Man pages for campsis
Generic PK/PD Simulation Platform CAMPSIS
| applyCompartmentCharacteristics | Apply compartment characteristics from model. In practice,... |
| applyScenario | Apply scenario to the given model or dataset. |
| Arm | Create a treatment arm. |
| arm-class | Arm class. |
| arms-class | Arms class. |
| assignDoseNumber | Assign dose number to each treatment entry. |
| BinomialDistribution | Binomial distribution. |
| Bolus | Create one or several bolus(es). |
| bolus-class | Bolus class. |
| bolus_wrapper-class | Bolus wrapper class. |
| Bootstrap | Create a bootstrap object. |
| bootstrap-class | Bootstrap class. |
| BootstrapDistribution | Create a bootstrap distribution. During function sampling,... |
| bootstrap_distribution-class | Bootstrap distribution class. |
| campsis_handler | Suggested Campsis handler for showing the progress bar. |
| checkIIandADDL | Check ii and addl arguments in addition to time. |
| computeIncrementalProgress | Compute incremental progress. |
| ConstantDistribution | Create a constant distribution. Its value will be constant... |
| constant_distribution-class | Constant distribution class. |
| convertTime | Convert numeric time vector based on the provided units. |
| counterBalanceLocfMode | Counter-balance LOCF mode for occasions & IOV. This function... |
| counterBalanceNocbMode | Counter-balance NOCB mode for occasions & IOV. This function... |
| Covariate | Create a non time-varying (fixed) covariate. |
| covariate-class | Covariate class. |
| covariates-class | Covariates class. |
| cutTableForEvent | Cut table according to given iteration. |
| CyclicSchedule | Cyclic schedule constructor. |
| cyclic_schedule-class | Cyclic schedule class. |
| Dataset | Create a dataset. |
| dataset-class | Dataset class. |
| DatasetConfig | Create a dataset configuration. This configuration allows... |
| dataset_config-class | Dataset configuration class. |
| DatasetSummary | Create a dataset summary (internal method). |
| days | Convert days to hours. |
| Declare | Create declare settings. |
| declare_settings-class | Declare settings class. |
| DiscreteDistribution | Discrete distribution. |
| distribution-class | Distribution class. See this class as an interface. |
| DoseAdaptation | Create a dose adaptation. |
| dose_adaptation-class | Dose adaptation class. |
| dose_adaptations-class | Dose adaptations class. |
| dosingOnly | Filter CAMPSIS output on dosing rows. |
| dropOthers | Return the 'DROP_OTHERS' string that may be used in the... |
| EtaDistribution | Create an ETA distribution. The resulting distribution is a... |
| Event | Create an interruption event. |
| event-class | Event class. |
| EventCovariate | Create an event covariate. These covariates can be modified... |
| event_covariate-class | Event covariate class. |
| EventIteration | Create an event iteration object. |
| EventRelatedObservations | Create an event-related observations list. Please note that... |
| Events | Create a list of interruption events. |
| events-class | Events class. |
| exportDelegate | Export delegate method. This method is common to RxODE and... |
| exportTableDelegate | Export table delegate. |
| factorScenarios | Factor scenarios columns if not done yet. |
| fillIOVOccColumns | Fill IOV/Occasion columns. |
| fixed_covariate-class | Fixed covariate class. |
| FixedDistribution | Create a fixed distribution. Each sample will be assigned a... |
| fixed_distribution-class | Fixed distribution class. |
| FunctionDistribution | Create a function distribution. During distribution sampling,... |
| function_distribution-class | Function distribution class. |
| generateIIV | Generate IIV matrix for the given Campsis model. |
| generateIIV_ | Generate IIV matrix for the given OMEGA matrix. |
| getAvailableTimeUnits | Return the list of available time units. |
| getColumn | Get data of given column unless if does not exist (return... |
| getCompartmentMapping | Get a mapping table with all possibilities of compartment... |
