Man pages for campsis
Generic PK/PD Simulation Platform Campsis

apply_action	Apply some action on the given object.
apply_compartment_characteristics	Apply compartment characteristics from model. In practice,...
apply_outfun	Apply output function(s) on the given Campsis results.
apply_scenario	Apply scenario to the given model or dataset.
Arm	Create a treatment arm.
arm-class	Arm class.
arms-class	Arms class.
as.numeric-time_sequence-method	Time sequence to numeric vector.
as.numeric-time_vector-method	Time vector to numeric vector.
assign_dose_number	Assign dose number to each treatment entry.
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,...
bootstrap_distribution-class	Bootstrap distribution class.
campsis_handler	Suggested Campsis handler for showing the progress bar.
campsis_metadata-class	Campsis metadata class.
campsis_tbl-class	Campsis table class (see this class as an interface)
check_ii_and_addl	Check ii and addl arguments in addition to time.
compute_incremental_progress	Compute incremental progress.
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...
constant_distribution-class	Constant distribution class.
convert_time	Convert numeric time vector based on the provided units.
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.
DefaultOutfun	Default output function (identity function).
default_outfun-class	Default output function 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.
dosing_only	Filter Campsis output on dosing rows.
DosingSchedule	Dosing schedule constructor.
dosing_schedule-class	Dosing schedule class.
dot-assert_variable_present	Assert that one or more variable columns are present in the...
dot-auto_colour_columns	Detect colour stratification columns automatically.
dot-auto_strata	Detect VPC stratification variable automatically.
dot-is_replicated	Does the data contain more than one replicate?
drop_others	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.
export_delegate	Export delegate method. This method is common to RxODE and...
export_table_delegate	Export table delegate.
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.
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_campsis_options	Get the Campsis options (R options).
get_column	Get data of given column unless if does not exist (return...
get_compartment_mapping	Get a mapping table with all possibilities of compartment...
get_covariates	Get all covariates (fixed / time-varying / event covariates).
getDatasetMaxTime	Get dataset max time.
get_event_covariates	Get all event-related covariates.
getEventIterations	Get list of event iterations.
get_fixed_covariates	Get all fixed covariates.
get_initial_conditions	Get initial conditions at simulation start-up.
get_iovs	Get all IOV objects.
get_occasions	Get all occasions.
get_random_seed_value	Get random seed value.
get_seed	Get seed value.
get_seed_for_dataset_export	Get seed for dataset export.
get_seed_for_iteration	Get seed for iteration.
get_seed_for_parameters_sampling	Get seed for parameter uncertainty sampling.
get_simulation_engine_type	Get simulation engine type.
get_splitting_configuration	Get splitting configuration for parallel export.
get_times	Get all distinct times for the specified object.
get_time_varying_covariates	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).
import_campsismod_to_namespace	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...
is_empty_bootstrap	Is the given bootstrap empty.
json_to_campsis_dataset	JSON to Campsis dataset.
json_to_campsis_settings	JSON to Campsis dataset.
left_join_iiv	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.
lognormal_distribution-class	Log normal distribution class.
make_vpc_summary	Make the VPC summary. Input data frame must contain the...
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.
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,...
NOCB	Create NOCB settings.
nocb_settings-class	NOCB settings class.
NormalDistribution	Create a normal distribution.
normal_distribution-class	Normal distribution class.
Observations	Create an observations list. Please note that the provided...
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-class	Occasion class.
occasions-class	Occasions class.
on_ci	Check if the current session is on CI (e.g. GitHub actions).
on_cran	Check if the current session is on CRAN. The objective is to...
open_json	Open JSON file.
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...
ParameterDistribution	Create a parameter distribution. The resulting distribution...
PI	Compute the prediction interval summary over time...
pi_campsis_tbl-class	Prediction Interval (PI) Campsis table class
PIOutfun	Create a prediction interval output function
pi_outfun-class	Prediction interval output function class.
preprocess_arm_column	Preprocess ARM column. Add ARM equation in model...
preprocess_dest	Pre-process destination engine. Throw an error message if the...
preprocess_dosing	Preprocess 'dosing' argument.
preprocess_events	Pre-process events.
preprocess_ids	Preprocess subjects ID's.
preprocessNocbvars	Preprocess 'nocbvars' argument.
preprocess_outfun	Pre-process outfun argument.
preprocess_outvars	Preprocess 'outvars' argument. 'Outvars' is a character...
