*f_N_2\tN*f_N_3\n", file = "model_files/pros.tsv")
cat("process\tN\n",
    "uptake\t-1\n", file = "model_files/stoi.tsv")
cat("pattern\treplacement\ttwoPhytoGroups\tthreePhytoGroups\n",
    "N\tNO3\tN_two\tN_three\n", file = "model_files/replacements.tsv")
cat("stagnation\tVE\n",
    "1\t10\n",
    "2\t20\n",
    file = "model_files/inputs.tsv")

# Define a dummy function_extended.f95 (can be empty for this example)
cat("SUBROUTINE dummy_ext()\nEND SUBROUTINE\n", file = "model_files/functions_extended.f95")

# Run model setup
model_obj <- model_setup(
  vars = "model_files/vars.tsv",
  pars = "model_files/pars.tsv",
  funs = "model_files/funs.tsv",
  pros = "model_files/pros.tsv",
  stoi = "model_files/stoi.tsv",
  repl = "model_files/replacements.tsv",
  datafile = "model_files/inputs.tsv",
  input_columns = c("stagnation", "VE"),
  sources = "model_files/functions_extended.f95",
  phyto_groups = 3
)

# Check if model is compiled (it should be)
print(model_obj$is_compiled())

# Clean up dummy files
unlink("model_files", recursive = TRUE)
} # }