Create a new individual

Create a new individual with the specified properties. All arguments are optional and will use default values if not provided.

Usage

create_individual(
  name = "New Individual",
  species = NULL,
  population = NULL,
  gender = NULL,
  age = NULL,
  weight = NULL,
  height = NULL,
  gestational_age = NULL,
  calculation_methods = NULL,
  disease_state = NULL,
  disease_state_parameters = NULL,
  seed = NULL,
  expression_profiles = NULL,
  description = NULL,
  parameters = NULL
)

Arguments

name

Character. Name of the individual

species

Character. Species of the individual (must be valid ospsuite Species)

population

Character. Population of the individual (must be valid ospsuite HumanPopulation)

gender

Character. Gender of the individual (must be valid ospsuite Gender)

age

An age() object, or NULL.

weight

A weight() object, or NULL.

height

A height() object, or NULL.

gestational_age

A gestational_age() object, or NULL (for infant/preterm individuals).

calculation_methods

Character vector. Calculation methods used for the individual

disease_state

Character. Disease-state name of the individual (optional). Together with disease_state_parameters it feeds the modern Disease object ({ Name, Parameters }) emitted under OriginData$Disease, matching create_expression_profile().

disease_state_parameters

List. Parameters for the disease state (optional), keyed on Name in the emitted Disease object.

seed

Integer. Simulation seed (optional)

expression_profiles

Character vector of expression-profile composite names (Molecule|Species|Category) to attach to the individual. Default NULL (no profiles).

description

Character. Free-text description of the individual. Default NULL (no description).

parameters

List of localized parameters (each created with create_parameter(path = ...)), or the equivalent raw list form the loader consumes, applied as the individual's Parameters overrides. Each entry must be path-bearing. Default NULL (no parameter overrides).

Value

An Individual object

See also

age(), weight(), height(), gestational_age() for the demographic value-object helpers.

Examples

# Create a minimal individual
individual <- create_individual(name = "Test Individual")

# Create a complete individual
individual <- create_individual(
  name = "John Doe",
  species = "Human",
  population = "European_ICRP_2002",
  gender = "MALE",
  age = age(30),
  weight = weight(70),
  height = height(175)
)

# Create an individual with calculation methods
individual <- create_individual(
  name = "Test Individual",
  calculation_methods = c("Method 1", "Method 2", "Method 3")
)

# Create an individual with disease state (emitted as the modern
# `Disease` object: `OriginData$Disease = { Name, Parameters }`)
individual <- create_individual(
  name = "Patient",
  disease_state = "CKD",
  disease_state_parameters = list(
    list(Name = "eGFR", Value = 45.0, Unit = "ml/min/1.73m²")
  )
)

# Create an individual referencing expression profiles with a localized
# parameter and a description
individual <- create_individual(
  name = "Subject 1",
  expression_profiles = c("CYP3A4|Human|Healthy", "P-gp|Human|Healthy"),
  description = "Reference healthy adult",
  parameters = list(
    create_parameter(
      path = "Organism|Liver|EHC continuous fraction",
      value = 1
    )
  )
)