Observer class for OSP snapshot observer sets

An R6 class that represents a single observer inside an ObserverSet. An observer is a simulation-time formula that computes a derived quantity from the underlying model (for example an amount observer or a container observer), used to expose values that are not natural model outputs.

In an OSP snapshot, each observer is one entry of the Observers array nested inside an ObserverSets building block. An observer is not itself a building block; it lives inside an ObserverSet.

Active bindings

data: The raw Observer list as it appears in the snapshot JSON (read-only).
name: The name of the observer. Writable: must be a non-empty scalar string.
type: The observer type. PK-Sim recognises "Amount" (an AmountObserverBuilder) and "Container" (a ContainerObserverBuilder). On assignment, a non-NULL value is validated against these two; assigning NULL removes the type.
dimension: The dimension of the observed quantity, resolved in PK-Sim via IDimensionRepository.DimensionByName(). Writable: must be a non-empty scalar string, or NULL to clear. There is no closed set of dimension names to validate against, so a required string is the strongest check available.
formula: The full ExplicitFormula object backing the observer, as a list with Name, Formula (the expression string), Dimension, and References (a list of FormulaUsablePath entries, each with Alias, Path, and Dimension). NULL when the observer carries no formula. Setting this field replaces the whole structure; pass NULL to drop it. For the inner expression string or dimension only, use formula_expression or formula_dimension.
formula_expression: The expression string of the underlying ExplicitFormula (Formula$Formula in the snapshot JSON). Setting writes back to the inner Formula$Formula field and preserves the sibling Name, Dimension, and References entries. To build a complete ExplicitFormula (including Name and References), assign to formula instead.
formula_dimension: The output dimension of the underlying ExplicitFormula (Formula$Dimension in the snapshot JSON), resolved in PK-Sim via IDimensionRepository.DimensionByName(). Setting writes back to the inner Formula$Dimension field.
formula_references: The References list of the underlying ExplicitFormula, where each entry is a named list with Alias, Path, and Dimension. Assign a list of create_formula_reference() outputs (or raw {Alias, Path, Dimension} lists) to replace it, preserving the sibling Formula$Name, Formula$Formula, and Formula$Dimension (the Formula is created if absent). Assign NULL to remove the references; when no Formula exists this is a no-op that does not create an empty Formula.
container_tags: The Tag values from the observer's ContainerCriteria, joined with |. There is no ContainerPath field in the snapshot JSON; this binding is synthesized from the tags found in ContainerCriteria. NULL when the observer carries no container criteria.
container_criteria: The full ContainerCriteria list, each entry a named list with Tag and (optionally) Type. Unlike container_tags, this preserves each condition's Type verbatim (including non-enum values such as "MatchTag"). Assign a list of create_descriptor_condition() outputs (or raw {Tag, Type} lists) to replace it; assign NULL to remove it.
molecule_list: The full MoleculeList object (ForAll, MoleculeNamesToInclude, MoleculeNamesToExclude) or NULL. Assign a create_molecule_list() output (or an equivalent raw list) to replace it; assign NULL to remove it.

Methods

`Observer$new()`

Create a new Observer object.

Usage

Observer$new(data = list())

Arguments

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

Returns

A new Observer object

`Observer$print()`

Print a short summary of the observer.

Usage

Observer$print(...)

Arguments

...: Additional arguments (unused).

Returns

Invisibly returns the Observer object.

`Observer$to_df()`

Convert the observer to a single-row tibble suitable for the tibble-layer exporter. Columns are name, type, dimension, formula_expression, formula_dimension, formula_references, and container_tags. formula_references collapses each FormulaUsablePath entry (Alias, Path, Dimension) to "alias=path" and joins entries with |; NA when the observer carries no references.

Usage

Observer$to_df()

Returns

A tibble with one row.

`Observer$clone()`

The objects of this class are cloneable with this method.

Usage

Observer$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples

observer <- Observer$new(list(
  Name = "brain_plasma_conc",
  Type = "Container",
  Dimension = "Concentration (molar)",
  Formula = list(
    Name = "brain_plasma_conc_formula",
    Formula = "Conc_Br",
    Dimension = "Concentration (molar)",
    References = list(list(
      Alias = "Conc_Br",
      Path = "Organism|Brain|Plasma|Drug|Concentration",
      Dimension = "Concentration (molar)"
    ))
  )
))
observer$name
#> [1] "brain_plasma_conc"
observer$type
#> [1] "Container"
observer$formula_expression
#> [1] "Conc_Br"
observer$formula_dimension
#> [1] "Concentration (molar)"
observer$formula_references
#> [[1]]
#> [[1]]$Alias
#> [1] "Conc_Br"
#> 
#> [[1]]$Path
#> [1] "Organism|Brain|Plasma|Drug|Concentration"
#> 
#> [[1]]$Dimension
#> [1] "Concentration (molar)"
#> 
#>