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Snapshot class for OSP snapshots

Snapshot.Rd

An R6 class that represents an OSP snapshot file. This class provides methods to access different components of the snapshot and visualize its structure.

Active bindings

data

The aggregated data of the snapshot from all components

pksim_version

The human-readable PKSIM version corresponding to the snapshot version

path

The path to the snapshot file relative to the working directory

compounds

List of Compound objects in the snapshot

expression_profiles

List of ExpressionProfile objects in the snapshot

individuals

List of Individual objects in the snapshot

formulations

List of Formulation objects in the snapshot

populations

List of Population objects in the snapshot

events

List of Event objects in the snapshot

protocols

List of Protocol objects in the snapshot

observed_data

List of DataSet objects (observed data) in the snapshot

Methods

Public methods

Method new()

Create a new Snapshot object from a JSON file or a list

Usage

Snapshot$new(input)

Arguments

input

Path to the snapshot JSON file, URL, template name, or a list containing snapshot data

Returns

A new Snapshot object

Method print()

Print a summary of the snapshot

Usage

Snapshot$print(...)

Arguments

...

Additional arguments passed to print methods

Returns

Invisibly returns the snapshot object

Method export()

Export the snapshot to a JSON file

Usage

Snapshot$export(path)

Arguments

path

Path to save the JSON file

Returns

Invisibly returns the object

Method add_individual()

Add an Individual object to the snapshot

Usage

Snapshot$add_individual(individual)

Arguments

individual

An Individual object created with create_individual()

Returns

Invisibly returns the object

Examples

\dontrun{
# Create a new individual
ind <- create_individual(name = "New Patient", age = 35, weight = 70)

# Add the individual to a snapshot
snapshot$add_individual(ind)
}

Method remove_individual()

Remove an individual from the snapshot by name

Usage

Snapshot$remove_individual(individual_name)

Arguments

individual_name

Character vector of individual name(s) to remove

Returns

Invisibly returns the object

Examples

\dontrun{
# Remove an individual from the snapshot
snapshot$remove_individual("Subject_001")
}

Method add_formulation()

Add a Formulation object to the snapshot

Usage

Snapshot$add_formulation(formulation)

Arguments

formulation

A Formulation object created with create_formulation()

Returns

Invisibly returns the object

Examples

\dontrun{
# Create a new formulation
form <- create_formulation(name = "Tablet", type = "Weibull")

# Add the formulation to a snapshot
snapshot$add_formulation(form)
}

Method remove_formulation()

Remove a formulation from the snapshot by name

Usage

Snapshot$remove_formulation(formulation_name)

Arguments

formulation_name

Character vector of formulation name(s) to remove

Returns

Invisibly returns the object

Examples

\dontrun{
# Remove a formulation from the snapshot
snapshot$remove_formulation("Tablet")
}

Method remove_population()

Remove a population from the snapshot by name

Usage

Snapshot$remove_population(population_name)

Arguments

population_name

Character vector of population name(s) to remove

Returns

Invisibly returns the object

Examples

\dontrun{
# Remove a population from the snapshot
snapshot$remove_population("pop_1")
}

Method add_expression_profile()

Add an ExpressionProfile object to the snapshot

Usage

Snapshot$add_expression_profile(expression_profile)

Arguments

expression_profile

An ExpressionProfile object

Returns

Invisibly returns the object

Examples

\dontrun{
# Create a new expression profile
profile_data <- list(
  Type = "Enzyme",
  Species = "Human",
  Molecule = "CYP3A4",
  Category = "Healthy",
  Parameters = list()
)
profile <- ExpressionProfile$new(profile_data)

# Add the expression profile to a snapshot
snapshot$add_expression_profile(profile)
}

Method remove_expression_profile()

Remove expression profiles from the snapshot by ID

Usage

Snapshot$remove_expression_profile(profile_id)

Arguments

profile_id

Character vector of expression profile IDs to remove

Returns

Invisibly returns the object

Examples

\dontrun{
# Remove an expression profile from the snapshot
snapshot$remove_expression_profile("CYP3A4|Human|Healthy")
}

Method add_observed_data()

Add a DataSet object (observed data) to the snapshot

Usage

Snapshot$add_observed_data(observed_data)

Arguments

observed_data

A DataSet object created from snapshot observed data

Returns

Invisibly returns the object

Method remove_observed_data()

Remove observed data from the snapshot by name

Usage

Snapshot$remove_observed_data(observed_data_name)

Arguments

observed_data_name

Character vector of observed data names to remove

Returns

Invisibly returns the object

Method clone()

The objects of this class are cloneable with this method.

Usage

Snapshot$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples


## ------------------------------------------------
## Method `Snapshot$add_individual`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Create a new individual
ind <- create_individual(name = "New Patient", age = 35, weight = 70)

# Add the individual to a snapshot
snapshot$add_individual(ind)
} # }

## ------------------------------------------------
## Method `Snapshot$remove_individual`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Remove an individual from the snapshot
snapshot$remove_individual("Subject_001")
} # }

## ------------------------------------------------
## Method `Snapshot$add_formulation`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Create a new formulation
form <- create_formulation(name = "Tablet", type = "Weibull")

# Add the formulation to a snapshot
snapshot$add_formulation(form)
} # }

## ------------------------------------------------
## Method `Snapshot$remove_formulation`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Remove a formulation from the snapshot
snapshot$remove_formulation("Tablet")
} # }

## ------------------------------------------------
## Method `Snapshot$remove_population`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Remove a population from the snapshot
snapshot$remove_population("pop_1")
} # }

## ------------------------------------------------
## Method `Snapshot$add_expression_profile`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Create a new expression profile
profile_data <- list(
  Type = "Enzyme",
  Species = "Human",
  Molecule = "CYP3A4",
  Category = "Healthy",
  Parameters = list()
)
profile <- ExpressionProfile$new(profile_data)

# Add the expression profile to a snapshot
snapshot$add_expression_profile(profile)
} # }

## ------------------------------------------------
## Method `Snapshot$remove_expression_profile`
## ------------------------------------------------

if (FALSE) { # \dontrun{
# Remove an expression profile from the snapshot
snapshot$remove_expression_profile("CYP3A4|Human|Healthy")
} # }