# Generic PK/PD Simulation Platform Campsis

## Documentation for package ‘campsis’ version 1.8.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N O P R S T U V W Y

## -- A --

applyAction | Apply some action on the given object.
applyAction-method | Apply some action on the given object.
applyCompartmentCharacteristics | Apply compartment characteristics from model. In practice, only compartment infusion duration needs to be applied.
Arm | Create a treatment arm.
arm-class | Arm class.
arms-class | Arms class.
as.numeric-method | Time sequence to numeric vector.
as.numeric-method | Time vector to numeric vector.

## -- B --

BinomialDistribution | Binomial distribution.
binomial_distribution-class | Binomial distribution class.
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, CAMPSIS will generate values depending on the given data and arguments.
bootstrap_distribution-class | Bootstrap distribution class.

## -- C --

campsis_handler | Suggested Campsis handler for showing the progress bar.
ConstantDistribution | Create a constant distribution. Its value will be constant across all generated samples.
constant_distribution-class | Constant distribution class.
convertTime | Convert numeric time vector based on the provided units.
Covariate | Create a non time-varying (fixed) covariate.
covariate-class | Covariate class.
covariates-class | Covariates class.
CyclicSchedule | Cyclic schedule constructor.
cyclic_schedule-class | Cyclic schedule class.

## -- D --

Dataset | Create a dataset.
dataset-class | Dataset class.
DatasetConfig | Create a dataset configuration. This configuration allows CAMPSIS to know which are the default depot and observed compartments.
dataset_config-class | Dataset configuration class.
days | Convert days to hours.
Declare | Create declare settings.
declare_settings-class | Declare settings class.
DefaultSettings | Create default settings.
default_settings-class | Default settings class.
DiscreteDistribution | Discrete distribution.
discrete_distribution-class | Discrete distribution class.
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.
DosingSchedule | Dosing schedule constructor.
dosing_schedule-class | Dosing schedule class.

## -- E --

EtaDistribution | Create an ETA distribution. The resulting distribution is a normal distribution, with mean=0 and sd=sqrt(OMEGA).
Event | Create an interruption event.
event-class | Event class.
EventCovariate | Create an event covariate. These covariates can be modified further in interruption events.
Events | Create a list of interruption events.
events-class | Events class.
event_covariate-class | Event covariate class.

## -- F --

FixedDistribution | Create a fixed distribution. Each sample will be assigned a fixed value coming from vector 'values'.
fixed_covariate-class | Fixed covariate class.
fixed_distribution-class | Fixed distribution class.
FunctionDistribution | 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")).
function_distribution-class | Function distribution class.

## -- G --

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.
getCampsisOption | Get Campsis option logic.
getCovariates | Get all covariates (fixed / time-varying / event covariates).
getCovariates-method | Get all covariates (fixed / time-varying / event covariates).
getEventCovariates | Get all event-related covariates.
getEventCovariates-method | Get all event-related covariates.
getFixedCovariates | Get all fixed covariates.
getFixedCovariates-method | Get all fixed covariates.
getIOVs | Get all IOV objects.
getIOVs-method | Get all IOV objects.
getOccasions | Get all occasions.
getOccasions-method | Get all occasions.
getSeedForDatasetExport | Get seed for dataset export.
getSeedForIteration | Get seed for iteration.
getSeedForParametersSampling | Get seed for parameter uncertainty sampling.
getSplittingConfiguration | Get splitting configuration for parallel export.
getTimes | Get all distinct times for the specified object.
getTimes-method | Get all distinct times for the specified object.
getTimeVaryingCovariates | Get all time-varying covariates.
getTimeVaryingCovariates-method | Get all time-varying covariates.

## -- H --

Hardware | Create hardware settings.
hardware_settings-class | Hardware settings class.
hours | Convert hours to hours (do nothing).

## -- I --

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 settings).
IOV | 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.

## -- L --

length-method | Return the number of subjects contained in this arm.
length-method | Return the number of repetition cycles.
length-method | Return the number of subjects contained in this dataset.
length-method | Return the number of repetition cycles.
LogNormalDistribution | Create a log normal distribution.
lognormal_distribution-class | Log normal distribution class.

