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Parse PKMODEL BLOCK data

Source: R/handle_spec_block.R
PKMODEL.Rd

Parse PKMODEL BLOCK data

Usage

PKMODEL(
  ncmt = 1,
  depot = FALSE,
  cmt = NULL,
  advan = NULL,
  trans = NULL,
  env = list(),
  pos = 1,
  ...
)

Arguments

ncmt

number of compartments; must be 1 (one-compartment, not including a depot dosing compartment), 2 (two-compartment model, not including a depot dosing compartment), or 3 (three-compartment model, not including a depot dosing compartment).

depot

logical indicating whether to add depot compartment.

cmt

compartment names as comma-delimited character.

advan

ADVAN subroutine number; can be 1, 2, 3, 4, 11, or 12; when specified, ncmt and depot are derived from the ADVAN number and the appropriate compartments are registered to the model unless specified elsewhere (see Details).

trans

the parameterization for the PK model; must be 1, 2, 4, or 11.

env

parse environment.

pos

block position number.

...

not used.

Details

When using $PKMODEL, certain symbols must be defined in the model specification depending on the value of ncmt, depot and trans.

  • ncmt 1, depot FALSE, trans 2: CL, V

  • ncmt 1, depot TRUE , trans 2: CL, V, KA

  • ncmt 2, depot FALSE, trans 4: CL, V1, Q, V2

  • ncmt 2, depot TRUE , trans 4: CL, V2, Q, V3, KA

  • ncmt 3, depot FALSE, trans 4: CL, V1, Q2, V2, Q3, V3

  • ncmt 3, depot TRUE , trans 4: CL, V2, Q3, V3, KA, Q4, V4

If trans=11 is specified, use the symbols listed above for the ncmt / depot combination, but append i at the end (e.g. CLi or Q2i or KAi).

If trans=1, the user must utilize the following symbols:

  • pred_CL for clearance

  • pred_V or pred_V2 for central compartment volume of distribution

  • pred_Q for intercompartmental clearance

  • pred_V3 for peripheral compartment volume of distribution

  • pred_KA for absorption rate constant

  • pred_Q2 for second intercompartmental clearance (3-cmt)

  • pred_VP2 or pred_V4 for second peripheral compartment volume of distribution (3-cmt)

When advan is supplied by the user, default compartments are registered in the model unless specified elsewhere. Compartment names are A1, A2, etc. to the number of compartments for the specified advan. These compartments will not be added in case (1) the model contains a $CMT block (2) the model contains a $INIT block or (3) no compartments have been registered in the model at the time $PKMODEL is processed (for example, via $YAML).

See also

BLOCK_PARSE

Examples

if (FALSE) { # \dontrun{
code <- '
$PARAM CL = 1, V2 = 20, Q = 2, V3 = 10, KA = 1
$PKMODEL ncmt = 2, depot = TRUE, cmt = "GUT CENT PERIPH"
'
mod <- mcode("pk2-example", code)

code <- '
$PARAM CL = 1, V2 = 20, Q3 = 2, V3 = 10, Q4 = 0.5, V4 = 50, KA = 1
$PKMODEL advan = 12
'
mod <- mcode("advan12-example", code)
} # }