Omega Labels Mis-Detected?

[billdenney]

(Hopefully this is unrelated, but I'm using @MikeKSmith 's #113.)

I think that this is an error with name detection of diagonal $OMEGA values.

I have the following $OMEGA block set in a model:

$OMEGA
 0.04   ; IIV KA
$OMEGA BLOCK(2)
 0.14  ; IIV CL
 -0.2  ; COV-IIV CL-V2
 0.4   ; IIV V2
$OMEGA
 0 FIX ; IIV Q3
 0 FIX ; IIV V3
 0 FIX ; IIV Q4
 0 FIX ; IIV V4

With it, I get the error:

> get_prm(xpdb=xpdb)
Returning parameter estimates from $prob no.1, subprob no.0, method lce
... # Some of the parameters here
# ... with 25 more rows
Warning message:
[$prob no.1, subprob no.0, lce] $OMEGA labels did not match the number of OMEGAs in the `.ext` file. 

As I looked, it appears to be an issue with off-diagonal $OMEGA values here such that they have blank names:

xpose/R/xpdb_access.R

Lines 426 to 433 in 74855b2

	n_omega <- sum(prms$type == 'ome' & prms$diagonal, na.rm = TRUE)
	omega_names <- data$prm_names$omega
	if (n_omega != length(omega_names)) {
	warning('[$prob no.', data$problem, ', subprob no.', data$subprob, ', ', data$method,
	'] $OMEGA labels did not match the number of OMEGAs in the `.ext` file.', call. = FALSE)
	} else {
	prms$label[prms$type == 'ome' & prms$diagonal] <- omega_names
	}

At that point, my omega names are:

[1] "IIV KA" "IIV CL" ""       "IIV V2" "IIV Q3" "IIV V3" "IIV Q4" "IIV V4"

while the number of diagonal omegas is accurately detected as 7.

[bguiastr]

Thanks for the detailed example. I need to rethink the way that blocks are parsed, xpose currently assumes that all blocks are written in their "triangle" form and not as a list. This is related to #87

[billdenney]

There is a project to make a full NONMEM parser: https://github.com/EightPillars/nmtranprocessorcpp

Might it be worthwhile to combine NONMEM parsing efforts into one rigorously tested parser that can be used across applications? (The linked effort is trying to make an ANTLR-based parser which would presumably be usable in many programming languages.)