[R] Issues with fa() function in "psych"
sagnik chakravarty
sagnik.stats at gmail.com
Mon Sep 1 12:05:37 CEST 2014
Hi William,
Recently I noticed that if the requested rotation is not available,
"principal" function also defaults to rotate=“none” without any WARNING.
You had earlier fixed the same issue with "fa" in version 1.4.4. Kindly
include the same for "principal" also.
Also, as I had pointed out earlier in my trailing mails, is there any
update on the following suggestion:
"The fa() function doesn't account for 'Heywood cases' (communality greater
than 1) and never ever throws out any error related to that which other
softwares do. This is a serious and common issue in iterative factor
analysis and hence should have been accounted for."
Awaiting your revert,
Thanks and Regards,
Sagnik
On Fri, May 16, 2014 at 10:54 AM, sagnik chakravarty <sagnik.stats at gmail.com
> wrote:
> Hi William,
>
> Thanks for the update. I see this package has so many capabilities ! I
> will suggest further for its development if anything else comes to my mind.
>
> Regards,
> Sagnik
>
>
> On Thu, May 15, 2014 at 6:34 AM, William Revelle <lists at revelle.net>
> wrote:
>
>> Sagnik,
>>
>> I did some more checking and in fact you can do equamax through GPA
>> rotation. (Gunter Nickel pointed this out in a post to R-help). I will
>> implement this in version 1.4.6 (1.4.5 is now working its way through the
>> various CRAN mirrors).
>>
>> You might like 1.4.5 in that I have added various ways of displaying
>> confidence intervals (cats eye plots) as well as upper and lower confidence
>> limits for correlations (cor.plot.upperLowerCi)
>>
>> Bill
>>
>> On Apr 10, 2014, at 1:22 AM, sagnik chakravarty <sagnik.stats at gmail.com>
>> wrote:
>>
>> > Thanks a lot Bill and Revelle for your helpful response.
>> > It would have been great if I could know when we can expect the release
>> of the edited version 1.4.4.
>> >
>> > Sagnik
>> >
>> >
>> > On Wed, Apr 9, 2014 at 8:05 PM, William Revelle <lists at revelle.net>
>> wrote:
>> > Sagnik raises the question as to why the psych package does not offer
>> the ‘equamax’ rotation.
>> > It is because all rotations are handled through the GPArotation package
>> which does not offer equamax.
>> >
>> > Sagnik also points out that if the requested rotation is not available,
>> fa defaults to rotate=“none” without any warning. I have fixed that for
>> the next release (1.4.4).
>> > (1.4.4 also will fix a bug in corr.test introduced into 1.4.3).
>> >
>> >
>> > The question about why printing just the loadings matrix leaves blank
>> cells? That is because the loadings matrix of class “loadings” which the
>> default print function prints with a cut = .3.
>> > Using the example from Sagnik, print(efa_pa$loadings,cut=0) will match
>> the output of efa_pa.
>> >
>> > The fm=“pa” option runs conventional principal axis factor analysis
>> (ala SPSS). As documented, this iterates max.iter times
>> >
>> > "Not all factor programs that do principal axes do iterative solutions.
>> The example from the SAS manual (Chapter 26) is such a case. To achieve
>> that solution, it is necessary to specify that the max.iterations = 1.
>> Comparing that solution to an iterated one (the default) shows that
>> iterations improve the solution. In addition, fm="minres" or fm="mle"
>> produces even better solutions for this example.”
>> >
>> > The com column is factor complexity using the index developed by
>> Hofmann (1978). It is a row wise measure of item complexity.
>> > I have added more documentation to this in 1.4.4
>> >
>> > Bill
>> >
>> >
>> > On Apr 8, 2014, at 2:28 AM, Pascal Oettli <kridox at ymail.com> wrote:
>> >
>> > > Hello,
>> > >
>> > > And what about submitting your suggestions directly to the package
>> > > author/maintainer?
>> > >
>> > > And please don't post in HTML.
>> > >
>> > > Regards,
>> > > Pascal
>> > >
>> > > On Tue, Apr 8, 2014 at 3:13 PM, sagnik chakravarty
>> > > <sagnik.stats at gmail.com> wrote:
>> > >> Hi Team,
>> > >>
>> > >> I was using your "psych" package for factor analysis and was also
>> comparing
>> > >> the results with SAS results. I have some suggestions and/or
>> confusions
>> > >> regarding the fa() function in the package:
>> > >>
>> > >> - The fa() function *doesn't account for Heywood cases*
>> (communality
>> > >> greater than 1) and never ever throws out any error related to
>> that which
>> > >> other softwares do. This is a serious and common issue in
>> iterative factor
>> > >> analysis and hence should have been accounted for.
