Man pages for Calvagone/campsis
Generic PK/PD Simulation Platform CAMPSIS

applyCompartmentCharacteristicsApply compartment characteristics from model. In practice,...
applyScenarioApply scenario to the given model or dataset.
ArmCreate a treatment arm.
arm-classArm class.
arms-classArms class.
assignDoseNumberAssign dose number to each treatment entry.
BinomialDistributionBinomial distribution.
BolusCreate one or several bolus(es).
bolus-classBolus class.
BootstrapCreate a bootstrap object.
bootstrap-classBootstrap class.
BootstrapDistributionCreate a bootstrap distribution. During function sampling,...
bootstrap_distribution-classBootstrap distribution class.
campsis_handlerSuggested Campsis handler for showing the progress bar.
checkIIandADDLCheck ii and addl arguments in addition to time.
computeIncrementalProgressCompute incremental progress.
ConstantDistributionCreate a constant distribution. Its value will be constant...
constant_distribution-classConstant distribution class.
counterBalanceLocfModeCounter-balance LOCF mode for occasions & IOV. This function...
counterBalanceNocbModeCounter-balance NOCB mode for occasions & IOV. This function...
CovariateCreate a non time-varying (fixed) covariate.
covariate-classCovariate class.
covariates-classCovariates class.
cutTableForEventCut table according to given iteration.
DatasetCreate a dataset.
dataset-classDataset class.
DatasetConfigCreate a dataset configuration. This configuration allows...
dataset_config-classDataset configuration class.
DatasetSummaryCreate a dataset summary (internal method).
DeclareCreate declare settings.
declare_settings-classDeclare settings class.
DiscreteDistributionDiscrete distribution.
distribution-classDistribution class. See this class as an interface.
DoseAdaptationCreate a dose adaptation.
dose_adaptation-classDose adaptation class.
dose_adaptations-classDose adaptations class.
dosingOnlyFilter CAMPSIS output on dosing rows.
dropOthersReturn the 'DROP_OTHERS' string that may be used in the...
EtaDistributionCreate an ETA distribution. The resulting distribution is a...
EventCreate an interruption event.
event-classEvent class.
EventCovariateCreate an event covariate. These covariates can be modified...
event_covariate-classEvent covariate class.
EventIterationCreate an event iteration object.
EventRelatedObservationsCreate an event-related observations list. Please note that...
EventsCreate a list of interruption events.
events-classEvents class.
exportDelegateExport delegate method. This method is common to RxODE and...
exportTableDelegateExport table delegate.
factorScenariosFactor scenarios columns if not done yet.
fillIOVOccColumnsFill IOV/Occasion columns.
fixed_covariate-classFixed covariate class.
FixedDistributionCreate a fixed distribution. Each sample will be assigned a...
fixed_distribution-classFixed distribution class.
FunctionDistributionCreate a function distribution. During distribution sampling,...
function_distribution-classFunction distribution class.
generateIIVGenerate IIV matrix for the given Campsis model.
generateIIV_Generate IIV matrix for the given OMEGA matrix.
getColumnGet data of given column unless if does not exist (return...
getCovariatesGet all covariates (fixed / time-varying / event covariates).
getDatasetMaxTimeGet dataset max time.
getEventCovariatesGet all event-related covariates.
getEventIterationsGet list of event iterations.
getFixedCovariatesGet all fixed covariates.
getFurrrSchedulingGet scheduling mode for furrr (see argument 'scheduling'...
getInitialConditionsGet initial conditions at simulation start-up.
getIOVsGet all IOV objects.
getOccasionsGet all occasions.
getRandomSeedValueGet random seed value.
getSeedGet seed value.
getSeedForDatasetExportGet seed for dataset export.
getSeedForIterationGet seed for iteration.
getSeedForParametersSamplingGet seed for parameter uncertainty sampling.
getSimulationEngineTypeGet simulation engine type.
getSplittingConfigurationGet splitting configuration for parallel export.
getTimesGet all distinct times for the specified object.
getTimeVaryingCovariatesGet all time-varying covariates.
getTimeVaryingVariablesGet all time-varying variables. These variables are likely to...
HardwareCreate hardware settings.
hardware_settings-classHardware settings class.
importCampsismodToNamespaceImport the whole campsismod package into NAMESPACE when...
InfusionCreate one or several infusion(s).
infusion-classInfusion class.
internal_settings-classInternal settings class (transient object from the simulation...
