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Submodel testing: Dropping single parameters in a matrix

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trinewa's picture
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Joined: 11/30/2009 - 06:35
Submodel testing: Dropping single parameters in a matrix

Hi,
I am testing submodels under a multivariate (3 variables) common pathways ADE model. I want to run a submodel where I drop the specific d for the first of the three variables, but I keep getting error messages. I hope someone could help me out with this.

I have tried various versions of the procedure below:

multiComPathAEad1eModel mxModel(ADE_Common_Fit$ADE,
mxMatrix( type="Diag", nrow=nvar, ncol=nvar, free[1,1]=FALSE, values[1,1]=0, name="ds" )
)
)
multiComPathAEad1eFit

The error messages I keep getting are:

Error: unexpected '=' in:
" mxModel(ADE_Common_Fit$ADE,
mxMatrix( type="Diag", nrow=nvar, ncol=nvar, free[1,1]="
> )
Error: unexpected ')' in " )"
> )
Error: unexpected ')' in ")"

mspiegel's picture
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Joined: 07/31/2009 - 15:24
When invoking a function, the

When invoking a function, the syntax foo(a = 1, b = 2, c = 3) assigns the values 1, 2, and 3 to the variables a, b, and c. Since the function invocation binds a value to a variable, the square brackets cannot be used on the left-hand side of the binding.

One method to drop a free parameter would be to do the following:

multiComPathAEad1eModel <- mxRename(ADE_Common_Fit, &nbsp;&nbsp;&nbsp;&nbsp;"multiComPathAEad1e")
multiComPathAEad1eModel$ADE.ds@free[1,1] <- FALSE
multiComPathAEad1eModel$ADE.ds@values[1,1] <- 0

trinewa's picture
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Joined: 11/30/2009 - 06:35
Thank you, that way it

Thank you, that way it works.

One follow-up question:
I seem to be having trouble getting confidence intervals on the parameters within the new model. using the following syntax:

multiComPathAEad1eModel multiComPathAEad1eModel$ADE.ds@free[1,1] multiComPathAEad1eModel$ADE.ds@values[1,1]

mxCI(c('multiComPathAEad1eModel$ADE.al', 'multiComPathAEad1eModel$ADE.dl','multiComPathAEad1eModel$ADE.el', 'multiComPathAEad1eModel$ADE.f','multiComPathAEad1eModel$ADE.as', 'multiComPathAEad1eModel$ADE.ds','multiComPathAEad1eModel$ADE.es'))
multiComPathADEad1eFit

This is the only output I get :
MxInterval
@reference: multiComPathAEad1eModel$ADE.al multiComPathAEad1eModel$ADE.dl multiComPathAEad1eModel$ADE.el multiComPathAEad1eModel$ADE.f multiComPathAEad1eModel$ADE.as multiComPathAEad1eModel$ADE.ds multiComPathAEad1eModel$ADE.es
@lowerdelta: 3.841459
@upperdelta: 3.841459

This syntax produces the same result:
mxCI(c('ADE.al', 'ADE.dl','ADE.el', 'ADE.f','ADE.as', 'ADE.ds','ADE.es'))

Any idea what's wrong?

mspiegel's picture
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Joined: 07/31/2009 - 15:24
Only one argument per

Only one argument per confidence interval for now. So you need to do:

intervals <- lapply(c('ADE.al', 'ADE.dl','ADE.el', 'ADE.f','ADE.as', 'ADE.ds','ADE.es'), mxCI)

tbates's picture
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Joined: 07/31/2009 - 14:25
won't this work? model =

won't this work?

model = mxModel(model, mxCI(c('ADE.al', 'ADE.dl','ADE.el', 'ADE.f','ADE.as', 'ADE.ds','ADE.es')) ) # add CIs to model
fit = mxRun(model, intervals=T)
summary(fit)

mspiegel's picture
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Joined: 07/31/2009 - 15:24
Oops. Yes, Tim Bates

Oops. Yes, Tim Bates suggestion is simpler and it will work.

trinewa's picture
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Joined: 11/30/2009 - 06:35
Thanks to both - that solved

Thanks to both - that solved the problems with the confidence intervals!

trinewa's picture
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Joined: 11/30/2009 - 06:35
I have tried the same syntax

I have tried the same syntax in order to drop the common D:

multiComPathAEad2eModel multiComPathAEad2eModel$ADE.d1@free multiComPathAEad2eModel$ADE.d1@values

but I get a new error message:

> multiComPathAEad2eModel$ADE.d1@free Error in checkSlotAssignment(object, name, value) :
"free" is not a slot in class "NULL"
> multiComPathAEad2eModel$ADE.d1@values Error in checkSlotAssignment(object, name, value) :
"values" is not a slot in class "NULL"

Writing free[1,1]
and values [1,1] does not help.

Why is this different, and what can I do if I want to drop one common factor and one of the parameters in the specific factors within the same sub model?

tbates's picture
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Joined: 07/31/2009 - 14:25
whenever an assignment like

whenever an assignment like that doesn't work, the thing to do is to try and access (rather than set) the path of interest, to make sure that you are addressing it correctly. Then if that is broken, go back up the chain of names to see where things are going wrong.

So if I saw
> multiComPathAEad2eModel$ADE.d1

return the error "free" is not a slot in class "NULL"

Then I think "so, d1 is coming back NULL - it doesn't exist." You can see this by saying:

   multiComPathAEad2eModel$ADE.d1

Then I would try

   multiComPathAEad2eModel$ADE

and see what is in there. My guess is the object you want is not called 'd1' but something else?

Finally, I bet you'd have a lot more luck doing this directly by building new matrices that do what you want and replacing the existing ones. So

newModel = mxModel(oldModel,name="new name",
mxMatrix( type="Diag", nrow=nvar, ncol=nvar, free=F, values=0, name="d1" )
)

that will give new a new model, with the d1 matrix fixed to 0 in place of whatever used to be there

best, tim

Steve's picture
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Joined: 07/30/2009 - 14:03
I would second Tim's advice.

I would second Tim's advice. That's the way to go about it. Each line encapsulates its meaning so that you have the best chance of understanding your script when you go back and read it years later.

In general, I would avoid directly changing parameters by using the @ syntax unless you _really_ know what you're doing. We have these functions like "mxMatrix" or "mxPath" in order to reduce the time you spend poking around trying to find what to change and to reduce the chance that you might break your model by not updating all of the parts of a matrix in consistent ways.

trinewa's picture
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Joined: 11/30/2009 - 06:35
You were right - the object's

You were right - the object's name was dl, not d1. Thanks for your patience, I will by me a new pair of glasses.

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