scarabee.analysis: Run a scaRabee Analysis
In scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

Description Usage Arguments Value Author(s) See Also

scarabee.analysis is the de facto gateway for running any kind of analysis with scaRabee. All other functions distributed with this package are secondary functions called directly or indirectly by scarabee.analysis.

Arguments for scarabee.analysis are best defined using the template distributed with the package.

  scarabee.analysis(files = NULL,
                    method = 'population',
                    runtype = NULL,
                    debugmode = FALSE,
                    estim.options = NULL,
                    npts = NULL,
                    alpha = NULL,
                    solver.options = list(method='lsoda'))

`files`	A list of input used for the analysis. The following elements are expected and none of them could be null: data A .csv file located in the working directory, which contains the dosing information, the observations of the dependent variable(s) to be modeled, and possibly covariate information. The expected format of this file is described in details in `vignette('scaRabee', package='scaRabee')`. param A .csv file located in the working directory, which contains the initial guess(es) for the model parameter(s) to be optimized or used for model simulation. The expected format of this file is described in details in `vignette('scaRabee',package='scaRabee')`. model A text file located in the working directory, which defines the model. Models specified with explicit, ordinary or delay differential equations are expected to respect a certain syntax and organization detailed in `vignette('scaRabee',package='scaRabee')`.
`method`	A character string, indicating the scale of the analysis. Should be 'population' or 'subject'.
`runtype`	A character string, indicating the type of analysis. Should be 'simulation', 'estimation', or 'gridsearch'.
`debugmode`	A logical value, indicating the debug mode should be turn on (`TRUE`) or off (default). Used only for estimation runs. If turn on, the user could have access to error message returned when the model and residual variability are evaluated in `fitmle` before the likelihood is computed.
`estim.options`	A list of estimation options containing two elements `maxiter` (the maximum number of iterations) and `maxeval` (the maximum number of function evaluations).
`npts`	Only necessary if `runtype` is set to 'gridsearch'; `npts` represents the number of points to be created by dimension of the grid search.
`alpha`	Only necessary if `runtype` is set to 'gridsearch'; `alpha` is a real number, representing the factor applied to the initial estimates of the model parameters to determine the lower and upper bounds to the grid search space.
`solver.options`	A list of differential equation solver options. Currently not modifiable by users.

Run an analysis until completion. See vignette('scaRabee',package='scaRabee') for more details about the expected outputs for an estimation, a simulation, or a gird search run.

Sebastien Bihorel (sb.pmlab@gmail.com)

fitmle

scaRabee documentation built on Feb. 4, 2022, 5:07 p.m.