IOVDefine inter-occasion variability (IOV) into the dataset. A...
isEmptyBootstrapIs the given bootstrap empty.
leftJoinIIVLeft-join IIV matrix.
length-arm-methodReturn the number of subjects contained in this arm.
length-dataset-methodReturn the number of subjects contained in this dataset.
LogNormalDistributionCreate a log normal distribution.
mergeTimeVaryingCovariatesMerge time-varying covariates into a single data frame. This...
mrgsolve_engine-classmrgsolve engine class.
nhanesNHANES database (demographics and body measure data combined,...
NOCBCreate NOCB settings.
nocb_settings-classNOCB settings class.
NormalDistributionCreate a normal distribution.
ObservationsCreate an observations list. Please note that the provided...
observations-classObservations class.
observations_set-classObservations set class.
obsOnlyFilter CAMPSIS output on observation rows.
OccasionDefine a new occasion. Occasions are defined by mapping...
occasion-classOccasion class.
occasions-classOccasions class.
ParameterDistributionCreate a parameter distribution. The resulting distribution...
PICompute the prediction interval summary over time.
preprocessArmColumnPreprocess ARM column. Add ARM equation in model...
preprocessDestPre-process destination engine. Throw an error message if the...
preprocessDosingPreprocess 'dosing' argument.
preprocessEventsPre-process events.
preprocessFunctionPre-process function argument.
preprocessIdsPreprocess subjects ID's.
preprocessNocbvarsPreprocess 'nocbvars' argument.
preprocessOutvarsPreprocess 'outvars' argument. 'Outvars' is a character...
preprocessReplicatesPreprocess 'replicates' argument.
preprocessScenariosPre-process scenarios.
preprocessSettingsPreprocess the simulation settings.
preprocessSlicesPreprocess 'slices' argument.
preprocessTSLDAndTDOSColumnPreprocess TSLD and TDOS columns according to given dataset...
processArmLabelsProcess arm labels. Arm identifiers in ARM column are...
processDropOthersProcess 'DROP_OTHERS'.
processSimulateArgumentsPreprocess arguments of the simulate method.
processTSLDAndTDOSColumnProcess TSLD and TDOS columns according to given dataset...
ProgressCreate progress settings.
progress_settings-classProgress settings class.
protocol-classProtocol class.
removeInitialConditionsRemove initial conditions.
reorderColumnsReorder output columns.
retrieveParameterValueRetrieve the parameter value (standardized) for the specified...
rxode_engine-classRxODE/rxode2 engine class.
sampleSample generic object.
sampleCovariatesListSample covariates list.
sampleDistributionAsTibbleSample a distribution and return a tibble.
sampleTimeVaryingCovariatesSample time-varying covariates.
scatterPlotScatter plot (or X vs Y plot).
ScenarioCreate an scenario.
scenario-classScenario class.
ScenariosCreate a list of scenarios.
scenarios-classScenarios class.
setLabelSet the label.
setSeedSet the seed. The goal of this method is to centralize all...
setSubjectsSet the number of subjects.
SettingsCreate advanced simulation settings.
setupPlanDefaultSetup default plan for the given simulation or hardware...
setupPlanSequentialSetup plan as sequential (i.e. no parallelisation).
shadedPlotShaded plot (or prediction interval plot).
simulateSimulate function.
simulateDelegateSimulation delegate (several replicates).
simulateDelegateCoreSimulation delegate core (single replicate).
simulateScenariosSimulation scenarios.
simulation_engine-classSimulation engine class.
SimulationProgressCreate a simulation progress object.
simulation_progress-classSimulation progress class.
simulation_settings-classSimulation settings class.
SolverCreate solver settings.
solver_settings-classSolver settings class. See ?mrgsolve::update. See...
spaghettiPlotSpaghetti plot.
splitDatasetSplit dataset according to config.
TimeVaryingCovariateCreate a time-varying covariate. This covariate will be...
time_varying_covariate-classTime-varying covariate class.
toDatasetSummaryConvert dataset to dataset summary (internal method).
toExplicitDistributionConvert user-given distribution to an explicit CAMPSIS...
treatment-classTreatment class.
treatment_iov-classTreatment IOV class.
treatment_iovs-classTreatment IOV's class.
undefined_distribution-classUndefined distribution class. This type of object is...
UniformDistributionCreate an uniform distribution.
uniteColumnsUnite the given column names.
VPCCompute the VPC summary. Input data frame must contain the...
vpcPlotVPC plot.
Calvagone/campsis documentation built on Feb. 25, 2024, 8:35 p.m.