atlantistools (version 0.4.3)

change_prm_cohort: Change biological parameterfile for parameters which expect multiple values.

Description

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

Usage

change_prm_cohort(prm_biol, select_acronyms, roc, parameter, relative = TRUE,
  save_to_disc = TRUE)

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

Matrix of multiplication factors which shall be applied to the old set of parameters. Please supply one row per selected group. Each row should have as many entries as the parameter itself. E.g. if you want to change the clearance rate for two fish groups you need to supply a matrix with 2 rows and 10 columns. In case you use different cohort numbers for age-structured groups supply a list of multiplication factors. Each list entry should be group specific.

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.

Value

parameterfile *.prm file with the new parameter values.

Examples

# NOT RUN {
d <- system.file("extdata", "setas-model-new-trunk", package = "atlantistools")

new_prm <- change_prm_cohort(prm_biol = file.path(d, "VMPA_setas_biol_fishing_Trunk.prm"),
                             select_acronyms = c("FPS", "FVS"),
                             roc = matrix(rep(2, times = 20), nrow = 2, ncol = 10),
                             parameter = "C",
                             save_to_disc = FALSE)
# C_FPS is in line 640. Old values are 0.0002 0.3 0.6 0.6 0.6 0.6 0.5 0.5 0.4 and 0.4.
new_prm[640:641]
# C_FVS is in line 652. Old values are 40.0 40.0 40.0 120.0 150.0 250.0 250.0 300.0 300.0 and 300.0.
new_prm[652:653]

# Also works for lists as argument
new_prm <- change_prm_cohort(prm_biol = file.path(d, "VMPA_setas_biol_fishing_Trunk.prm"),
                             select_acronyms = c("FPS", "FVS"),
                             roc = list(rep(3, times = 10), rep(2, times = 10)),
                             parameter = "C",
                             save_to_disc = FALSE)
# }