read_extfile

Reads .ext files generated by NONMEM

At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP
<doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors'
package in the 'Monolix' installation, as described at the following url
<https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>.
When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required
Chart Data instead of exporting it from the 'Monolix' gui.

Matthew Fidler

ggPMX

'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models

read_extfile function

<dl><dt>run</dt>
<dd>run a run number or run identifier</dd>
<dt>project</dt>
<dd>project the NONMEM project directory</dd>
<dt>file</dt>
<dd>file the `ext` file name</dd>
<dt>path</dt>
<dd>path full path and file name for `ext` file</dd>
<dt>read_fun</dt>
<dd>read_fun function to read the `ext` file</dd>
<dt>quiet</dt>
<dd>Logical, if <code>FALSE</code> messages are printed to the console.</dd></dl>

Arguments

This function is based on read_nmext from mrgsolve, Original Author: Kyle T Baron.
This function has some changes to the original code:
Addition of param, "quiet", (option of pmx_msg function, from xpose package) (Line: 27)
The code was slightly adjusted to check for multiple tables and also extract SE (ITERATION == 1000000001) (Line: 44-58, Line: 86-96, respectively)
The output was also slightly adjusted to fit ggPMX output (df and df2) (Line: 105,106)
as_bmat was replaced by bmat_like to create the diagonal matrix (Line 116:142)

Author

Reads .ext files generated by NONMEM — read_extfile

<dl>

<dt>run</dt>
<dd>run a run number or run identifier</dd>


<dt>project</dt>
<dd>project the NONMEM project directory</dd>


<dt>file</dt>
<dd>file the `ext` file name</dd>


<dt>path</dt>
<dd>path full path and file name for `ext` file</dd>


<dt>read_fun</dt>
<dd>read_fun function to read the `ext` file</dd>


<dt>quiet</dt>
<dd>Logical, if <code>FALSE</code> messages are printed to the console.</dd>

</dl>

read_extfile: Reads .ext files generated by NONMEM

Description

Usage

Value

Arguments

Author

Examples