Generic PK/PD Simulation Platform Campsis

Documentation for package ‘campsis’ version 1.9.0

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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.