andy00000000000 / nonmem2mrgsolve Goto Github PK

SAME option in omega will work to translate w/ nonmem2mrgsolve. But if sigdigs is specified by user, SAME ETA(s) are treated as Fixed and not rounded to specified significant digits. The ETA the SAME ETA(s) are based off of is rounded (treated as estimated, not "Fixed")

R.yml file needs updating; currently checks are failing

Not able to read in EXT correctly when multiple $EST blocks in CTL, since NONMEM appends the header after each.

Hi Andrew,

Nice work - just want to point that the function nonmem2mrgsolve::nonmem2mrgsolve assumes the model file ends in .ctl extension. Very commonly the model extension is instead .mod, which is not recognized for now.

Identify lines implementing IOV and comment out or remove the IOV portions. Remove IOV etas from Omega block.

line 100: tmpom <- tmpom[1, which(tmpom != 0)]
breaks code when there is only 1 non-zero omega term since it is converting from named matrix to numeric value

similar issue may occur if no omegas or if all omegas are fixed to 0

Currently no conversion of T, TSFD, TIME to SOLVERTIME or sef.time(). May need to move line locations to ODE block.

Remove duplicate help articles for nonmem2mrgsolve function
Update README

add to readme

Currently works for user defined odes (ADVAN13, etc.). Build in the others.

real examples of workflow

convert using only ctl instead of ext or cnv

Hello!

I'm trying to convert rxode2 models to mrgsolve, and to do that:

1. I'm using babelmixr2 to convert the RxODE model to NONMEM (as a ctl file)
2. Then the idea was to use your package to convert the ctl file to an mrgsolve compatible format.

The issue is, I only have the model file, not the data field for the classic babelmixr conversion.

As such, I'm using the result of this comment (which can be used as a working example btw) to write a ctl file, before using that file to convert to mrgsolve.

Currently, I realized that your package required both the ctl and ext files. As I currently have only the ctl file, how could I handle this "automatically"?

Thank you by advance!

Wrote as NA=NA.

Option to use cnv file for final estimates instead of ext when using alternative estimation routines.

Variables declared within a conditional statement will be missing "double" from second condition (following "else") if applicable.

Add option for output filename directly from nonmem2mrgsolve call

Set up so future commits are "Verified"

Needs creating.

Create R Shiny app to run and display both codes

some parameters at times listed twice

See pkpd alt model for Mohamed's project.

NONMEM covariance step is necessary to identify which parameters are fixed from ext file. Future version should incorporate a workaround using just the ctl file

breaking translation error. Incorrect brackets and blank parameter declaration

They are not being pulled backwards from PK block into PARAM if appear as R_[cmt] or D_[cmt] = RATE or DUR; would need to be renamed so not using reserved words

minor bug

Checks fail due to fake examples listed in R help guides

read in input csv and nm tbl, sim w/ nocb, compare evid=0

Example:

"FIRST
" USE PRDATA, ONLY: MXSTP01
" MXSTP01=2147483647

add to improve validation and future reproducibility