| getCovariates | Get all covariates (fixed / time-varying / event covariates). |
| getDatasetMaxTime | Get dataset max time. |
| getEventCovariates | Get all event-related covariates. |
| getEventIterations | Get list of event iterations. |
| getFixedCovariates | Get all fixed covariates. |
| getFurrrScheduling | Get scheduling mode for furrr (see argument 'scheduling'... |
| getInitialConditions | Get initial conditions at simulation start-up. |
| getIOVs | Get all IOV objects. |
| getOccasions | Get all occasions. |
| getRandomSeedValue | Get random seed value. |
| getSeed | Get seed value. |
| getSeedForDatasetExport | Get seed for dataset export. |
| getSeedForIteration | Get seed for iteration. |
| getSeedForParametersSampling | Get seed for parameter uncertainty sampling. |
| getSimulationEngineType | Get simulation engine type. |
| getSplittingConfiguration | Get splitting configuration for parallel export. |
| getTimes | Get all distinct times for the specified object. |
| getTimeVaryingCovariates | Get all time-varying covariates. |
| getTimeVaryingVariables | Get all time-varying variables. These variables are likely to... |
| Hardware | Create hardware settings. |
| hardware_settings-class | Hardware settings class. |
| hours | Convert hours to hours (do nothing). |
| importCampsismodToNamespace | Import the whole campsismod package into NAMESPACE when... |
| Infusion | Create one or several infusion(s). |
| infusion-class | Infusion class. |
| infusion_wrapper-class | Infusion wrapper class. |
| internal_settings-class | Internal settings class (transient object from the simulation... |
| IOV | Define inter-occasion variability (IOV) into the dataset. A... |
| isEmptyBootstrap | Is the given bootstrap empty. |
| leftJoinIIV | Left-join IIV matrix. |
| length-arm-method | Return the number of subjects contained in this arm. |
| length-cyclic_schedule-method | Return the number of repetition cycles. |
| length-dataset-method | Return the number of subjects contained in this dataset. |
| length-repeat_at_schedule-method | Return the number of repetition cycles. |
| LogNormalDistribution | Create a log normal distribution. |
| mergeTimeVaryingCovariates | Merge time-varying covariates into a single data frame. This... |
| minutes | Convert minutes to hours. |
| months | Convert pharma months (1 month = 4 weeks) to hours. |
| mrgsolve_engine-class | mrgsolve engine class. |
| nhanes | NHANES database (demographics and body measure data combined,... |
| NOCB | Create NOCB settings. |
| nocb_settings-class | NOCB settings class. |
| NormalDistribution | Create a normal distribution. |
| Observations | Create an observations list. Please note that the provided... |
| observations-class | Observations class. |
| observations_set-class | Observations set class. |
| obsOnly | Filter CAMPSIS output on observation rows. |
| Occasion | Define a new occasion. Occasions are defined by mapping... |
| occasion-class | Occasion class. |
| occasions-class | Occasions class. |
| onCI | Check if the current session is on CI (e.g. GitHub actions). |
| onCran | Check if the current session is on CRAN. The objective is to... |
| Outfun | Create a new output function |
| output_function-class | Output function class. |
| ParameterDistribution | Create a parameter distribution. The resulting distribution... |
| PI | Compute the prediction interval summary over time. |
| preprocessArmColumn | Preprocess ARM column. Add ARM equation in model... |
| preprocessDest | Pre-process destination engine. Throw an error message if the... |
| preprocessDosing | Preprocess 'dosing' argument. |
| preprocessEvents | Pre-process events. |
| preprocessIds | Preprocess subjects ID's. |
| preprocessNocbvars | Preprocess 'nocbvars' argument. |
| preprocessOutfun | Pre-process outfun argument. |
| preprocessOutvars | Preprocess 'outvars' argument. 'Outvars' is a character... |
| preprocessReplicates | Preprocess 'replicates' argument. |
| preprocessScenarios | Pre-process scenarios. |