## -- M --

minutes | Convert minutes to hours.
months | Convert pharma months (1 month = 4 weeks) to hours.
mrgsolve_engine-class | mrgsolve engine class.

## -- N --

nhanes | NHANES database (demographics and body measure data combined, from 2017-2018).
NOCB | Create NOCB settings.
nocb_settings-class | NOCB settings class.
NormalDistribution | Create a normal distribution.
normal_distribution-class | Normal distribution class.

## -- O --

Observations | Create an observations list. Please note that the provided 'times' will automatically be sorted. Duplicated times will be removed.
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 values to dose numbers. A new column will automatically be created in the exported dataset.
occasion-class | Occasion class.
occasions-class | Occasions class.
Outfun | Create a new output function
output_function-class | Output function class.

## -- P --

ParameterDistribution | Create a parameter distribution. The resulting distribution is a log-normal distribution, with meanlog=log(THETA) and sdlog=sqrt(OMEGA).
PI | Compute the prediction interval summary over time.
Progress | Create progress settings.
progress_settings-class | Progress settings class.
protocol-class | Protocol class.

## -- R --

RepeatAtSchedule | 'Repeat at' schedule constructor. Note that the time 0 for the base pattern will be added by default if not provided.
repeated_schedule-class | Repeated schedule class. See this class as an interface.
repeatSchedule | Repeat schedule.
repeatSchedule-method | Repeat schedule.
repeat_at_schedule-class | 'Repeat at' schedule class.
ReplaceAction | Create a replace action.
replace_action-class | Replace action class.
retrieveParameterValue | Retrieve the parameter value (standardized) for the specified parameter name.
rxode_engine-class | RxODE/rxode2 engine class.

## -- S --

sample | Sample generic object.
sample-method | Sample generic object.
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.
scenario_action-class | Scenario action class.
scenario_actions-class | Scenario actions class.
seconds | Convert seconds to hours.
setLabel | Set the label.
setLabel-method | Set the label.
setSubjects | Set the number of subjects.
setSubjects-method | Set the number of subjects.
Settings | Create advanced simulation settings.
setupPlanDefault | 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)
setupPlanSequential | Setup plan as sequential (i.e. no parallelisation).
shadedPlot | Shaded plot (or prediction interval plot).
simulate | Simulate function.
simulate-method | Simulate function.
SimulationProgress | Create a simulation progress object.
simulation_engine-class | Simulation engine class.
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 ?rxode2::rxSolve.
spaghettiPlot | Spaghetti plot.
standardiseTime | Standardise time to hours.

## -- T --

TimeSequence | Instantiate a new time sequence.
TimeVaryingCovariate | Create a time-varying covariate. This covariate will be implemented using EVID=2 rows in the exported dataset and will not use interruption events.
TimeVector | Instantiate a new time vector
time_sequence-class | Time sequence class.
time_varying_covariate-class | Time-varying covariate class.
time_vector-class | Time vector class.
treatment-class | Treatment class.
treatment_iov-class | Treatment IOV class.
treatment_iovs-class | Treatment IOV's class.

## -- U --

undefined_distribution-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_schedule-class | Undefined schedule class.
UniformDistribution | Create an uniform distribution.
uniform_distribution-class | Uniform distribution class.
unwrapTreatment | Unwrap treatment.
unwrapTreatment-method | Unwrap treatment.
updateADDL | Update the number of additional doses (ADDL).
updateADDL-method | Update the number of additional doses (ADDL).
updateAmount | Update amount.
updateAmount-method | Update amount.
updateII | Update the inter-dose interval (II).
updateII-method | Update the inter-dose interval (II).
updateRepeat | Update the repeat field (argument 'rep' in Bolus and Infusion constructors).
updateRepeat-method | Update the repeat field (argument 'rep' in Bolus and Infusion constructors).

## -- V --

VPC | 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
vpcPlot | VPC plot.

## -- W --

weeks | Convert weeks to hours.

## -- Y --

years | Convert pharma years (1 year = 12*4 weeks) to hours.