[R] FIML using lavaan returns zeroes for coefficients

Joshua Wiley jwiley.psych at gmail.com
Mon Jul 23 20:59:58 CEST 2012

Hi Andrew,

I do not think there is a reason to avoid it for univariate regression
other than:

1) as was stated the predictors must be continuous
2) it will be slower (non issue for a handful of regressions on a few
thousand cases but for people doing thousands of regression on
millions of observations, a big concern)

In the next month or so, I may have a beta version of a package
primarily providing helper functions for fitting SEM models, but could
also include an lm()ish wrapper to lavaan.  It would use the
traditional formula interface, but issue a warning if factor variables
or variables with insufficient unique values were used (as either
predictors or outcomes).  If anyone would be interested in beta
testing, feel free to email me.  Once I have a basic package working,
it will go up on github.



On Mon, Jul 23, 2012 at 6:07 AM, Andrew Miles <rstuff.miles at gmail.com> wrote:
> Thanks for the helpful explanation.
> As to your question, I sometimes use lavaan to fit univariate regressions simply because it can handle missing data using FIML rather than listwise deletion.  Are there reasons to avoid this?
> BTW, thanks for the update in the development version.
> Andrew Miles
> On Jul 21, 2012, at 12:59 PM, yrosseel wrote:
>> On 07/20/2012 10:35 PM, Andrew Miles wrote:
>>> Hello!
>>> I am trying to reproduce (for a publication) analyses that I ran
>>> several months ago using lavaan, I'm not sure which version, probably
>>> 0.4-12. A sample model is given below:
>>> pathmod='mh30days.log.w2 ~ mh30days.log + joingroup + leavegroup +
>>> alwaysgroup + grp.partic.w2 + black + age + bivoc + moved.conf +
>>> local.noretired + retired + ds + ministrytime + hrswork +
>>> nomoralescore.c + negint.c + cong.conflict.c + nomoraleXjoin +
>>> nomoraleXleave + nomoraleXalways + negintXjoin + negintXleave +
>>> negintXalways + conflictXjoin + conflictXleave + conflictXalways '
>>> mod1 = sem(pathmod, data=sampledat, missing="fiml", se="robust")
>>> At the time, the model ran fine.  Now, using version 0.4-14, the
>>> model returns all 0's for coefficients.
>> What happened is that since 0.4-14, lavaan tries to 'detect' models that are just univariate regression, and internally calls lm.fit, instead of the lavaan estimation engine, at least when the missing="ml" argument is NOT used. (BTW, I fail to understand why you would use lavaan if you just want to fit a univariate regression).
>> When missing="ml" is used, lavaan normally checks if you have fixed x covariates (which you do), and if fixed.x=TRUE (which is the default). In 0.4, lavaan internally switches to fixed.x=FALSE (which implicitly assumes that all your predictors are continuous, but I assume you would not using missing="ml" otherwise). Unfortunately, for the 'special' case of univariate regression, it fails to do this. This behavior will likely change in 0.5, where, by default, only endogenous/dependent variables will be handled by missing="ml", not exogenous 'x' covariates.
>> To fix it: simply add the fixed.x=FALSE argument, or revert to 0.4-12 to get the old behavior.
>> Hope this helps,
>> Yves.
>> http://lavaan.org
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Joshua Wiley
Ph.D. Student, Health Psychology
Programmer Analyst II, Statistical Consulting Group
University of California, Los Angeles

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