OriginData class for OSP snapshot individuals — OriginData • osp.snapshots

An R6 class that represents the demographic starting point of an Individual: species, population, gender, and the physiological parameters (age, gestational age, weight, height) that PK-Sim uses when creating the subject. The set of calculation methods used while deriving the individual is exposed as a CalculationMethods object. Optional disease state metadata is preserved as-is for round-trip fidelity.

In an OSP snapshot, the JSON object is named OriginData and lives under each entry of the Individuals array.

Active bindings

data: The raw OriginData list as it appears in the snapshot JSON, refreshed from the embedded CalculationMethods object (read-only).
species: The species of the individual.
population: The population of the individual.
gender: The gender of the individual.
age: Numeric age value of the individual (in age_unit). Writable: assign an age() object to set the value and unit together. A bare numeric scalar is rejected; use age() instead.
age_unit: Unit string for age.
gestational_age: Numeric gestational age value (in gestational_age_unit), used for preterm individuals. Writable: assign a gestational_age() object to set the value and unit together. A bare numeric scalar is rejected; use gestational_age() instead.
gestational_age_unit: Unit string for gestational_age.
weight: Numeric weight value of the individual (in weight_unit). Writable: assign a weight() object to set the value and unit together. A bare numeric scalar is rejected; use weight() instead.
weight_unit: Unit string for weight.
height: Numeric height value of the individual (in height_unit). Writable: assign a height() object to set the value and unit together. A bare numeric scalar is rejected; use height() instead.
height_unit: Unit string for height.
calculation_methods: A CalculationMethods object holding the calculation methods PK-Sim applies while creating the individual.
disease_state: Optional disease-state name. Read from the modern Disease object (Disease$Name) or, for a loaded legacy snapshot, the legacy DiseaseState key. Writing sets the modern Disease$Name.
disease_state_parameters: Optional list of disease-state parameters. Read from the modern Disease object (Disease$Parameters) or, for a loaded legacy snapshot, the legacy DiseaseStateParameters key. Writing sets the modern Disease$Parameters.

Methods

`OriginData$new()`

Create a new OriginData object

Usage

OriginData$new(data = list())

Arguments

data: Raw OriginData list from a snapshot. May be NULL or an empty list, both of which create an empty OriginData.

Returns

A new OriginData object

`OriginData$print()`

Print a summary of the origin data

Usage

OriginData$print(...)

Arguments

...: Additional arguments passed to print methods

Returns

Invisibly returns the OriginData object

`OriginData$clone()`

The objects of this class are cloneable with this method.

Usage

OriginData$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.