Bugs

Unresolved Bugs

Saving new simulation variables
Upon saving, Xpose asks if new variables should always be added to the corresponding table. Unfortunately, this choice is not saved.
Improper Shrinkage Calculation
Includes ETA values that are zero when calculating shrinkage. Most of the time this is inconsequential.

Resolved Bugs

0.12

Multiple records per line
According to NONMEM's user guide, there may be multiple records per line. This has been added in.
Xpose R script generating -Inf errors
Fixed log-plot issues with -Inf.
Extended variables mismatch
When replacing an extended variable label that is the

same as a variable defined in one of the model blocks ($PK, $PRED, etc.) and that variable is defined on the same line as the model block, EsN did not know that this variable was off limit for substitution later. This has been fixed.

0.11

80 Character problems
When enabling the display 80 characters and then disabling it, the 80 character highlighting remains and cannot be edited. Fixed in Version 0.11.
Occasional slash problems
When files contained a period than slash, these slashes were changed to backward slashes occasionally in windows. Fixed in Version 0.11 (Due to updating file-names).
Prompting for version control when saving
When version control is disabled and a new user attempts to edit the control stream, esn tries to place the control stream in version control. This bug was due to menu mis-labeling. The menu has been labeled and changed according to the functions needed. There is "Automatically place model under version control" and "Automatically generate a description for the version control." Previously these had the same labels and were in different locations. This is fixed in Verison 0.11
Not detecting the correct estimation method
When the estimation method is at

the end of the $EST record, EsN did not calculate the correct estimation method. Now the correct estimation has been calculated.

Not detecting certain variables
EsN did not detect variables that are defined on the same line as the $ERROR, $PK and $PRED statements. This has been resolved.

Changes

0.12

  • Changed header code to support 5 different styles of headers: (1) PLT tools header, (2) PDx pop header, (3) Pirana, (4) Census style headers, and (5) anything else.
  • Added better error handling by using lisp save-restriction more often.
  • Added new behavior for backspace and delete in the editable region of the comments.
  • Added a magic * key that will start a list in an editable region of the header.
  • Changed delete and backspace to be advised functions to conform with any key-binding changes that the user wishes.
  • Allowed THETA, ETA, and EPS to be renumbered with the explicit comment THETA(1) - Comment
  • Allowed extended control streams to ignore THETA, ETA, EPS, etc statements before variable label.
  • Changed the automatic generation of the PLT graphics script to only occur when:
    • There is no graphics script associated with that file.
    • If there is a graphics script, that graphics script was last generated by Emacs Speaks NONMEM (should have EsN in the comment)
  • Added hyperlinks to control streams
  • Added renumbering of A_0.
  • Added Icons to launch or run files in NMQual, PDx pop, Census, etc.

0.11

  • Changed emacs to recognize NONMEM files when opend as files that start with a $PROBLEM statement (regardless of the extension). In text files (like files ending with .txt), or with files that Emacs does not recognize, when typing $PRO at the beginning of the control stream, Emacs will then recognize the file as a control stream. Note that the .txt extension collides with outputs in NONMEM 7 unless the $ESTIMATION step specifies a different output.
  • Changed Emacs Speaks NONMEM to autoload (only loads when a control stream is openend or recognized), speeding up initial Emacs load.
  • Changed Key binding menu (windows keys, emacs keys, etc.) to be a different file that is no longer loaded by default.
  • Added more files to version control. These are names that are output by default in NONMEM 7. Assuming a base file name of root, these files are:
    • root.txt
    • root.cov
    • root.coi
    • root.cor
    • root.phi
  • Added the new Fortran 95 operators (supported by NONMEM 7)
  • Added .res as a default NONMEM output file
  • Allow input to be 50 data items per record (supported by NONMEM 7)
  • Added warning highlighting if output variables are over the maximum specified.
  • Added highlighting (in warning face) of continuation & of Fortran95 that may be used with NONMEM 7.
  • Added different types of PRED/WRES/RES output in NONMEM 7
  • Added ADVAN13 the new LSODA differential equation solver for NONMEM 7.
  • Added SIGL step size to $EST for NONMEM 7.
  • Added iterative two-stage methods (ITS), Monte-Carlo Importance Sampling (IMP), Monte-Carlo Importance Sampling EM assisted by Mode a Posteriori/MAP estimation (IMPMAP), Stochastic Approximation Expectation Maximization Method (SAEM), and Full Markov Chain Monte Carlo/MCMC Bayesian Analysis Method (BAYES) which are included in NONMEM 7.
  • Added extended control stream support of MU variables.
  • Moved the NONMEM assumed version to two places on the menu tree.
  • Added support for PLT tools.

To Do

  • Automatic checks/generation for mu-variables.
  • Automatic checks/Generation of GRD for Bayes IMP/IMPMAP/SAEM errors to speed up calculation.
  • Automatic output of estimation files. (FO would be control-fo-01.txt, control-fo-02.txt, BAYES would be control-bayes-01.txt, etc. )