| Apply some action on the given object. | apply_action apply_action,campsis_model,replace_action-method apply_action,dataset,replace_action-method |
| Apply compartment characteristics from model. In practice, only compartment infusion duration needs to be applied. | apply_compartment_characteristics |
| Apply output function(s) on the given Campsis results. | apply_outfun apply_outfun,outfun-method apply_outfun,outfuns-method |
| Create a treatment arm. | Arm |
| Arm class. | arm-class |
| Arms class. | arms-class |
| Time sequence to numeric vector. | as.numeric,time_sequence-method |
| Time vector to numeric vector. | as.numeric,time_vector-method |
| Binomial distribution class. | binomial_distribution-class |
| Binomial distribution. | BinomialDistribution |
| Create one or several bolus(es). | Bolus |
| Bolus wrapper class. | bolus_wrapper-class |
| 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 |
| Campsis metadata class. | campsis_metadata-class |
| Campsis table class (see this class as an interface) | campsis_tbl campsis_tbl-class |
| Compute the prediction interval summary over time. | compute_pi |
| Compute generic statistics over time. | compute_stats |
| 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. | convert_time |
| Create a non time-varying (fixed) covariate. | Covariate |
| Covariate class. | covariate-class |
| Covariates class. | covariates-class |
| Cyclic schedule class. | cyclic_schedule-class |
| Cyclic schedule constructor. | CyclicSchedule |
| 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 |
| Default output function class. | default_outfun-class |
| Default settings class. | default_settings-class |
| Default output function (identity function). | DefaultOutfun |
| Create default settings. | DefaultSettings |
| Discrete distribution class. | discrete_distribution-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. | dosing_only |
| Dosing schedule class. | dosing_schedule-class |
| Dosing schedule constructor. | DosingSchedule |
| 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. | generate_iiv |
| Generate IIV matrix for the given OMEGA matrix. | generate_iiv_ |
| Return the list of available time units. | get_available_time_units |
| Get Campsis option logic. | get_campsis_option |
| Get all covariates (fixed / time-varying / event covariates). | get_covariates get_covariates,arm-method get_covariates,arms-method get_covariates,covariates-method get_covariates,dataset-method |
| Get all event-related covariates. | get_event_covariates get_event_covariates,arm-method get_event_covariates,arms-method get_event_covariates,covariates-method get_event_covariates,dataset-method |
| Get all fixed covariates. | get_fixed_covariates get_fixed_covariates,arm-method get_fixed_covariates,arms-method get_fixed_covariates,covariates-method get_fixed_covariates,dataset-method |
| Get all IOV objects. | get_iovs get_iovs,arm-method get_iovs,arms-method get_iovs,dataset-method |
| Get all occasions. | get_occasions get_occasions,arm-method get_occasions,arms-method get_occasions,dataset-method |
| Get splitting configuration for parallel export. | get_splitting_configuration |
| Get all time-varying covariates. | get_time_varying_covariates get_time_varying_covariates,arm-method get_time_varying_covariates,arms-method get_time_varying_covariates,covariates-method get_time_varying_covariates,dataset-method |
| Get all distinct times for the specified object. | get_times get_times,arm-method get_times,arms-method get_times,dataset-method get_times,events-method get_times,observations-method get_times,observations_set-method get_times,treatment-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 wrapper class. | infusion_wrapper-class |
| 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 |
| Treatment IOV class. | iov-class |
| Return the number of subjects contained in this arm. | length,arm-method |
| Return the number of repetition cycles. | length,cyclic_schedule-method |
| Return the number of subjects contained in this dataset. | length,dataset-method |
| Return the number of repetition cycles. | length,repeat_at_schedule-method |
| Log normal distribution class. | lognormal_distribution-class |
| 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 |
| NCA table output function class. | nca_table_outfun-class |
| Create a NCA table output function | NCATableOutfun |
| NHANES database (demographics and body measure data combined, from 2017-2018). | nhanes |
| Create NOCB settings. | NOCB |
| NOCB settings class. | nocb_settings-class |
| Normal distribution class. | normal_distribution-class |
| Create a normal distribution. | NormalDistribution |
| Filter Campsis output on observation rows. | obs_only |
| 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 |
| 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. | outfun-class |
| Create a collection of output functions. | Outfuns |
| Output functions class (i.e. a collection of output functions). | outfuns-class |
| Create a parameter distribution. The resulting distribution is a log-normal distribution, with meanlog=log(THETA) and sdlog=sqrt(OMEGA). | ParameterDistribution |
| Prediction Interval (PI) Campsis table class | pi_campsis_tbl pi_campsis_tbl-class |
| Prediction interval output function class. | pi_outfun-class |
| Create a prediction interval output function | PIOutfun |
| Create progress settings. | Progress |
| Progress settings class. | progress_settings-class |
| Protocol class. | protocol-class |
| 'Repeat at' schedule class. | repeat_at_schedule-class |
| Repeat schedule. | repeat_schedule repeat_schedule,numeric,cyclic_schedule-method repeat_schedule,numeric,repeat_at_schedule-method repeat_schedule,numeric,undefined_schedule-method |
| 'Repeat at' schedule constructor. Note that the time 0 for the base pattern will be added by default if not provided. | RepeatAtSchedule |
