Create a new schema item — create_schema

Create a SchemaItem for an Advanced Protocol from named arguments. This is a thin factory around SchemaItem$new() that builds the raw list shape for you.

A schema item is one application inside a Schema of an Advanced Protocol. It carries an application type, an optional formulation key, target organ and compartment, and the application-level parameters (dose, start time, ...).

Usage

create_schema_item(
  name,
  application_type,
  formulation_key = NULL,
  target_organ = NULL,
  target_compartment = NULL,
  parameters = NULL,
  dose = NULL,
  dose_unit = "mg",
  start_time = NULL,
  start_time_unit = "h"
)

Arguments

name: Character. Name of the schema item (required).
application_type: Character. Application type for the schema item (required). Must be one of the canonical PK-Sim application types: "Oral", "Intravenous", "IntravenousBolus", or "UserDefined".
formulation_key: Character. Formulation key linking the schema item to a formulation selection in the owning simulation.
target_organ: Character. Target organ for the application. Only valid when application_type is "UserDefined".
target_compartment: Character. Target compartment for the application. Only valid when application_type is "UserDefined".
parameters: List of Parameter objects (created with create_parameter()) or raw parameter lists. These become the application-level parameters (dose, start time, ...). The promoted dose and start_time arguments flow into the same "InputDose" and "Start time" parameters, so supplying a setting both as a promoted argument and as the matching parameters entry is an error.
dose: Numeric scalar dose for the application, written as a single InputDose parameter. NULL (default) emits no dose parameter. The dose family (plain dose, per body weight, or per body surface area) is selected by dose_unit.
dose_unit: Character. Unit for dose, default "mg". Must be a dose-family unit (a Mass, Amount, dose-per-body-weight, or dose-per-body-surface-area unit, for example "mg", "mg/kg", or "mg/m²"). Consulted only when dose is supplied.
start_time: Numeric scalar application start time, written as a "Start time" parameter. NULL (default) emits no start-time parameter. Zero and negative values are allowed.
start_time_unit: Character. Unit for start_time, default "h", validated against the "Time" dimension. Consulted only when start_time is supplied.

Value

A SchemaItem object.

Examples

# An oral schema item using the promoted dose and start-time arguments
item <- create_schema_item(
  name = "Item 1",
  application_type = "Oral",
  dose = 10,
  dose_unit = "mg",
  start_time = 0
)

# The same, authored through the free-form `parameters` escape hatch
item <- create_schema_item(
  name = "Item 1",
  application_type = "Oral",
  parameters = list(
    create_parameter(name = "Start time", value = 0, unit = "h"),
    create_parameter(name = "InputDose", value = 10, unit = "mg")
  )
)

# A user-defined schema item targeting the venous blood plasma
item <- create_schema_item(
  name = "User defined",
  application_type = "UserDefined",
  target_organ = "VenousBlood",
  target_compartment = "Plasma",
  dose = 5
)