Documentation

Kronecker product
I had not realised that %x% was the way of indicating Kronecker product, and so had thought it was a typo for %*%
Would be good to add a comment to the script where this first appears to clarify.
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Explaining how standard errors are estimated
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How would ordinary mortals access trunk/models/passing etc

Debugging sphinx documentation
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Link Documentation directly to Example Scripts/Data
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?

documentation-wide discussion (layout, how to include code, etc.)

demo files
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UnivariateTwinAnalysis_MatrixRaw.R
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:
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hangovers from Mx
So in
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'
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Lower exists now
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"
+ )
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