| Repeated schedule class. See this class as an interface. | repeated_schedule-class |
| Replace action class. | replace_action-class |
| Create a replace action. | ReplaceAction |
| Retrieve the parameter value (standardized) for the specified parameter name. | retrieve_parameter_value |
| rxode2 engine class. | rxode_engine-class |
| Sample generic object. | sample sample,bolus,integer-method sample,bootstrap,integer-method sample,bootstrap_distribution,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 (S3 generic). | scatter_plot |
| Scatter plot for standard Campsis simulation output. | scatter_plot.std_campsis_tbl |
| Create an scenario. | Scenario |
| Scenario action class. | scenario_action-class |
| Scenario actions class. | scenario_actions-class |
| Scenario class. | scenario-class |
| Create a list of scenarios. | Scenarios |
| Scenarios class. | scenarios-class |
| Convert seconds to hours. | seconds |
| Set the label. | set_label set_label,arm,character-method set_label,dataset,character-method |
| Set the number of subjects. | set_subjects set_subjects,arm,integer-method set_subjects,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) | setup_plan_default |
| Setup plan as sequential (i.e. no parallelisation). | setup_plan_sequential |
| Shaded plot / prediction interval plot (S3 generic). | shaded_plot |
| Shaded plot for standard Campsis simulation output. | shaded_plot.std_campsis_tbl |
| Simulate function. | simulate simulate,campsis_model,data.frame,character,events,scenarios,function,character,outfuns,integer,integer,logical,simulation_settings-method simulate,campsis_model,dataset,character,events,scenarios,function,character,outfuns,integer,integer,logical,simulation_settings-method simulate,campsis_model,tbl_df,character,events,scenarios,function,character,outfuns,integer,integer,logical,simulation_settings-method simulate,campsis_model,tbl_df,mrgsolve_engine,events,scenarios,function,character,outfuns,integer,integer,logical,simulation_settings-method simulate,campsis_model,tbl_df,rxode_engine,events,scenarios,function,character,outfuns,integer,integer,logical,simulation_settings-method simulate,replicated_campsis_model,dataset,character,events,scenarios,function,character,outfuns,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 (S3 generic). | spaghetti_plot |
| Spaghetti plot for standard Campsis simulation output. | spaghetti_plot.std_campsis_tbl |
| Standardise time to hours. | standardise_time |
| Statistics Campsis table class | stats_campsis_tbl stats_campsis_tbl-class |
| Statistics output function class. | stats_outfun-class |
| Create a statistics output function | StatsOutfun |
| Standard Campsis table class | std_campsis_tbl std_campsis_tbl-class |
| Time sequence class. | time_sequence-class |
| Time-varying covariate class. | time_varying_covariate-class |
| Time vector class. | time_vector-class |
| Instantiate a new time sequence. | TimeSequence |
| 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 |
| Instantiate a new time vector | TimeVector |
| Treatment IOV's class. | treatment_iovs-class |
| Treatment class. | treatment-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_distribution-class |
| Undefined schedule class. | undefined_schedule-class |
| Uniform distribution class. | uniform_distribution-class |
| Create an uniform distribution. | UniformDistribution |
| Unwrap treatment. | unwrap_treatment unwrap_treatment,arm-method unwrap_treatment,arms-method unwrap_treatment,bolus-method unwrap_treatment,bolus_wrapper-method unwrap_treatment,dataset-method unwrap_treatment,infusion-method unwrap_treatment,infusion_wrapper-method unwrap_treatment,treatment-method |
| Update the number of additional doses (ADDL). | update_addl update_addl,arm,integer,character-method update_addl,arms,integer,character-method update_addl,bolus,integer,character-method update_addl,bolus_wrapper,integer,character-method update_addl,dataset,integer,character-method update_addl,infusion,integer,character-method update_addl,infusion_wrapper,integer,character-method update_addl,treatment,integer,character-method |
| Update amount. | update_amount update_amount,arm,numeric,character-method update_amount,arms,numeric,character-method update_amount,bolus,numeric,character-method update_amount,bolus_wrapper,numeric,character-method update_amount,dataset,numeric,character-method update_amount,infusion,numeric,character-method update_amount,infusion_wrapper,numeric,character-method update_amount,treatment,numeric,character-method |
| Update the inter-dose interval (II). | update_ii update_ii,arm,numeric,character-method update_ii,arms,numeric,character-method update_ii,bolus,numeric,character-method update_ii,bolus_wrapper,numeric,character-method update_ii,dataset,numeric,character-method update_ii,infusion,numeric,character-method update_ii,infusion_wrapper,numeric,character-method update_ii,treatment,numeric,character-method |
| Update the repeat field (argument 'rep' in Bolus and Infusion constructors). | update_repeat update_repeat,arm,repeated_schedule,character-method update_repeat,arms,repeated_schedule,character-method update_repeat,bolus,repeated_schedule,character-method update_repeat,bolus_wrapper,repeated_schedule,character-method update_repeat,dataset,repeated_schedule,character-method update_repeat,infusion,repeated_schedule,character-method update_repeat,infusion_wrapper,repeated_schedule,character-method update_repeat,treatment,repeated_schedule,character-method |
| VPC plot (S3 generic). | vpc_plot |
| VPC plot for prediction-interval Campsis output. | vpc_plot.pi_campsis_tbl |
| VPC plot for standard Campsis simulation output. | vpc_plot.std_campsis_tbl |
| Convert weeks to hours. | weeks |
| Convert pharma years (1 year = 12*4 weeks) to hours. | years |