>> > >>
>> > >>
>> > >> - The fa() function doesn't provide "equamax" rotation in its
>> rotation
>> > >> list and still if you specify "*rotation=equamax*", it will run
>> without
>> > >> throwing out any error and even mentioning in the result that
>> "equamax" has
>> > >> been applied. But I have thoroughly compared results from "
>> > >> *rotation=none*" and "*rotation=equamax*" options and they are
>> exactly
>> > >> same. *That means fa() is not doing the rotation at all and yet
>> telling
>> > >> that it is doing that!!* I have even mentioned "*rotation=crap*"
>> option
>> > >> just to check and surprisingly it ran(without any error) with the
>> result
>> > >> showing:
>> > >>
>> > >> *Factor Analysis using method = gls*
>> > >> * Call: fa(r = cor_mat, nfactors = 4, n.obs = 69576,
>> rotate =
>> > >> "crap", fm = "gls")*
>> > >>
>> > >> I hope you understand the severity of this bug and hence
>> > >> request you to correct this.
>> > >>
>> > >> - To my sense, there might be some problem with "fm=ml" and "fm=pa"
>> > >> options since the convergence issue should be with MLE method and
>> not PA
>> > >> method but while running factor analysis with PA, I am getting the
>> > >> following warning:
>> > >>
>> > >> *maximum iteration exceeded*
>> > >> * The estimated weights for the factor scores are probably
>> > >> incorrect. Try a different factor extraction method.*
>> > >>
>> > >> If I compare the results of R and SAS,* I am getting
>> > >> convergence error for MLE in SAS whereas I am getting the same error
>> for PA
>> > >> in R *!! I am not being able to understand this mismatch.
>> > >>
>> > >> - If I call the *loading matrix like efa_pa$loadings, the matrix
>> shown
>> > >> has many blank cells whereas the final result showing the loadings
>> doesn't
>> > >> have so* !!
>> > >>
>> > >> *Loadings:*
>> > >> * PA1 PA2 PA3 PA4 *
>> > >> *Var1 0.401 -0.243*
>> > >> *Var2 0.336 -0.104 0.710*
>> > >> *Var3 0.624 0.123 0.170 *
>> > >>
>> > >>
>> > >> - Could you please explain* what the "com" column means* in the
>> output:?
>> > >>
>> > >>
>> > >> * PA1 PA3 PA2 PA4 h2 u2 com*
>> > >> *Var1 0.44 0.14 -0.03 -0.10 0.22665 0.773 1.3*
>> > >> *Var2 0.08 0.11 0.02 0.78 0.62951 0.370 1.1*
>> > >> *Var3 0.62 0.12 0.15 0.14 0.43578 0.564 1.3*
>> > >>
>> > >> - Request you to add option for *"equamax" rotation* also if
>> possible.
>> > >>
>> > >>
>> > >> I have come across the above issues until now. Please do correct me
>> if I am
>> > >> wrong.
>> > >>
>> > >> Awaiting your revert which would clear out my confusions,
>> > >>
>> > >> Thanks for your valuable time,
>> > >>
>> > >> Sagnik
>> > >>
>> > >> --
>> > >> Regards,
>> > >>
>> > >> *SAGNIK CHAKRAVARTY*
>> > >>
>> > >> *Mob:* +919972865435
>> > >> *Email:* sagnik.stats at gmail.com
>> > >> sagnik.739 at gmail.com
>> > >>
>> > >> [[alternative HTML version deleted]]
>> > >>
>> > >> ______________________________________________
>> > >> R-help at r-project.org mailing list
>> > >> https://stat.ethz.ch/mailman/listinfo/r-help
>> > >> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > >> and provide commented, minimal, self-contained, reproducible code.
>> > >
>> > >
>> > >
>> > > --
>> > > Pascal Oettli
>> > > Project Scientist
>> > > JAMSTEC
>> > > Yokohama, Japan
>> > >
>> > > ______________________________________________
>> > > R-help at r-project.org mailing list
>> > > https://stat.ethz.ch/mailman/listinfo/r-help
>> > > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > > and provide commented, minimal, self-contained, reproducible code.
>> > >
>> >
>> > William Revelle
>> http://personality-project.org/revelle.html
>> > Professor
>> http://personality-project.org
>> > Department of Psychology http://www.wcas.northwestern.edu/psych/
>> > Northwestern University http://www.northwestern.edu/
>> > Use R for psychology http://personality-project.org/r
>> > It is 5 minutes to midnight http://www.thebulletin.org
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > --
>> > Regards,
>> >
>> > SAGNIK CHAKRAVARTY
>> >
>> > Mob: +919972865435
>> > Email: sagnik.stats at gmail.com
>> > sagnik.739 at gmail.com
>>
>> William Revelle
>> http://personality-project.org/revelle.html
>> Professor http://personality-project.org
>> Department of Psychology http://www.wcas.northwestern.edu/psych/
>> Northwestern University http://www.northwestern.edu/
>> Use R for psychology http://personality-project.org/r
>> It is 5 minutes to midnight http://www.thebulletin.org
>>
>>
>>
>>
>>
>
>
> --
> Regards,
>
> *SAGNIK CHAKRAVARTY*
>
> *Mob:* +919972865435
> *Email:* sagnik.stats at gmail.com
> sagnik.739 at gmail.com
>
--
Regards,
SAGNIK CHAKRAVARTY
Statistician, India
sagnik.stats at gmail.com
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