| Apply compartment characteristics from model. In practice, only compartment infusion duration needs to be applied. | applyCompartmentCharacteristics |
| Create a treatment arm. | Arm |
| Arm class. | arm-class |
| Arms class. | arms-class |
| Binomial distribution. | BinomialDistribution |
| Create one or several bolus(es). | Bolus |
| Bolus class. | bolus-class |
| Create a bootstrap object. | Bootstrap |
| Bootstrap distribution class. | bootstrap_distribution-class |
| Bootstrap class. | bootstrap-class |
| Create a bootstrap distribution. During function sampling, CAMPSIS will generate values depending on the given data and arguments. | BootstrapDistribution |
| Suggested Campsis handler for showing the progress bar. | campsis_handler |
| Constant distribution class. | constant_distribution-class |
| Create a constant distribution. Its value will be constant across all generated samples. | ConstantDistribution |
| Convert numeric time vector based on the provided units. | convertTime |
| Create a non time-varying (fixed) covariate. | Covariate |
| Covariate class. | covariate-class |
| Covariates class. | covariates-class |
| Create a dataset. | Dataset |
| Dataset configuration class. | dataset_config-class |
| Dataset class. | dataset-class |
| Create a dataset configuration. This configuration allows CAMPSIS to know which are the default depot and observed compartments. | DatasetConfig |
| Convert days to hours. | days |
| Create declare settings. | Declare |
| Declare settings class. | declare_settings-class |
| Discrete distribution. | DiscreteDistribution |
| Distribution class. See this class as an interface. | distribution-class |
| Dose adaptation class. | dose_adaptation-class |
| Dose adaptations class. | dose_adaptations-class |
| Create a dose adaptation. | DoseAdaptation |
| Filter CAMPSIS output on dosing rows. | dosingOnly |
| Create an ETA distribution. The resulting distribution is a normal distribution, with mean=0 and sd=sqrt(OMEGA). | EtaDistribution |
| Create an interruption event. | Event |
| Event covariate class. | event_covariate-class |
| Event class. | event-class |
| Create an event covariate. These covariates can be modified further in interruption events. | EventCovariate |
| Create a list of interruption events. | Events |
| Events class. | events-class |
| Fixed covariate class. | fixed_covariate-class |
| Fixed distribution class. | fixed_distribution-class |
| Create a fixed distribution. Each sample will be assigned a fixed value coming from vector 'values'. | FixedDistribution |
| Function distribution class. | function_distribution-class |
| Create a function distribution. During distribution sampling, the provided function will be responsible for generating values for each sample. If first argument of this function is not the size (n), please tell which argument corresponds to the size 'n' (e.g. list(size="n")). | FunctionDistribution |
| Generate IIV matrix for the given Campsis model. | generateIIV |
| Generate IIV matrix for the given OMEGA matrix. | generateIIV_ |
| Return the list of available time units. | getAvailableTimeUnits |
| Get all covariates (fixed / time-varying / event covariates). | getCovariates getCovariates,arm-method getCovariates,arms-method getCovariates,covariates-method getCovariates,dataset-method |
| Get all event-related covariates. | getEventCovariates getEventCovariates,arm-method getEventCovariates,arms-method getEventCovariates,covariates-method getEventCovariates,dataset-method |
| Get all fixed covariates. | getFixedCovariates getFixedCovariates,arm-method getFixedCovariates,arms-method getFixedCovariates,covariates-method getFixedCovariates,dataset-method |
| Get all IOV objects. | getIOVs getIOVs,arm-method getIOVs,arms-method getIOVs,dataset-method |
| Get all occasions. | getOccasions getOccasions,arm-method getOccasions,arms-method getOccasions,dataset-method |
| Get seed for dataset export. | getSeedForDatasetExport |
| Get seed for iteration. | getSeedForIteration |
| Get seed for parameter uncertainty sampling. | getSeedForParametersSampling |
| Get splitting configuration for parallel export. | getSplittingConfiguration |
| Get all distinct times for the specified object. | getTimes getTimes,arm-method getTimes,arms-method getTimes,dataset-method getTimes,events-method getTimes,observations_set-method |
| Get all time-varying covariates. | getTimeVaryingCovariates getTimeVaryingCovariates,arm-method getTimeVaryingCovariates,arms-method getTimeVaryingCovariates,covariates-method getTimeVaryingCovariates,dataset-method |
| Create hardware settings. | Hardware |
| Hardware settings class. | hardware_settings-class |
| Convert hours to hours (do nothing). | hours |
| Create one or several infusion(s). | Infusion |
| Infusion class. | infusion-class |
| Internal settings class (transient object from the simulation settings). | internal_settings-class |
| Define inter-occasion variability (IOV) into the dataset. A new variable of name 'colname' will be output into the dataset and will vary at each dose number according to the given distribution. | IOV |
| Return the number of subjects contained in this arm. | length,arm-method |
| Return the number of subjects contained in this dataset. | length,dataset-method |
