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Change biological parameterfile to simplify automated ATLANTIS calibrations.

Source: R/change-prm.R
change_prm.Rd

This function is used to help automate the calibration routine for ATLANTIS models.

Usage

change_prm(
  prm_biol,
  select_acronyms,
  roc,
  parameter,
  relative = TRUE,
  save_to_disc = TRUE,
  version_flag = 2
)

Arguments

prm_biol

Character string giving the connection to the biological parameterfile. The filename usually contains biol_fishing and does end in .prm.

select_acronyms

Character vector of functional groups which shall be read in. Names have to match the ones used in the *.prm file. Check column "Code" in "functionalGroups.csv" for clarification.

roc

Vector of multiplication factors which shall be applied to the old set of parameters. Please supply one value per selected group. In case relative is FALSE the new absolute values can be passed as roc.

parameter

Character value of the model parameter which shall be changed. Only one parameter can be selected per function call.

relative

Logical if TRUE values are changed relative to base values. If FALSE new values can be passed directly. Default is TRUE.

save_to_disc

Logical indicating if the resulting prm file should be overwritten (TRUE) or not (FALSE). Defaults to TRUE.

version_flag

The version of ATLANTIS model. 1 for bec_dev, 2 for trunk. default is 2..

Value

parameterfile *.prm file with the new parameter values.

Examples

d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")
prm_biol <- file.path(d, "VMPA_setas_biol_fishing_Trunk.prm")

new_prm <- change_prm(prm_biol,
                      select_acronyms = c("FPS", "FVS"),
                      roc = c(2,3),
                      parameter = "KWRR",
                      save_to_disc = FALSE)