I have a quite large model built in the previous PHX 1.3/NLME 1.2 version, and have recently migrated to PHX 1.4/NLME 1.3. I am now experiencing problems running my model and suspect it do be due a change in the "enable" command. I have
used in rigorously to manually turn covariates on/off during model development.
For instance, I have this statement :
tvFTOTadj=(tvFTOT*(1+Mix1Sep2ontvFTOT*(Mix1Sep2==1))*(1+InsDosontvFTOT*InsDos)*(1+InsSmontvFTOT*InsSm))
stparm(FTOT = 1/(1+exp(log(1/tvFTOTadj-1)+nFTOT)))
…
fixef(tvFTOT = c(, 0.53,))
…
#FTOT
fixef(Mix1Sep2ontvFTOT(enable=0)=c(,0.1,))
fixef(InsDosontvFTOT(enable=0)=c(,0.000025,)) # level is 4000 pM, ie. 0.000025*4000=0.1
fixef(InsSmontvFTOT(enable=0)=c(,0.1,))
where I’d be manually testing three difference covariates on FTOT. In the base case, they would all be turned off with enable=0.
This is in agreement with the the modelling reference language manual for PHX v. 1.3 p. 43ff, where it states:
6 f(enable=1) = c(0.01, 0.1, 5)
…
Line 6 is like line 4, but the fixed effect f is enabled within an estimation run. This
is used in covariate effect modeling procedures. Enabling the fixed effect means
that it is estimated. The enable value is 1 if it is enabled and 0 (zero) if it is disabled
and not estimated.
After a model is fit, the statement on line 6 can be rewritten as
f(enable=0) = c(0.01, 0.1, 5)
to set the enable value to zero and disable the fixed effect estimation.
In the modelling reference language manual for PHX v. 1.4 p. 41ff, it now states:
6 f(enable=c(1)) = c(0.01, 0.1, 5)
…
Line 6 is like line 4, but the fixed effect f is enabled within an estimation run. This
is used in covariate effect modeling procedures. Enabling the fixed effect means
that it is estimated. If a fixed effect is disabled, that means its value is frozen to
0.0 and it is not estimated. There is a command-line argument, /xe, that determines
which variables are chosen to be disabled. If there is no such argument, all
fixed effects having an enable clause are disabled.
It seems that now there is syntax change, so that the assignment should be =c(1) for enabling. Would it be =c(0) for disabling? It doesnt seem to work, however, since my script - running i v. 13 - is not running properly now. The fixed effects are still being estimted, though enable=c(0).
Also, the part in the manual text highliged in bold seems unclear, hence:
-“if a fixed effect is disabled” - does this mean "if enable=c(0) is stated for that fixed effect"?
-what is this /xe argument, and where do I see it /check if its there
-"If there is no such argument, all fixed effects having an enable clause are
disabled". What does this mean - that just the word enable will trigger diablement?
In short, how do I get the enable functionality as it was in version 1.3. Ie. so can build the compete "shell" and easily turn on of off the fixed effect I want to test but setting enable to 1 or 0, w/o having to comment out the effect out entirely and set to 0.
I did get an answer from Bendt, but I did not understand it, alas (sorry, Berndt!).
Thank you in advance !
Edited by Thomas Klitgaard, 10 July 2015 - 08:53 AM.