initialize.report: Initialize Report Files

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

Description

initialize.report is a secondary function called during direct grid search or estimation runs.

For direct grid search runs, initialize.report creates the report file in the results & backup directory. This report file reports information about the run, including a summary table of the grid search which gives the value of the objective function for the different vector of estimates tested.

For estimation runs, initialize.report creates the log file and the report file in the results & backup directory. The log file stores, for each subject in the analysis, the values of the objective function and the parameter estimates at each iteration of the estimation process. The report file reports information about the estimation run, including the final estimates and some related statistics.

initialize.report is typically not called directly by users.

Usage

  initialize.report(problem = NULL,
                   param = NULL,
                   files = NULL,
                   isgrid = 0)

Arguments

problem	A list containing the following 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. method A character string, indicating the scale of the analysis. Should be 'population' or 'subject'. init A data.frame of parameter data with the following columns: 'names', 'type', 'value', 'isfix', 'lb', and 'ub'. debugmode Logical indicator of debugging mode. modfun Model function.
param	A data.frame containing the values of fixed and variable parameter estimates. Expected to contain the 'names', 'type', 'value', 'isfix', 'lb', and 'ub' columns.
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. 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). pred A .csv file reporting the predictions and calculated residuals for each individual in the dataset. est A .csv file reporting the final parameter estimates for each individual in the dataset. sim A .csv file reporting the simulated model predictions for each individual in the dataset. (Not used for estimation runs).
isgrid	Indicator of direct grid search runs.

Author(s)

Sebastien Bihorel ([e-mail])

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