Hi folks, I am just pasting in here some email discussion between Greg Carey and myself concerning the language interface. In the thread we drifted off to talk about models of assortative mating.
Greg Carey's email:
just looked at openMx and am worried that things might get unnecessarily complicated when dealing with large multivariate problems.
imagine data on twins and families on the WAIS and a factor model. the proposed GUI is like Amos--you will spend so much time drawing paths from 13 variables to X latent factors for father (including 13 specifics), X latent factors for mother (13 more specifics), for son 1, son 2 ... to daughter k that the actual canvas cannot accommodate the number of necessary symbols. in addition, the 13 x 13 covariance matrix between husband's WAIS and wife's WAIS should be predicted by the model of marital assortment. try to express this in jack's RAM notation--it is possible but the only practical way (that i can see) is to define blocks of the path-coefficient matrix and the exogenous-residual covariance matrix in terms of other, more specific matrices.
anyway, what everyone is doing is perfectly fine--for simple models. for complicated models, i suspect that a different interface is required (one that may, in fact, be accommodated by expansion of the python script, mxParser.py). in terms of a positive contribution, i suggest that the old logic of Mx be followed but in the following way:
(1) define the parameter matrices containing free and/or fixed parameters [e.g., what is typically done in Group 1]
covA sy 3 fr
D di 3 fi
StdE di 3
WhatEver fu 3 6
(2) parse a series of statements that fix, free, equate, etc. elements of the above matrices. these would include the FI, FR, EQ, PA, MA, SP statements of Mx
0 1 1
23.6 4 9.3
.3 .8 .7 0 0 0
0 .7 .3 .2 0 0
0 0 0 0 .8 .5
FI Whatever 1 1 2 1 3 2
(3) give the algebra (as in the first group in usual Mx Code) but in R syntax
Example = Stde %*% WhatEver %*% transpose(Whatever)
(4) assign the predicted matrices from (3) to the groups in the model
(5) from the above information, it is possible to construct two different numeric vectors:
xfandf = vector of all free and fixed parameters
xf = compact vector of free parameters,
so do the following in the minimization function passed into NAG E04???
(5.a) take the vector xf passed from E04??? and put the appropriate elements into vector xfandf
(5.b) from vector xfandf, construct the parameter matrices specified in BEGIN MATRICES and BEGIN WHATEVER
(5.c) perform the algebra specified in step (3) above
----- CHECK THIS CODE OUT ----------------------------------------------
npheno <- 5
Va sy npheno
sigE di npheno
Re st npheno
eta sy npheno
1 1 1 0 0
1 1 1 0 0
1 1 1 0 0
0 0 0 1 1
0 0 0 1 1
ST 2.5 DIAG(Va)
ST 0.4 OFFDIAG(Va)
ST 3.0 sigE
Vp <- Va + sigE %*% Re %*% sigE
covE <- sigE %*% eta %*% sigE
1 rbind (cbind(Vp, Va + covE), cbind(Va + covE, Vp))
2 rbind (cbind(Vp, .5*Va + covE), cbind(.5*Va + covE, Vp))
----- END OF CODE --------------------------------------------------------
bottom line = if you implement this in the existing openMx framework, it will take pages of code. a suitable preprocessor in python, perl, or (if really interested in a potential gui with web interfaces) java can have a user enter the code and have it translated into Mx equivalent using the above rules.
anyway, just trying to help out.
Editorial Note from Mike Neale: the Pattern command, which is rarely used in Mx, simply identifies which elements should be free parameters without actually assigning parameter numbers (labels in OpenMx) to them. It is equivalent to free=c(T,F,T) syntax in OpenMx.