# Generic PK/PD Simulation Platform Campsis

## Documentation for package ‘campsis’ version 1.9.0

- 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 --

apply_action | Apply some action on the given object.
apply_action-method | Apply some action on the given object.
apply_compartment_characteristics | Apply compartment characteristics from model. In practice, only compartment infusion duration needs to be applied.
apply_outfun | Apply output function(s) on the given Campsis results.
apply_outfun-method | Apply output function(s) on the given Campsis results.
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.
campsis_metadata-class | Campsis metadata class.
campsis_tbl | Campsis table class (see this class as an interface)
campsis_tbl-class | Campsis table class (see this class as an interface)
compute_pi | Compute the prediction interval summary over time.
compute_stats | Compute generic statistics over time.
ConstantDistribution | Create a constant distribution. Its value will be constant across all generated samples.
constant_distribution-class | Constant distribution class.
convert_time | 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.
DefaultOutfun | Default output function (identity function).
DefaultSettings | Create default settings.
default_outfun-class | Default output function class.
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.
DosingSchedule | Dosing schedule constructor.
dosing_only | Filter Campsis output on dosing rows.
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 --

generate_iiv | Generate IIV matrix for the given Campsis model.
generate_iiv_ | Generate IIV matrix for the given OMEGA matrix.
get_available_time_units | Return the list of available time units.
get_campsis_option | Get Campsis option logic.
get_covariates | Get all covariates (fixed / time-varying / event covariates).
get_covariates-method | Get all covariates (fixed / time-varying / event covariates).
get_event_covariates | Get all event-related covariates.
get_event_covariates-method | Get all event-related covariates.
get_fixed_covariates | Get all fixed covariates.
get_fixed_covariates-method | Get all fixed covariates.
get_iovs | Get all IOV objects.
get_iovs-method | Get all IOV objects.
get_occasions | Get all occasions.
get_occasions-method | Get all occasions.
get_splitting_configuration | Get splitting configuration for parallel export.
get_times | Get all distinct times for the specified object.
get_times-method | Get all distinct times for the specified object.
get_time_varying_covariates | Get all time-varying covariates.
get_time_varying_covariates-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 --

NCATableOutfun | Create a NCA table output function
nca_table_outfun-class | NCA table output function class.
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.
obs_only | 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
outfun-class | Output function class.
Outfuns | Create a collection of output functions.
outfuns-class | Output functions class (i.e. a collection of output functions).

## -- P --

ParameterDistribution | Create a parameter distribution. The resulting distribution is a log-normal distribution, with meanlog=log(THETA) and sdlog=sqrt(OMEGA).
PIOutfun | Create a prediction interval output function
pi_campsis_tbl | Prediction Interval (PI) Campsis table class
pi_campsis_tbl-class | Prediction Interval (PI) Campsis table class
pi_outfun-class | Prediction interval output function class.
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.
repeat_at_schedule-class | 'Repeat at' schedule class.
repeat_schedule | Repeat schedule.
repeat_schedule-method | Repeat schedule.
ReplaceAction | Create a replace action.
replace_action-class | Replace action class.
retrieve_parameter_value | Retrieve the parameter value (standardized) for the specified parameter name.
rxode_engine-class | rxode2 engine class.

## -- S --

sample | Sample generic object.
sample-method | Sample generic object.
scatter_plot | Scatter plot (S3 generic).
scatter_plot.std_campsis_tbl | Scatter plot for standard Campsis simulation output.
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.
Settings | Create advanced simulation settings.
setup_plan_default | 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)
setup_plan_sequential | Setup plan as sequential (i.e. no parallelisation).
set_label | Set the label.
set_label-method | Set the label.
set_subjects | Set the number of subjects.
set_subjects-method | Set the number of subjects.
shaded_plot | Shaded plot / prediction interval plot (S3 generic).
shaded_plot.std_campsis_tbl | Shaded plot for standard Campsis simulation output.
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.
spaghetti_plot | Spaghetti plot (S3 generic).
spaghetti_plot.std_campsis_tbl | Spaghetti plot for standard Campsis simulation output.
standardise_time | Standardise time to hours.
StatsOutfun | Create a statistics output function
stats_campsis_tbl | Statistics Campsis table class
stats_campsis_tbl-class | Statistics Campsis table class
stats_outfun-class | Statistics output function class.
std_campsis_tbl | Standard Campsis table class
std_campsis_tbl-class | Standard Campsis table class

## -- 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 to_explicit_distribution() 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.
unwrap_treatment | Unwrap treatment.
unwrap_treatment-method | Unwrap treatment.
update_addl | Update the number of additional doses (ADDL).
update_addl-method | Update the number of additional doses (ADDL).
update_amount | Update amount.
update_amount-method | Update amount.
update_ii | Update the inter-dose interval (II).
update_ii-method | Update the inter-dose interval (II).
update_repeat | Update the repeat field (argument 'rep' in Bolus and Infusion constructors).
update_repeat-method | Update the repeat field (argument 'rep' in Bolus and Infusion constructors).

## -- V --

vpc_plot | VPC plot (S3 generic).
vpc_plot.pi_campsis_tbl | VPC plot for prediction-interval Campsis output.
vpc_plot.std_campsis_tbl | VPC plot for standard Campsis simulation output.

## -- W --

weeks | Convert weeks to hours.

## -- Y --

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