BLOCK_PARSE: Functions to parse code blocks

In mrgsolve: Simulate from ODE-Based Models

Functions to parse code blocks

Description

Most of the basic blocks are listed in this help topic. But see also PKMODEL() which has more-involved options and is documented separately.

Usage

PARAM(
  x,
  env,
  pos = 1,
  annotated = FALSE,
  object = NULL,
  as_object = FALSE,
  covariates = FALSE,
  input = FALSE,
  tag = NULL,
  ...
)

FIXED(x, env, pos = 1, annotated = FALSE, ...)

THETA(
  x,
  env,
  pos = 1,
  annotated = FALSE,
  object = NULL,
  as_object = FALSE,
  name = "THETA",
  fill = NULL,
  ...
)

INIT(x, env, pos = 1, annotated = FALSE, object = NULL, as_object = FALSE, ...)

CMT(
  x,
  env,
  pos = 1,
  annotated = FALSE,
  object = NULL,
  as_object = FALSE,
  number = NULL,
  prefix = "A",
  ...
)

CAPTURE(x, env, pos = 1, annotated = FALSE, etas = NULL, ...)

HANDLEMATRIX(
  x,
  env,
  pos = 1,
  annotated = FALSE,
  object = NULL,
  as_object = FALSE,
  name = "...",
  type = NULL,
  oclass = "",
  prefix = "",
  labels = NULL,
  unlinked = FALSE,
  ...
)

Arguments

x	data
env	parse environment
pos	block position
annotated	logical
object	the name of an object in ENV
as_object	indicates that object code is being provided
covariates	logical; mark as covariates and potentially required data input
input	logical; mark as potentially required data input
tag	space or comma-separated user-defined tags for the parameter block
...	passed
name	block name
fill	deprecated; not used
number	number of compartments to create
prefix	a prefix to add to the label
etas	allows for block capture of ETAs in the simulated output; this should be R code that will get parsed and evaluated; the result should be an integer-like vector which identifies which ETAs will be captured.
type	internal use
oclass	internal use
labels	aliases to use for simulated ETA values
unlinked	internal use

Details

When using object or as_object populate the block contents, the following types are required

• PARAM: a named list

• INIT : a named list

• THETA : a numeric vector; names are ignored

• CMT: a character vector

• OMEGA: matrix; set rownames on the matrix to create ETA labels; setting rownames is the only way to specify labels when working through the object or as_object directives

• SIGMA: matrix; set rownames on the matrix to create EPS labels; setting rownames is the only way to specify labels when working through the object or as_object directives

See Also

PKMODEL()

mrgsolve documentation built on Oct. 18, 2024, 5:12 p.m.