Protocol class for OSP snapshot protocols — Protocol • osp.snapshots

An R6 class that represents a protocol in an OSP snapshot. This class provides methods to access different properties of a protocol and display a summary of its information. Protocols can be either simple (with dosing intervals) or advanced (with schemas and schema items).

An Advanced Protocol's schemas are exposed as a named list of Schema objects, each of which owns a list of SchemaItem objects. Simple Protocols expose their single application directly through the application_type, dosing_interval, and parameters fields.

Active bindings

data: The raw data of the protocol, refreshed from the wrapped Schema objects so mutations through the R6 surface flow back into the snapshot payload (read-only).
name: The name of the protocol. Writable: must be a non-empty scalar string.
is_advanced: Whether the protocol is advanced (schema-based)
application_type: The application type (for simple protocols). Writable: must be one of the canonical PK-Sim application types (see create_protocol()'s application_type argument), or NULL to clear.
dosing_interval: The dosing interval (for simple protocols). Writable: must be one of the fixed PK-Sim dosing intervals (see create_protocol()'s dosing_interval argument), or NULL to clear.
time_unit: The time unit for the protocol. Writable: must be a valid unit for dimension "Time", or NULL to clear.
parameters: The parameters of the protocol (for simple protocols). Writable: must be a list, or NULL to clear.
schemas: A named list of Schema objects for advanced protocols. Names are taken from each schema's name field (duplicates are disambiguated by make.unique). Simple protocols return an empty list.

Methods

`Protocol$new()`

Create a new Protocol object

Usage

Protocol$new(data)

Arguments

data: Raw protocol data from a snapshot

Returns

A new Protocol object

`Protocol$print()`

Print a summary of the protocol including its properties and parameters.

Usage

Protocol$print(...)

Arguments

...: Additional arguments passed to print methods

Returns

Invisibly returns the Protocol object for method chaining

`Protocol$to_df()`

Convert protocol data to a single consolidated tibble. Advanced protocols emit one row per SchemaItem and join back to the protocol via protocol_name. Simple protocols emit a single row.

Usage

Protocol$to_df()

Returns

A tibble containing all protocol data in a single data frame

`Protocol$get_human_application_type()`

Get human-readable application type

Usage

Protocol$get_human_application_type()

Returns

Character string with human-readable application type

`Protocol$get_human_dosing_interval()`

Get human-readable dosing interval

Usage

Protocol$get_human_dosing_interval()

Returns

Character string with human-readable dosing interval

`Protocol$clone()`

The objects of this class are cloneable with this method.

Usage

Protocol$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.