scarabee.read.data: Read scaRabee Data File

In sbihorel/scaRabee: Optimization Toolkit for Pharmacokinetic-Pharmacodynamic Models

Description

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

Usage

  scarabee.read.data(files = NULL,
                     method = NULL)

Arguments

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).

method

A character string, indicating the scale of the analysis. Should be 'population' or 'subject'.

Value

Return a list with 2 levels:

data

A list which content depends on the scope of the analysis. If the analysis was run at the level of the subject, data contains as many levels as the number of subjects in the dataset, plus the ids level containing the vector of identification numbers of all subjects included in the analysis population. If the analysis was run at the level of the population, data contains only one level of data and ids is set to 1.

Each subject-specific level contains as many levels as there are treatment levels for this subject, plus the trts level listing all treatments for this subject, and the id level giving the identification number of the subject.

Each treatment-specific levels is a list containing the following levels:

cov

mij x 3 data.frame containing the times of observations of the dependent variables (extracted from the TIME variable), the indicators of the type of dependent variables (extracted from the CMT variable), and the actual dependent variable observations (extracted from the DV variable) for this particular treatment and this particular subject.

cov

mij x c data.frame containing the times of observations of the dependent variables (extracted from the TIME variable) and all the covariates identified for this particular treatment and this particular subject.

bolus

bij x 4 data.frame providing the instantaneous inputs for a treatment and individual.

infusion

fij x (4+c) data.frame providing the zero-order inputs for a treatment and individual.

trt

the particular treatment identifier.

new

A logical indicator defining whether or not a modified data file has been created based upon the original file. This is the case if and if only the time of first data record for one or more individuals in the original data file is not 0. The new data file is created such as the TIME variable is modified so that time of the first data record for all individuals is 0; the time of later records is modified accordingly.

Author(s)

Sebastien Bihorel ([e-mail])

See Also

scarabee.analysis

sbihorel/scaRabee documentation built on Feb. 7, 2022, 9:50 p.m.