Package: osp.snapshots 1.1.0

Felix MIL

osp.snapshots: Import and Manipulate Open Systems Pharmacology Project Snapshots

Provides a convenient R interface for working with PKSIM project snapshots exported as JSON files. You provide the snapshot file, and 'osp.snapshots' handles the complex nested structure, allowing you to easily import, navigate, modify, and export snapshot data. Building blocks can be converted to data frames for integration with the 'ospsuite' R framework and broader R ecosystem.

Authors:Felix MIL [aut, cre], Diane Lefaudeux [aut], ESQlabs, GmbH [cph, fnd]

osp.snapshots_1.1.0.tar.gz
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osp.snapshots_1.1.0.tar.gz(r-4.7-any)osp.snapshots_1.1.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
osp.snapshots/json (API)

# Install 'osp.snapshots' in R:
install.packages('osp.snapshots', repos = c('https://esqlabs.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/esqlabs/osp.snapshots/issues

Pkgdown/docs site:https://esqlabs.github.io

On CRAN:

Conda:

3.04 score 1 stars 112 exports 74 dependencies

Last updated from:72ea69e028 (on v1.1.0). Checks:5 ERROR, 3 WARNING, 1 FAIL. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR329
source / vignettesERROR291
linux-releaseERROR320
macos-releaseERROR231
macos-oldrelERROR271
windows-develWARNING329
windows-releaseWARNING331
windows-oldrelWARNING342
wasm-releaseFAIL246

Exports:add_compoundadd_eventadd_expression_profileadd_formulationadd_individualadd_observed_dataadd_observer_setadd_populationadd_protocoladd_simulationAdvancedParameterageas_tibblesCalculationMethodsCompoundCompoundProcessSelectionconvert_ospsuite_time_to_durationconvert_ospsuite_time_unit_to_lubridatecreate_compoundcreate_compound_process_selectioncreate_descriptor_conditioncreate_eventcreate_event_selectioncreate_expression_profilecreate_formula_referencecreate_formulationcreate_formulation_selectioncreate_individualcreate_molecule_listcreate_observed_datacreate_observercreate_observer_setcreate_observer_set_selectioncreate_output_intervalcreate_output_mappingcreate_output_schemacreate_parametercreate_populationcreate_processcreate_protocolcreate_protocol_selectioncreate_schemacreate_schema_itemcreate_snapshotcreate_solver_settingserrorEventEventSelectionexport_snapshotExpressionProfileFormulationFormulationSelectionfraction_unboundgestational_ageget_compounds_dfsget_default_alternativeget_events_dfsget_expression_profiles_dfsget_formulations_dfsget_individuals_dfsget_observed_data_dfsget_observer_sets_dfsget_populations_dfsget_protocols_dfsheightIndividualintestinal_permeabilitylipophilicityload_snapshotloadDataSetFromSnapshotLocalizedParameterObservedDataObserverObserverSetObserverSetSelectionOriginDataosp_modelsOutputIntervalOutputMappingOutputSchemaParameterpermeabilityPopulationProcessProtocolProtocolSelectionrangeRangeremove_compoundremove_eventremove_expression_profileremove_formulationremove_individualremove_observed_dataremove_observer_setremove_populationremove_protocolremove_simulationSchemaSchemaItemSimulationSnapshotsolubilitySolverSettingstimevalidate_gendervalidate_populationvalidate_snapshotvalidate_speciesvalidate_unitvaluesweight

Dependencies:backportsbitbit64checkmateclicliprcommonmarkcowplotcpp11crayoncurldata.tabledplyrfarverfitdistrplusfsgenericsggh4xggnewscaleggplot2ggtextgluegridtextgtablehmsisobandjpegjsonlitelabelinglatticelifecyclelitedownloggerlubridatemagrittrmarkdownMASSMatrixopenxlsxospsuiteospsuite.plotsospsuite.utilspatchworkpillarpkgconfigpngprettyunitsprogresspurrrR6RColorBrewerRcppreadrrlangrSharpS7scalesstringistringrsurvivaltibbletidyrtidyselecttimechangetlftzdbutf8vctrsviridisLitevroomwithrxfunxml2zip

