Documentation

Posted on
Picture of user. Dorothy Bishop Joined: 02/04/2010

Kronecker product

Forums
Sorry - just realised that an earlier correction I suggested to the manual was in error.
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.

Posted on
Picture of user. Dorothy Bishop Joined: 02/04/2010

Explaining how standard errors are estimated

Forums
I've written a bit for my simplified manual for beginners (see Wiki) to try and explain to the uninitiated how standard errors are estimated. My own understanding of this topic is primitive and probably wrong, so I want to run this pass the experts before incorporating it in the SMB. It's very short: could somebody who understands these things please take a look and tell me what needs changing. Thanks
Posted on
Picture of user. neale Joined: 07/31/2009

How would ordinary mortals access trunk/models/passing etc

Forums
Sometimes the models in trunk/models/passing, failing, etc. are useful to link to, even if they are not part of the official docs (yet). How does one compose a URL to get to these directories?
Posted on
Picture of user. mspiegel Joined: 07/31/2009

Debugging sphinx documentation

Forums
After writing some documentation in a ReStructured Text (.rst) file, the next step is to run "make html" or "make latex" to build this documentation. The Sphinx build system likes to generate warning messages. Even though a warning is not an error, a warning should be fixed because it signals that there could be an error in the documentation markup. In my experience, fixing warnings generated by Sphinx can be a somewhat tricky. First off, the messages are somewhat cryptic.
Posted on
No user picture. Hermine Joined: 07/31/2009

Link Documentation directly to Example Scripts/Data

Forums
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?

Posted on
Picture of user. tbates Joined: 07/31/2009

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

Forums
Topic for discussing things that pertain to most or all of the documentation, such as software for figures, or code formatting...
Posted on
Picture of user. tbates Joined: 07/31/2009

demo files

Forums
for talking about the demo files
Posted on
Picture of user. tbates Joined: 07/31/2009

UnivariateTwinAnalysis_MatrixRaw.R

Forums
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:

Posted on
Picture of user. tbates Joined: 07/31/2009

hangovers from Mx

Forums
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'
Posted on
Picture of user. tbates Joined: 07/31/2009

Lower exists now

Forums
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"
+ )