scarabee.read.parms: Read scaRabee Parameter File
In scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

Description Usage Arguments Value Author(s) See Also

scarabee.read.parms is a secondary function called at each scaRabee run. It reads and checks the information contained in the specified parameter file.scarabee.read.parms is typically not called directly by users.

1	scarabee.read.parms(files = NULL)

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').
iter: A .csv file reporting the values of the objective function and estimates of model parameters at each iteration. (Not used for simulation runs).
report: A text file reporting for each individual in the dataset the final parameter estimates for structural model parameters, residual variability and secondary parameters as well as the related statistics (coefficients of variation, confidence intervals, covariance and correlation matrix). (Not used for simulation runs).
pred: A .csv file reporting the predictions and calculated residuals for each individual in the dataset. (Not used for simulation runs).
est: A .csv file reporting the final parameter estimates for each individual in the dataset. (Not used for simulation runs).
sim: A .csv file reporting the simulated model predictions for each individual in the dataset. (Not used for estimation runs).

If the content of the parameter file is valid, scarabee.read.parms returns a data.frame with the same content. The names of the data.frame columns are: names, type, value, isfix, lb, and ub.

Sebastien Bihorel (sb.pmlab@gmail.com)

scarabee.analysis

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