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

osp_models(): Browse available OSPSuite building block templates

Core Classes

Main classes for working with snapshots and building blocks

Snapshot: Snapshot class for OSP snapshots

Individual: Individual class for OSP snapshot individuals

Compound: Compound class for OSP snapshot compounds

Formulation: Formulation class for OSP snapshot formulations

Population: Population class for OSP snapshot populations

Protocol: Protocol class for OSP snapshot protocols

Event: Event class for OSP snapshot events

ExpressionProfile: ExpressionProfile class for OSP snapshot expression profiles

Parameter: Parameter class for OSP snapshot parameters

AdvancedParameter: AdvancedParameter class for Population advanced parameters

range(): Create a range object for physiological parameters

Create Building Blocks

Functions to create new building blocks from scratch

create_individual(): Create a new individual

create_formulation(): Create a new formulation

create_parameter(): Create a new parameter

Manage Building Blocks

Add and remove building blocks from snapshots

add_individual(): Add an individual to a snapshot

add_formulation(): Add a formulation to a snapshot

add_expression_profile(): Add an expression profile to a snapshot

remove_individual(): Remove individuals from a snapshot

remove_formulation(): Remove formulations from a snapshot

remove_population(): Remove populations from a snapshot

remove_expression_profile(): Remove expression profiles from a snapshot

Data Frame Conversion

Convert building blocks to data frames for analysis

get_individuals_dfs(): Get all individuals in a snapshot as data frames

get_compounds_dfs(): Get all compounds in a snapshot as data frames

get_formulations_dfs(): Get all formulations 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

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_observed_data_dfs(): Get all observed data in a snapshot as data frames

Observed Data

Work with clinical and experimental data

loadDataSetFromSnapshot(): Load DataSet from OSP snapshot observed data

Validation and Utilities

Helper functions for validation and data conversion

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_calculation_methods>): Print method for compound calculation methods

print(<compound_collection>): S3 print method for compound collections

print(<compound_processes>): S3 print method for compound processes

print(<event_collection>): S3 print method for event collections

print(<expression_profile_collection>): S3 print method for expression profile collections

print(<formulation_collection>): S3 print method for formulation collections

print(<hepatic_clearance>): Print method for hepatic clearance processes

print(<individual_collection>): S3 print method for individual collections

print(<induction>): Print method for induction processes

print(<inhibition>): Print method for inhibition processes

print(<metabolizing_enzymes>): Print method for metabolizing enzymes

print(<observed_data_collection>): Print method for observed data collection

print(<parameter_collection>): Print method for parameter collections

print(<physicochemical_property>): S3 print method for physicochemical properties

print(<population_collection>): S3 print method for population collections

print(<protein_binding_partners>): Print method for protein binding partners

print(<protocol_collection>): S3 print method for protocol collections

print(<renal_clearance>): Print method for renal clearance processes

print(<transporter_proteins>): Print method for transporter proteins