AdvancedProtocol

Description of an advanced administration protocol

Active bindings

UUID

Unique identifier (read-only)

Name

Protocol name

Schemas

List of schemas for the advanced protocol

Path

Prefix path for the administration to create default path, otherwise for custom pkmls path should be provided for each schema item protocol

Formulations

Formulations used with protocol

FormulationKey

Formulations Key used with protocol

Methods

Public methods

• AdvancedProtocol$new()

• AdvancedProtocol$addSchema()

• AdvancedProtocol$addProtocolToSchema()

• AdvancedProtocol$extractProtocol()

• AdvancedProtocol$getAllParameterPaths()

• AdvancedProtocol$toSnapshot()

• AdvancedProtocol$print()

• AdvancedProtocol$clone()

---

Method new()

Initialize a new instance of the class

Usage

AdvancedProtocol$new(name = "Protocol", path = NULL)

Arguments

name

Name of the protocol

path

Prefix for the path of administration in the simulations

Returns

A new AdvancedProtocol object.

---

Method addSchema()

Add a schema of administration

Usage

AdvancedProtocol$addSchema(
  startTime,
  numberOfRepetitions,
  timeBetweenRepetitions,
  timeUnit,
  schemaName
)

Arguments

startTime

Starting time of the schema

numberOfRepetitions

Number of repetitions of the schema

timeBetweenRepetitions

Time between repetitions of the schema

timeUnit

Time unit for startTime and timeBetweenRepetitions of the schema

schemaName

Name of the schema

Returns

The updated AdvancedProtocol object.

---

Method addProtocolToSchema()

Add a protocol of administration to an existing schema

Usage

AdvancedProtocol$addProtocolToSchema(protocol, schemaName)

Arguments

protocol

The protocol to add to the schema

schemaName

Name of the schema to add the protocol to

Returns

The updated AdvancedProtocol object.

---

Method extractProtocol()

Extract all single administration to be applied by a protocol. For easier mapping to path in the simulation pkml.

Usage

AdvancedProtocol$extractProtocol(path = self$Path)

Arguments

path

Prefix path for the administration.

Returns

A tibble with the type of administration, time of administration, parameters of the administration and the formulation name.

---

Method getAllParameterPaths()

Extract all parameter paths needed to be changed in the simulation

Usage

AdvancedProtocol$getAllParameterPaths(path = self$Path)

Arguments

path

Prefix path for the administration.

Returns

A character vector with all parameter paths.

---

Method toSnapshot()

Convert to snapshot

Usage

AdvancedProtocol$toSnapshot()

---

Method print()

Print the object to the console

Usage

AdvancedProtocol$print()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

AdvancedProtocol$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.