Readme and manuals

Help Manual

Help pageTopics
Add one or more compounds to a snapshotadd_compound
Add one or more events to a snapshotadd_event
Add one or more expression profiles to a snapshotadd_expression_profile
Add one or more formulations to a snapshotadd_formulation
Add one or more individuals to a snapshotadd_individual
Add one or more observed-data entries to a snapshotadd_observed_data
Add one or more observer sets to a snapshotadd_observer_set
Add one or more populations to a snapshotadd_population
Add one or more protocols to a snapshotadd_protocol
Build a simulation from a snapshot and attach itadd_simulation
AdvancedParameter class for Population advanced parametersAdvancedParameter
Age value objectage
Convert a snapshot collection to a tibble or list of tibblesas_tibbles
CalculationMethods class for OSP snapshotsCalculationMethods
Compound class for OSP snapshot compoundsCompound
CompoundProcessSelection class for compound process selectionsCompoundProcessSelection
Convert time value and unit to lubridate durationconvert_ospsuite_time_to_duration
Convert ospsuite time units to lubridate-compatible unitsconvert_ospsuite_time_unit_to_lubridate
Create a new compoundcreate_compound
Create a compound process selectioncreate_compound_process_selection
Create a container criterion for an observercreate_descriptor_condition
Create a new eventcreate_event
Create an event selection for a simulationcreate_event_selection
Create a new expression profilecreate_expression_profile
Create a formula reference for an observercreate_formula_reference
Create a new formulationcreate_formulation
Create a formulation selection for a simulation compoundcreate_formulation_selection
Create a new individualcreate_individual
Create a molecule list for an observercreate_molecule_list
Create a new observed data setcreate_observed_data
Create a new observercreate_observer
Create a new observer setcreate_observer_set
Create an observer-set selection for a simulationcreate_observer_set_selection
Create an output interval for a simulation output schemacreate_output_interval
Create an output-to-observed-data mapping for a simulationcreate_output_mapping
Create an output schema for a simulationcreate_output_schema
Create a new parametercreate_parameter
Create a new populationcreate_population
Create a new compound processcreate_process
Create a new protocolcreate_protocol
Create a protocol selection for a simulation compoundcreate_protocol_selection
Create a new schemacreate_schema
Create a new schema itemcreate_schema_item
Create an empty snapshotcreate_snapshot
Create a solver settings object for a simulationcreate_solver_settings
Error series value objecterror
Event class for OSP snapshot eventsEvent
EventSelection class for Simulation event referencesEventSelection
Export a snapshot to a JSON fileexport_snapshot
ExpressionProfile class for OSP snapshot expression profilesExpressionProfile
Formulation class for OSP snapshot formulationsFormulation
FormulationSelection class for Simulation compound formulationsFormulationSelection
Fraction unbound value objectfraction_unbound
Gestational age value objectgestational_age
Get all compounds in a snapshot as data framesget_compounds_dfs
Get the default alternative of a compound propertyget_default_alternative
Get all events in a snapshot as data framesget_events_dfs
Get all expression profiles in a snapshot as data framesget_expression_profiles_dfs
Get all formulations in a snapshot as data framesget_formulations_dfs
Get all individuals in a snapshot as data framesget_individuals_dfs
Get all observed data in a snapshot as a tibbleget_observed_data_dfs
Get all observer sets in a snapshot as data framesget_observer_sets_dfs
Get all populations in a snapshot as data framesget_populations_dfs
Get all protocols in a snapshot as a single consolidated data frameget_protocols_dfs
Height value objectheight
Individual class for OSP snapshot individualsIndividual
Intestinal permeability value objectintestinal_permeability
Lipophilicity value objectlipophilicity
Load a snapshot from various sourcesload_snapshot
Load DataSet from OSP snapshot observed dataloadDataSetFromSnapshot ObservedData
LocalizedParameter class for path-bearing OSP snapshot parametersLocalizedParameter
Observer class for OSP snapshot observer setsObserver
ObserverSet class for OSP snapshot observer setsObserverSet
ObserverSetSelection class for Simulation observer-set referencesObserverSetSelection
OriginData class for OSP snapshot individualsOriginData
Browse available OSPSuite building block templatesosp_models
OutputInterval class for Simulation output schemasOutputInterval
OutputMapping class for simulation output-to-observed-data mappingsOutputMapping
OutputSchema class for Simulation output schedulesOutputSchema
Parameter class for OSP snapshot parametersParameter
Permeability value objectpermeability
Population class for OSP snapshot populationsPopulation
Print method for biliary clearance processesprint.biliary_clearance
Print method for compound additional parametersprint.compound_additional_parameters
S3 print method for compound processesprint.compound_processes
Print method for hepatic clearance processesprint.hepatic_clearance
Print method for induction processesprint.induction
Print method for inhibition processesprint.inhibition
Print method for metabolizing enzymesprint.metabolizing_enzymes
Print method for parameter collectionsprint.parameter_collection
S3 print method for physicochemical propertiesprint.physicochemical_property
Print method for protein binding partnersprint.protein_binding_partners
Print method for renal clearance processesprint.renal_clearance
Generic print method for snapshot collectionsprint.snapshot_collection
Print method for transporter proteinsprint.transporter_proteins
Process class for OSP snapshot compound processesProcess
Protocol class for OSP snapshot protocolsProtocol
ProtocolSelection class for Simulation compound protocol assignmentsProtocolSelection
Create a range object for physiological parametersrange
Range class for physiological parametersRange Range-class
Remove compounds from a snapshotremove_compound
Remove events from a snapshotremove_event
Remove expression profiles from a snapshotremove_expression_profile
Remove formulations from a snapshotremove_formulation
Remove individuals from a snapshotremove_individual
Remove observed data from a snapshotremove_observed_data
Remove observer sets from a snapshotremove_observer_set
Remove populations from a snapshotremove_population
Remove protocols from a snapshotremove_protocol
Remove simulations from a snapshotremove_simulation
Schema class for OSP advanced protocolsSchema
SchemaItem class for OSP advanced protocolsSchemaItem
Simulation class for OSP snapshot simulationsSimulation
Snapshot class for OSP snapshotsSnapshot
Solubility value objectsolubility
SolverSettings class for simulation solver configurationSolverSettings
Time series value objecttime
Validate that a gender is validvalidate_gender
Validate that a population is validvalidate_population
Validate that an object is a Snapshotvalidate_snapshot
Validate that a species is validvalidate_species
Validate that a unit is valid for a given dimensionvalidate_unit
Measurement values series value objectvalues
Weight value objectweight