[R] polycor package

[yrosseel]

Dear Laura,

John is correct. The error is produced by the sem() function in the 
lavaan package. The reason is that you did not use proper names for the 
function arguments. The correct call should be:

sem.cdu= sem(cdu, sample.cov=hetcor, sampl.nobs=1861, 
meanstructure=F,fixed.x=F)

But more importantly, using a polychoric correlation as input, and using 
ML estimation will not produce correct standard errors and test 
statistics. A better approach is to use the categorical capabilities of 
lavaan and provide the full data to sem(), indicating which variables 
can be considered as 'ordered'. For example:

sem.cdu= sem(cdu, data=germany2009, ordered=c("cdupid", "MERKELLIKE", 
"CDULIKE", "MERKELPROX", "CDUPROX"))

Here, I assumed all variables can be considered as ordered. If some of 
them should be treated as conintuous/numeric, omit them from the 
ordered= argument.

By default, lavaan will use the WLSMV estimator when ordered variables 
are involved.

Yves.


On 11/16/2012 10:13 PM, John Fox wrote:
> Dear Laura,
>
> As I explained to you when you wrote to me directly, you're not
> having trouble with the polycor package, since you have AFAICS
> successfully computed polychoric correlation among your variables.
> The error is produced when you call sem(), apparently in the lavaan
> package (though you don't mention that), and you should address your
> question to the author of that package (or use an appropriate title
> line in your r-help posting).
>
> Best, John
>
> ------------------------------------------------ John Fox Sen.
> William McMaster Prof. of Social Statistics Department of Sociology
> McMaster University Hamilton, Ontario, Canada
> http://socserv.mcmaster.ca/jfox/  On Fri, 16 Nov 2012 12:58:03 +0000
> Laura Maria Schwirz <schwirzl at tcd.ie> wrote:
>> I am currently working with R's polycor package and I have
>> encountered a problem. I tried to follow the steps as outlined in
>> the sem.pdf file where a CFA model is run using polychoric
>> correlations. Every time I run the command sem(model, data, N=.), I
>> get the following warning message: Warning message: In if
>> (orthogonal) { : the condition has length > 1 and only the first
>> element will be used
>>
>> Below is the code that I am using for my dataset. I also tried to
>> copy and paste the code from the sem.pdf file using data from CNES
>> but I still get an error message. Any help would be much
>> appreciated.
>>
>>
>>
>>> germany2009 <- read.dta("StataforR.dta") #attach(germany2009)
>>> viewData(germany2009) # hcor <- function(data) hetcor(data,
>>> std.err=F, pd=T)$correlations hetcor=hcor(germany2009) hetcor
>> cdupid MERKELLIKE    CDULIKE MERKELPROX    CDUPROX cdupid
>> 1.0000000  0.5073577  0.6070514 -0.4064925 -0.4146810 MERKELLIKE
>> 0.5073577  1.0000000  0.7832340 -0.4405571 -0.4200360 CDULIKE
>> 0.6070514  0.7832340  1.0000000 -0.4868895 -0.5042006 MERKELPROX
>> -0.4064925 -0.4405571 -0.4868895  1.0000000  0.8789219 CDUPROX
>> -0.4146810 -0.4200360 -0.5042006  0.8789219  1.0000000
>>> viewData(hetcor) cdu= ' CDULIKE ~ cdupid + CDUPROX
>> +   MERKELLIKE ~ cdupid + MERKELPROX +   CDUPROX ~ ~ cdupid +
>> cdupid ~ ~ MERKELPROX +   CDUPROX ~ ~ MERKELPROX +   MERKELLIKE ~
>> 1 +   CDULIKE ~1 '
>>> sem.cdu= sem(cdu, hetcor, N=1861, meanstructure=F,fixed.x=F)
>> Warning message: In if (orthogonal) { : the condition has length >
>> 1 and only the first element will be used