Documentation

I would like to link all the OpenMx scripts directly to the documentation, but don't know where they physically reside, and can't find them from the website.

Ideally, if a user clicks on a (linked) script, it should open immediately in their R application so it can be run with just two clicks (assuming the user has R installed). Could/should this be done and if so, how?

Topic for discussing things that pertain to most or all of the documentation, such as software for figures, or code formatting...

for talking about the demo files

There are close to zero comments on this script, and much of it is quite obscure.

1. There are still places with T instead of TRUE and unlabeled parameters relying on being in the right place:

mxMatrix("Full", 1, 2, T, 20, "mean", dimnames=list(NULL, selVars), name="expMeanMZ"),

2. Most matrices need a comment about what it is they are holding, i.e.:

mxMatrix("Full", nrow=1, ncol=1, free=TRUE, values=.6, label="a", name="X") # what is this for?

mxAlgebra(X %*% t(X), name="A"), # what does this do?

Proposing an algebra for the the groups is critical and needs a comment:

There are places in the demo scripts that inherit things from Mx that are not necessary: like the fact that Mx couldn't read files with a labels line..

So in , we see:

data(twinData)
twinVars <- c('fam','age','zyg','part','wt1','wt2','ht1','ht2','htwt1','htwt2','bmi1','bmi2')

Much easier to say

data(twinData)
twinVars = names(twinData) 
# maybe with a comment so people know what is going on
# 'fam','age','zyg','part','wt1','wt2','ht1','ht2','htwt1','htwt2','bmi1','bmi2'

http://openmx.psyc.virginia.edu/docs/OpenMx/latest/Introduction.html#simple-openmx-script

Says "PS a lower triangular matrix doesn’t exist yet so we specify it explicitly"

scripts using the newer types amongst ‘Diag’, ‘Full’, ‘Iden’, ‘Lower’, ‘Sdiag’, ‘Stand’, ‘Symm’, ‘Unit’, or ‘Zero’ should change

Also "True" is not a defined variable in R. TRUE is.

so the snippet fails to execute

> mxMatrix(
+ type="Full",
+ nrow=1,
+ ncol=2,
+ free=True,
+ values=c(0,0),
+ dimnames=list(NULL, selVars),
+ name="expMean"
+ )