EsN - PLT Tools

PLT Tools Support

Requirements:

To run from emacs, Emacs must be installed in a directory without spaces.

Features not supported in PLT Tools-mode (PLT does not directly support these features):

Splitting of variables into multiple runs to output over 20 or 50 $PRED generated variables is not supported when using the PLT tools.
- When using the suggested msfooutputfile, PLT tools stores the MSFO in the MISCELLANEOUS/MSFO directory as msfo.TIMESTAMP. This would require some way to get each MSFO file involved in the multiple-control stream run and then merging the tables together.
- When specifying a different MSFO file, the MSFO file is retained in the working directory. At first glance this may seem like merging together tables would be feasible. However, when there are over 20 to 50 output items, EsN modifies the control stream to output slightly different table names. Using PLT tools AllRecords and FirstRecords, files such as AllRecords.txt~0 and FirstRecords.txt~0 should be stored in the home-directory. Therefore with multiple runs with over 20 or 50 items, these files would be overwritten. However one run could be merged back to AllRecords.txt and FirstRecords.txt. When this occurs, it would be in the working directory, and would not be created in PLT tools, nor stored within its system. Therefore, all graphics of PLT tools would be unable to run, and the AllRecords.txt or FirstRecords.txt would not be stored in PLT's system automatically.
Does not support multiple all sub-problems control streams. This is implied by having the same output file for every $PROBLEM in the control stream.

Notes for Windows

This has only been tested on Windows. The most recent version of PLT tools does not launch correctly unless launched outside of Emacs. One way to run PLT tools is to associate plta files with PLT tools. Afterward you may have Emacs "open" the automation file instead of launching PLT tools and opening the file. This option may be toggled under windows. It requires w32-browser to be in the load path. This should be included in EmacsPortable.

Automatic Updating of AllRecords.txt and FirstRecords.txt

Time Dependent Parameters

The automatic updating of parameters assumes that each parameter is the same throughout the subject. If there are time-varying covariates, or inter-occasion variability this does not hold true. For these cases, manually move the variable from the FirstRecords.txt to the AllRecords.txt. Emacs Speaks NONMEM will respect this, and not force the variable to be in FirstRecords.txt if the variable is already in AllRecords.txt.

Automatic PLT Tools Graphic Script Creation

Based on information in the file, including input variable specifications, and variable labels, EsN generates a template graphic script that may be edited and changed in PLT tools. It assumes that your input file is your covariate file, and fills out variable labels from the control stream. Once saved in PLT tools, Emacs Speaks NONMEM will not edit the script again.

Commenting Records for Brief Summary document

Note that if you run PLT tools, and use the ;C comment to include the $THETA, $OMEGA and $SIGMA labels, the final document may be little confusing. For example, with:

$THETA (0,150.,)  ;C THETA(1) - popE0
$THETA (0,200.,)  ;C THETA2 - popEMAX
$THETA (.001,10,) ;C THETA[3] - popEC50
$OMEGA 0.5 ;C ETA(1) - etaE0
$OMEGA 0.5 ;C  ETA(2) - etaEMAX
$OMEGA 0.5 ;C OMEGA3 -  etaEC50
$SIGMA 100 ;C SIGMA1 errSD

This would become:

ETA (0,150.,)  ;C THETA(1) - popE0
ETA (0,200.,)  ;C THETA2 - popEMAX
ETA (.001,10,) ;C THETA[3] - popEC50
EGA 0.5 ;C ETA(1) - etaE0
EGA 0.5 ;C  ETA(2) - etaEMAX
EGA 0.5 ;C OMEGA3 -  etaEC50
GMA 100 ;C SIGMA1 errSD

PLT tools 2.3.0 build 1589 takes drops the first 3 characters of the line recognized to be have comment text. Therefore the $THETA blocks becomes ETA, though it does not code for ETA variables. One way to overcome this is by having the code on each comment on a line without the record. In this example, we would have:

$THETA
       (0,150.,)  ;C THETA(1) - popE0
       (0,200.,)  ;C THETA2 - popEMAX
       (.001,10,) ;C THETA[3] - popEC50
$OMEGA
       0.5 ;C ETA(1) - etaE0
       0.5 ;C  ETA(2) - etaEMAX
       0.5 ;C OMEGA3 -  etaEC50
$SIGMA
       100 ;C SIGMA1 errSD

would result in unambiguous comments in the Brief Summary pdf:

    (0,150.,)  ;C THETA(1) - popE0
    (0,200.,)  ;C THETA2 - popEMAX
    (.001,10,) ;C THETA[3] - popEC50
    0.5 ;C ETA(1) - etaE0
    0.5 ;C  ETA(2) - etaEMAX
    0.5 ;C OMEGA3 -  etaEC50
    100 ;C SIGMA1 errSD

As of PLT tools 2.3.0 build 1589, this is no longer an issue (thanks Dennis!)

This has been fixed in the most recent version of PLT tools.

Emacs Speaks NONMEM's UserDefinedScript.R

Links in PLT tools

Links in PLT tools require grep to be installed on the system. It is installed by default on max and unix systems. It is also installed in the EmacsPortable distribution.

esnm

Emacs Speaks NONMEM

PLT Tools