| preprocessSettings | Preprocess the simulation settings. |
| preprocessSlices | Preprocess 'slices' argument. |
| preprocessTablefun | Pre-process tablefun argument. |
| preprocessTSLDAndTDOSColumn | Preprocess TSLD and TDOS columns according to given dataset... |
| processAllTimeColumns | Process time-related columns according to given dataset... |
| processArmLabels | Process arm labels. Arm identifiers in ARM column are... |
| processDropOthers | Process 'DROP_OTHERS'. |
| processSimulateArguments | Preprocess arguments of the simulate method. |
| Progress | Create progress settings. |
| progress_settings-class | Progress settings class. |
| protocol-class | Protocol class. |
| removeInitialConditions | Remove initial conditions. |
| reorderColumns | Reorder output columns. |
| RepeatAtSchedule | 'Repeat at' schedule constructor. Note that the time 0 for... |
| repeat_at_schedule-class | 'Repeat at' schedule class. |
| repeated_schedule-class | Repeated schedule class. See this class as an interface. |
| repeatSchedule | Repeat schedule. |
| retrieveParameterValue | Retrieve the parameter value (standardized) for the specified... |
| rxode_engine-class | RxODE/rxode2 engine class. |
| sample | Sample generic object. |
| sampleCovariatesList | Sample covariates list. |
| sampleDistributionAsTibble | Sample a distribution and return a tibble. |
| sampleTimeVaryingCovariates | Sample time-varying covariates. |
| scatterPlot | Scatter plot (or X vs Y plot). |
| Scenario | Create an scenario. |
| scenario-class | Scenario class. |
| Scenarios | Create a list of scenarios. |
| scenarios-class | Scenarios class. |
| seconds | Convert seconds to hours. |
| setLabel | Set the label. |
| setSeed | Set the seed. The goal of this method is to centralize all... |
| setSubjects | Set the number of subjects. |
| Settings | Create advanced simulation settings. |
| setupPlanDefault | Setup default plan for the given simulation or hardware... |
| setupPlanSequential | Setup plan as sequential (i.e. no parallelisation). |
| shadedPlot | Shaded plot (or prediction interval plot). |
| simulate | Simulate function. |
| simulateDelegate | Simulation delegate (several replicates). |
| simulateDelegateCore | Simulation delegate core (single replicate). |
| simulateScenarios | Simulation scenarios. |
| simulation_engine-class | Simulation engine class. |
| SimulationProgress | Create a simulation progress object. |
| simulation_progress-class | Simulation progress class. |
| simulation_settings-class | Simulation settings class. |
| Solver | Create solver settings. |
| solver_settings-class | Solver settings class. See ?mrgsolve::update. See... |
| spaghettiPlot | Spaghetti plot. |
| splitDataset | Split dataset according to config. |
| standardiseTime | Standardise time to hours. |
| TimeVaryingCovariate | Create a time-varying covariate. This covariate will be... |
| time_varying_covariate-class | Time-varying covariate class. |
| toDatasetSummary | Convert dataset to dataset summary (internal method). |
| toExplicitDistribution | Convert user-given distribution to an explicit CAMPSIS... |
| treatment-class | Treatment class. |
| treatment_iov-class | Treatment IOV class. |
| treatment_iovs-class | Treatment IOV's class. |
| undefined_distribution-class | Undefined distribution class. This type of object is... |
| undefined_schedule-class | Undefined schedule class. |
| UniformDistribution | Create an uniform distribution. |
| uniteColumns | Unite the given column names. |
| unwrapTreatment | Unwrap treatment. |
| updateADDL | Update the number of additional doses (ADDL). |
| updateAmount | Update amount. |
| updateII | Update the inter-dose interval (II). |
| updateRepeat | Update the repeat field (argument 'rep' in Bolus and Infusion... |
| VPC | Compute the VPC summary. Input data frame must contain the... |
| vpcPlot | VPC plot. |
| weeks | Convert weeks to hours. |
| years | Convert pharma years (1 year = 12*4 weeks) to hours. |
