Update a BioCro model definition

Following an optimization, it is typically necessary to update the initial values and/or parameters of a base model definition with new values determined during the optimization. The update_model function helps to streamline this process. It is expected that this function will be called after objective_function.

Usage

update_model(
    base_model_definition,
    independent_args,
    new_ind_arg_values,
    dependent_arg_function = NULL
  )

Arguments

base_model_definition

The same value that was passed to objective_function.

independent_args

The same value that was passed to objective_function.

new_ind_arg_values

A numeric vector representing new values of the independent arguments, typically determined by an optimizer.

dependent_arg_function

The same value that was passed to objective_function.

Value

A list based on base_model_definition but with new values of some of its initial_values and parameters, as specified by the elements of independent_args and new_ind_arg_values.

Examples

if (require(BioCro)) {
  # Update the default Soybean-BioCro model with new values of `Leaf` (an
  # initial value) and `alphaStem` (a parameter)
  base_model <- BioCro::soybean

  new_model <- update_model(
    base_model,
    list(Leaf = 1, alphaLeaf = 2), # The values here will not be used
    c(1000, 2000)                  # These are the actual new values
  )

  # Compare the two models
  cat('\n\nComparing initial Leaf values:\n')
  print(base_model$initial_values$Leaf)
  print(new_model$initial_values$Leaf)

  cat('\n\nComparing alphaLeaf values:\n')
  print(base_model$parameters$alphaLeaf)
  print(new_model$parameters$alphaLeaf)
}
#> 
#> 
#> Comparing initial Leaf values:
#> [1] 0.06312
#> [1] 1000
#> 
#> 
#> Comparing alphaLeaf values:
#> [1] 23.8895
#> [1] 2000