Package index • osp.snapshots

Import and export

Load snapshots and export modifications

load_snapshot(): Load a snapshot from various sources
export_snapshot(): Export a snapshot to a JSON file
create_snapshot(): Create an empty snapshot
osp_models(): Browse available OSPSuite building block templates

Building blocks

R6 classes wrapping the PK-Sim building blocks and the root snapshot

Snapshot: Snapshot class for OSP snapshots
Compound: Compound class for OSP snapshot compounds
Event: Event class for OSP snapshot events
ExpressionProfile: ExpressionProfile class for OSP snapshot expression profiles
Formulation: Formulation class for OSP snapshot formulations
Individual: Individual class for OSP snapshot individuals
ObserverSet: ObserverSet class for OSP snapshot observer sets
Population: Population class for OSP snapshot populations
Protocol: Protocol class for OSP snapshot protocols
Simulation: Simulation class for OSP snapshot simulations

Leaf and sub-structure types

Reusable R6 leaf classes and sub-structures held inside building blocks

AdvancedParameter: AdvancedParameter class for Population advanced parameters
CalculationMethods: CalculationMethods class for OSP snapshots
CompoundProcessSelection: CompoundProcessSelection class for compound process selections
EventSelection: EventSelection class for Simulation event references
FormulationSelection: FormulationSelection class for Simulation compound formulations
LocalizedParameter: LocalizedParameter class for path-bearing OSP snapshot parameters
Observer: Observer class for OSP snapshot observer sets
ObserverSetSelection: ObserverSetSelection class for Simulation observer-set references
OriginData: OriginData class for OSP snapshot individuals
OutputInterval: OutputInterval class for Simulation output schemas
OutputMapping: OutputMapping class for simulation output-to-observed-data mappings
OutputSchema: OutputSchema class for Simulation output schedules
Parameter: Parameter class for OSP snapshot parameters
Process: Process class for OSP snapshot compound processes
ProtocolSelection: ProtocolSelection class for Simulation compound protocol assignments
Schema: Schema class for OSP advanced protocols
SchemaItem: SchemaItem class for OSP advanced protocols
SolverSettings: SolverSettings class for simulation solver configuration
range(): Create a range object for physiological parameters
Range-class Range: Range class for physiological parameters

Factories

Construct building blocks and leaves from named arguments

create_compound(): Create a new compound
create_compound_process_selection(): Create a compound process selection
create_descriptor_condition(): Create a container criterion for an observer
create_event(): Create a new event
create_event_selection(): Create an event selection for a simulation
create_expression_profile(): Create a new expression profile
create_formula_reference(): Create a formula reference for an observer
create_formulation(): Create a new formulation
create_formulation_selection(): Create a formulation selection for a simulation compound
create_individual(): Create a new individual
create_molecule_list(): Create a molecule list for an observer
create_observed_data(): Create a new observed data set
create_observer(): Create a new observer
create_observer_set(): Create a new observer set
create_observer_set_selection(): Create an observer-set selection for a simulation
create_output_interval(): Create an output interval for a simulation output schema
create_output_mapping(): Create an output-to-observed-data mapping for a simulation
create_output_schema(): Create an output schema for a simulation
create_parameter(): Create a new parameter
create_population(): Create a new population
create_process(): Create a new compound process
create_protocol(): Create a new protocol
create_protocol_selection(): Create a protocol selection for a simulation compound
create_schema(): Create a new schema
create_schema_item(): Create a new schema item
create_solver_settings(): Create a solver settings object for a simulation

Value-object helpers

Bundle a value, unit, and field-specific extras for the create_* factory arguments

lipophilicity(): Lipophilicity value object
fraction_unbound(): Fraction unbound value object
solubility(): Solubility value object
intestinal_permeability(): Intestinal permeability value object
permeability(): Permeability value object
age(): Age value object
weight(): Weight value object
height(): Height value object
gestational_age(): Gestational age value object
time(): Time series value object
values(): Measurement values series value object
error(): Error series value object

Mutators

Add and remove building blocks on a snapshot

add_compound(): Add one or more compounds to a snapshot
add_event(): Add one or more events to a snapshot
add_expression_profile(): Add one or more expression profiles to a snapshot
add_formulation(): Add one or more formulations to a snapshot
add_individual(): Add one or more individuals to a snapshot
add_observed_data(): Add one or more observed-data entries to a snapshot
add_observer_set(): Add one or more observer sets to a snapshot
add_population(): Add one or more populations to a snapshot
add_protocol(): Add one or more protocols to a snapshot
add_simulation(): Build a simulation from a snapshot and attach it
remove_compound(): Remove compounds from a snapshot
remove_event(): Remove events from a snapshot
remove_expression_profile(): Remove expression profiles from a snapshot
remove_formulation(): Remove formulations from a snapshot
remove_individual(): Remove individuals from a snapshot
remove_observed_data(): Remove observed data from a snapshot
remove_observer_set(): Remove observer sets from a snapshot
remove_population(): Remove populations from a snapshot
remove_protocol(): Remove protocols from a snapshot
remove_simulation(): Remove simulations from a snapshot

Tibble exporters

Convert building blocks to tibbles for analysis

as_tibbles(): Convert a snapshot collection to a tibble or list of tibbles
get_compounds_dfs(): Get all compounds in a snapshot as data frames
get_events_dfs(): Get all events in a snapshot as data frames
get_expression_profiles_dfs(): Get all expression profiles in a snapshot as data frames
get_formulations_dfs(): Get all formulations in a snapshot as data frames
get_individuals_dfs(): Get all individuals in a snapshot as data frames
get_observed_data_dfs(): Get all observed data in a snapshot as a tibble
get_observer_sets_dfs(): Get all observer sets in a snapshot as data frames
get_populations_dfs(): Get all populations in a snapshot as data frames
get_protocols_dfs(): Get all protocols in a snapshot as a single consolidated data frame

Observed data

Bridge between PK-Sim observed data and ospsuite

loadDataSetFromSnapshot(): Load DataSet from OSP snapshot observed data

Validators and utilities

Helpers for validation and data conversion

get_default_alternative(): Get the default alternative of a compound property
validate_snapshot(): Validate that an object is a Snapshot
validate_species(): Validate that a species is valid
validate_population(): Validate that a population is valid
validate_gender(): Validate that a gender is valid
validate_unit(): Validate that a unit is valid for a given dimension
convert_ospsuite_time_unit_to_lubridate(): Convert ospsuite time units to lubridate-compatible units
convert_ospsuite_time_to_duration(): Convert time value and unit to lubridate duration

Print methods

Formatted display methods for building block collections

print(<biliary_clearance>): Print method for biliary clearance processes
print(<compound_additional_parameters>): Print method for compound additional parameters
print(<compound_processes>): S3 print method for compound processes
print(<hepatic_clearance>): Print method for hepatic clearance processes
print(<induction>): Print method for induction processes
print(<inhibition>): Print method for inhibition processes
print(<metabolizing_enzymes>): Print method for metabolizing enzymes
print(<parameter_collection>): Print method for parameter collections
print(<physicochemical_property>): S3 print method for physicochemical properties
print(<protein_binding_partners>): Print method for protein binding partners
print(<renal_clearance>): Print method for renal clearance processes
print(<snapshot_collection>): Generic print method for snapshot collections
print(<transporter_proteins>): Print method for transporter proteins