| Create a log normal distribution. | LogNormalDistribution |
| Convert minutes to hours. | minutes |
| Convert pharma months (1 month = 4 weeks) to hours. | months |
| mrgsolve engine class. | mrgsolve_engine-class |
| NHANES database (demographics and body measure data combined, from 2017-2018). | nhanes |
| Create NOCB settings. | NOCB |
| NOCB settings class. | nocb_settings-class |
| Create a normal distribution. | NormalDistribution |
| Create an observations list. Please note that the provided 'times' will automatically be sorted. Duplicated times will be removed. | Observations |
| Observations set class. | observations_set-class |
| Observations class. | observations-class |
| Filter CAMPSIS output on observation rows. | obsOnly |
| Define a new occasion. Occasions are defined by mapping occasion values to dose numbers. A new column will automatically be created in the exported dataset. | Occasion |
| Occasion class. | occasion-class |
| Occasions class. | occasions-class |
| Create a new output function | Outfun |
| Output function class. | output_function-class |
| Create a parameter distribution. The resulting distribution is a log-normal distribution, with meanlog=log(THETA) and sdlog=sqrt(OMEGA). | ParameterDistribution |
| Compute the prediction interval summary over time. | PI |
| Create progress settings. | Progress |
| Progress settings class. | progress_settings-class |
| Protocol class. | protocol-class |
| Retrieve the parameter value (standardized) for the specified parameter name. | retrieveParameterValue |
| RxODE/rxode2 engine class. | rxode_engine-class |
| Sample generic object. | sample sample,bolus,integer-method sample,bootstrap,integer-method sample,bootstrap_distribution,integer-method sample,campsis_model,integer-method sample,constant_distribution,integer-method sample,covariate,integer-method sample,fixed_distribution,integer-method sample,function_distribution,integer-method sample,infusion,integer-method sample,observations,integer-method |
| Scatter plot (or X vs Y plot). | scatterPlot |
| Create an scenario. | Scenario |
| Scenario class. | scenario-class |
| Create a list of scenarios. | Scenarios |
| Scenarios class. | scenarios-class |
| Convert seconds to hours. | seconds |
| Set the label. | setLabel setLabel,arm,character-method |
| Set the number of subjects. | setSubjects setSubjects,arm,integer-method setSubjects,dataset,integer-method |
| Create advanced simulation settings. | Settings |
| Setup default plan for the given simulation or hardware settings. This plan will prioritise the distribution of workers in the following order: 1) Replicates (if 'replicate_parallel' is enabled) 2) Scenarios (if 'scenario_parallel' is enabled) 3) Dataset export / slices (if 'dataset_export' or 'slice_parallel' is enabled) | setupPlanDefault |
| Setup plan as sequential (i.e. no parallelisation). | setupPlanSequential |
| Shaded plot (or prediction interval plot). | shadedPlot |
| Simulate function. | simulate simulate,campsis_model,data.frame,character,events,scenarios,function,character,output_function,integer,integer,logical,simulation_settings-method simulate,campsis_model,dataset,character,events,scenarios,function,character,output_function,integer,integer,logical,simulation_settings-method simulate,campsis_model,tbl_df,character,events,scenarios,function,character,output_function,integer,integer,logical,simulation_settings-method simulate,campsis_model,tbl_df,mrgsolve_engine,events,scenarios,function,character,output_function,integer,integer,logical,simulation_settings-method simulate,campsis_model,tbl_df,rxode_engine,events,scenarios,function,character,output_function,integer,integer,logical,simulation_settings-method |
| Simulation engine class. | simulation_engine-class |
| Simulation progress class. | simulation_progress-class |
| Simulation settings class. | simulation_settings-class |
| Create a simulation progress object. | SimulationProgress |
| Create solver settings. | Solver |
| Solver settings class. See ?mrgsolve::update. See ?rxode2::rxSolve. | solver_settings-class |
| Spaghetti plot. | spaghettiPlot |
| Standardise time to hours. | standardiseTime |
| Time-varying covariate class. | time_varying_covariate-class |
| Create a time-varying covariate. This covariate will be implemented using EVID=2 rows in the exported dataset and will not use interruption events. | TimeVaryingCovariate |
| Treatment IOV class. | treatment_iov-class |
| Treatment IOV's class. | treatment_iovs-class |
| Treatment class. | treatment-class |
| Undefined distribution class. This type of object is automatically created in method toExplicitDistribution() when the user does not provide a concrete distribution. This is because S4 objects do not accept NULL values. | undefined_distribution-class |
| Create an uniform distribution. | UniformDistribution |
| Compute the VPC summary. Input data frame must contain the following columns: - replicate: replicate number - low: low percentile value in replicate (and in scenario if present) - med: median value in replicate (and in scenario if present) - up: up percentile value in replicate (and in scenario if present) - any scenario column | VPC |
| VPC plot. | vpcPlot |
| Convert weeks to hours. | weeks |
| Convert pharma years (1 year = 12*4 weeks) to hours. | years |