preprocess_replicates	Preprocess 'replicates' argument.
preprocess_scenarios	Pre-process scenarios.
preprocess_settings	Preprocess the simulation settings.
preprocess_slices	Preprocess 'slices' argument.
preprocess_tablefun	Pre-process tablefun argument.
preprocessTSLDAndTDOSColumn	Preprocess TSLD and TDOS columns according to given dataset...
processAllTimeColumns	Process time-related columns according to given dataset...
process_arm_labels	Process arm labels. Arm identifiers in ARM column are...
process_drop_others	Process 'DROP_OTHERS'.
process_simulate_arguments	Preprocess arguments of the simulate method.
Progress	Create progress settings.
progress_settings-class	Progress settings class.
protocol-class	Protocol class.
remove_initial_conditions	Remove initial conditions.
reorder_columns	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.
repeat_schedule	Repeat schedule.
ReplaceAction	Create a replace action.
replace_action-class	Replace action class.
retrieve_parameter_value	Retrieve the parameter value (standardized) for the specified...
rxode_engine-class	rxode2 engine class.
sample	Sample generic object.
sample_covariates_list	Sample covariates list.
sample_distribution_as_tibble	Sample a distribution and return a tibble.
sampleTimeVaryingCovariates	Sample time-varying covariates.
scatter_plot	Scatter plot (S3 generic).
scatterPlot	Scatter plot (or X vs Y plot).
scatter_plot.std_campsis_tbl	Scatter plot for standard Campsis simulation output.
Scenario	Create an scenario.
scenario_action-class	Scenario action class.
scenario_actions-class	Scenario actions class.
scenario-class	Scenario class.
Scenarios	Create a list of scenarios.
scenarios-class	Scenarios class.
seconds	Convert seconds to hours.
set_label	Set the label.
setLabel	Set the label.
set_seed	Set the seed. The goal of this method is to centralize all...
set_subjects	Set the number of subjects.
setSubjects	Set the number of subjects.
Settings	Create advanced simulation settings.
setup_plan_default	Setup default plan for the given simulation or hardware...
setupPlanDefault	Setup default plan for the given simulation or hardware...
setup_plan_sequential	Setup plan as sequential (i.e. no parallelisation).
setupPlanSequential	Setup plan as sequential (i.e. no parallelisation).
shaded_plot	Shaded plot / prediction interval plot (S3 generic).
shadedPlot	Shaded plot (or prediction interval plot).
shaded_plot.std_campsis_tbl	Shaded plot for standard Campsis simulation output.
simulate	Simulate function.
simulate_delegate	Simulation delegate (several replicates).
simulate_delegate_core	Simulation delegate core (single replicate).
simulate_scenarios	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...
spaghetti_plot	Spaghetti plot (S3 generic).
spaghettiPlot	Spaghetti plot.
spaghetti_plot.std_campsis_tbl	Spaghetti plot for standard Campsis simulation output.
splitDataset	Split dataset according to config.
standardise_time	Standardise time to hours.
stats_campsis_tbl-class	Statistics Campsis table class
StatsOutfun	Create a statistics output function
stats_outfun-class	Statistics output function class.
std_campsis_tbl-class	Standard Campsis table class
TimeSequence	Instantiate a new time sequence.
time_sequence-class	Time sequence class.
TimeVaryingCovariate	Create a time-varying covariate. This covariate will be...
time_varying_covariate-class	Time-varying covariate class.
TimeVector	Instantiate a new time vector
time_vector-class	Time vector class.
toDatasetSummary	Convert dataset to dataset summary (internal method).
to_explicit_distribution	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.
uniform_distribution-class	Uniform distribution class.
unite_columns	Unite the given column names.
unwrap_treatment	Unwrap treatment.
update_addl	Update the number of additional doses (ADDL).
update_amount	Update amount.
update_ii	Update the inter-dose interval (II).
update_repeat	Update the repeat field (argument 'rep' in Bolus and Infusion...
vec_restore.campsis_tbl	Restore a campsis_tbl object
vpc_plot	VPC plot (S3 generic).
vpcPlot	VPC plot.
vpc_plot.pi_campsis_tbl	VPC plot for prediction-interval Campsis output.
vpc_plot.std_campsis_tbl	VPC plot for standard Campsis simulation output.
weeks	Convert weeks to hours.
years	Convert pharma years (1 year = 12*4 weeks) to hours.