Generic PK/PD Simulation Platform CAMPSIS
Apply compartment characteristics from model. In practice, only compar...
Apply scenario to the given model or dataset.
Arm class.
Create a treatment arm.
Arms class.
Assign dose number to each treatment entry.
Binomial distribution.
Bolus class.
Create one or several bolus(es).
Bootstrap distribution class.
Bootstrap class.
Create a bootstrap object.
Create a bootstrap distribution. During function sampling, CAMPSIS wil...
Suggested Campsis handler for showing the progress bar.
Check ii and addl arguments in addition to time.
Compute incremental progress.
Constant distribution class.
Create a constant distribution. Its value will be constant across all ...
Convert numeric time vector based on the provided units.
Counter-balance LOCF mode for occasions & IOV. This function will simp...
Counter-balance NOCB mode for occasions & IOV. This function will simp...
Covariate class.
Create a non time-varying (fixed) covariate.
Covariates class.
Cut table according to given iteration.
Dataset configuration class.
Dataset class.
Create a dataset.
Create a dataset configuration. This configuration allows CAMPSIS to k...
Create a dataset summary (internal method).
Convert days to hours.
Declare settings class.
Create declare settings.
Discrete distribution.
Distribution class. See this class as an interface.
Dose adaptation class.
Dose adaptations class.
Create a dose adaptation.
Filter CAMPSIS output on dosing rows.
Return the 'DROP_OTHERS' string that may be used in the 'outvars' vect...
Create an ETA distribution. The resulting distribution is a normal dis...
Event covariate class.
Event class.
Create an interruption event.
Create an event covariate. These covariates can be modified further in...
Create an event iteration object.
Create an event-related observations list. Please note that the provid...
Events class.
Create a list of interruption events.
Export delegate method. This method is common to RxODE and mrgsolve.
Export table delegate.
Factor scenarios columns if not done yet.
Fill IOV/Occasion columns.
Fixed covariate class.
Fixed distribution class.
Create a fixed distribution. Each sample will be assigned a fixed valu...
Function distribution class.
Create a function distribution. During distribution sampling, the prov...
Generate IIV matrix for the given OMEGA matrix.
Generate IIV matrix for the given Campsis model.
Return the list of available time units.
Get data of given column unless if does not exist (return NULL in that...
Get all covariates (fixed / time-varying / event covariates).
Get dataset max time.
Get all event-related covariates.
Get list of event iterations.
Get all fixed covariates.
Get scheduling mode for furrr (see argument 'scheduling' available in ...
Get initial conditions at simulation start-up.
Get all IOV objects.
Get all occasions.
Get random seed value.
Get seed value.
Get seed for dataset export.
Get seed for iteration.
Get seed for parameter uncertainty sampling.
Get simulation engine type.
Get splitting configuration for parallel export.
Get all distinct times for the specified object.
Get all time-varying covariates.
Get all time-varying variables. These variables are likely to be influ...
Hardware settings class.
Create hardware settings.
Convert hours to hours (do nothing).
Import the whole campsismod package into NAMESPACE when parsed by 'rox...
Infusion class.
Create one or several infusion(s).
Internal settings class (transient object from the simulation settings...
Define inter-occasion variability (IOV) into the dataset. A new variab...
Is the given bootstrap empty.
Left-join IIV matrix.
Return the number of subjects contained in this arm.
Return the number of subjects contained in this dataset.
Create a log normal distribution.
Merge time-varying covariates into a single data frame. This last data...
Convert minutes to hours.
Convert pharma months (1 month = 4 weeks) to hours.
mrgsolve engine class.
NOCB settings class.
Create NOCB settings.
Create a normal distribution.
Observations set class.
Observations class.
Create an observations list. Please note that the provided 'times' wil...
Filter CAMPSIS output on observation rows.
Occasion class.
Define a new occasion. Occasions are defined by mapping occasion value...
Occasions class.
Create a new output function
Output function class.
Create a parameter distribution. The resulting distribution is a log-n...
Compute the prediction interval summary over time.
Preprocess ARM column. Add ARM equation in model automatically.
Pre-process destination engine. Throw an error message if the destinat...
Preprocess 'dosing' argument.
Pre-process events.
Preprocess subjects ID's.
Preprocess 'nocbvars' argument.
Pre-process outfun argument.
Preprocess 'outvars' argument. 'Outvars' is a character vector which t...
Preprocess 'replicates' argument.
Pre-process scenarios.
Preprocess the simulation settings.
Preprocess 'slices' argument.
Pre-process tablefun argument.
Preprocess TSLD and TDOS columns according to given dataset configurat...
Process time-related columns according to given dataset configuration.
Process arm labels. Arm identifiers in ARM column are replaced by arm ...
Process 'DROP_OTHERS'.
Preprocess arguments of the simulate method.
Progress settings class.
Create progress settings.
Protocol class.
Remove initial conditions.
Reorder output columns.
Retrieve the parameter value (standardized) for the specified paramete...
RxODE/rxode2 engine class.
Sample generic object.
Sample covariates list.
Sample a distribution and return a tibble.
Sample time-varying covariates.
Scatter plot (or X vs Y plot).
Scenario class.
Create an scenario.
Scenarios class.
Create a list of scenarios.
Convert seconds to hours.
Set the label.
Set the seed. The goal of this method is to centralize all calls to th...
Set the number of subjects.
Create advanced simulation settings.
Setup default plan for the given simulation or hardware settings. This...
Setup plan as sequential (i.e. no parallelisation).
Shaded plot (or prediction interval plot).
Simulate function.
Simulation delegate (several replicates).
Simulation delegate core (single replicate).
Simulation scenarios.
Simulation engine class.
Simulation progress class.
Simulation settings class.
Create a simulation progress object.
Solver settings class. See ?mrgsolve::update. See ?rxode2::rxSolve.
Create solver settings.
Spaghetti plot.
Split dataset according to config.
Standardise time to hours.
Time-varying covariate class.
Create a time-varying covariate. This covariate will be implemented us...
Convert dataset to dataset summary (internal method).
Convert user-given distribution to an explicit CAMPSIS distribution. P...
Treatment IOV class.
Treatment IOV's class.
Treatment class.
Undefined distribution class. This type of object is automatically cre...
Create an uniform distribution.
Unite the given column names.
Compute the VPC summary. Input data frame must contain the following c...
VPC plot.
Convert weeks to hours.
Convert pharma years (1 year = 12*4 weeks) to hours.
A generic, easy-to-use and intuitive pharmacokinetic/pharmacodynamic (PK/PD) simulation platform based on R packages 'rxode2' and 'mrgsolve'. CAMPSIS provides an abstraction layer over the underlying processes of writing a PK/PD model, assembling a custom dataset and running a simulation. CAMPSIS has a strong dependency to the R package 'campsismod', which allows to read/write a model from/to files and adapt it further on the fly in the R environment. Package 'campsis' allows the user to assemble a dataset in an intuitive manner. Once the user’s dataset is ready, the package is in charge of preparing the simulation, calling 'rxode2' or 'mrgsolve' (at the user's choice) and returning the results, for the given model, dataset and desired simulation settings.
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