Re: [R] Issues with fa() function in psych
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.st...@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 li...@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.st...@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 li...@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 kri...@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.st...@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
Re: [R] Issues with fa() function in psych
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 li...@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.st...@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 li...@revelle.net wrote: Sagnik raises the question as to why the psych package does not offer the âequamaxâ 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=ânoneâ 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 âloadingsâ 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=âpaâ 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.â 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 kri...@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.st...@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
Re: [R] Issues with fa() function in psych
Hi Sagnik, sagnik chakravarty wrote - Request you to add option for *equamax rotation* also if possible. As GPApackage doesn't provide an explicit function termed Equamax you may want to use Crawford-Ferguson rotation from the GPApackage ( cfT). With the additional argument kappa=m*/(2*p), where m is the number of factors and p the number of variables/items, you'll be able to achieve a Equamax rotation. On the equivalence of orthogonal CF with Orthomax family please refer to Browne, 2001, An overview fo Analytic Rotation in Exploratory Factor Analysis, Multivariate Behavioural Research, 36 (1), 111-150 Cheers, Gunter -- View this message in context: http://r.789695.n4.nabble.com/Issues-with-fa-function-in-psych-tp4688378p4690511.html Sent from the R help mailing list archive at Nabble.com. __ R-help@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.
Re: [R] Issues with fa() function in psych
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.st...@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 li...@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 kri...@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.st...@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$loadings, the matrix shown has many blank cells whereas the final result showing the loadings doesn't have so* !! *Loadings:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 0.123 0.170 * - Could you please explain* what the com column means* in the output:? *
Re: [R] Issues with fa() function in psych
Thanks a lot Bill and Revelle for your helpful response. It would have been great if I could know when we can expect the release of the edited version 1.4.4. Sagnik On Wed, Apr 9, 2014 at 8:05 PM, William Revelle li...@revelle.net wrote: Sagnik raises the question as to why the psych package does not offer the 'equamax' rotation. It is because all rotations are handled through the GPArotation package which does not offer equamax. Sagnik also points out that if the requested rotation is not available, fa defaults to rotate=none without any warning. I have fixed that for the next release (1.4.4). (1.4.4 also will fix a bug in corr.test introduced into 1.4.3). The question about why printing just the loadings matrix leaves blank cells? That is because the loadings matrix of class loadings which the default print function prints with a cut = .3. Using the example from Sagnik, print(efa_pa$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 kri...@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.st...@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$loadings, the matrix shown has many blank cells whereas the final result showing the loadings doesn't have so* !! *Loadings:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 0.123 0.170 * - Could you please explain* what the com column means* in the output:? * PA1 PA3 PA2 PA4 h2 u2 com* *Var1 0.44 0.14 -0.03 -0.10 0.22665 0.773 1.3* *Var2 0.08 0.11 0.02 0.78 0.62951 0.370 1.1* *Var3 0.62 0.12 0.15 0.14 0.43578 0.564 1.3* - Request you to add option for *equamax rotation* also if possible. I have come across the above issues until now. Please do correct me if I am wrong. Awaiting your revert which would clear out my confusions, Thanks for your valuable time, Sagnik -- Regards, *SAGNIK CHAKRAVARTY* *Mob:* +919972865435
Re: [R] Issues with fa() function in psych
I am probably going to push it to CRAN today or tomorrow. Bill On Apr 10, 2014, at 1:22 AM, sagnik chakravarty sagnik.st...@gmail.com wrote: Thanks a lot Bill and Revelle for your helpful response. It would have been great if I could know when we can expect the release of the edited version 1.4.4. Sagnik On Wed, Apr 9, 2014 at 8:05 PM, William Revelle li...@revelle.net wrote: Sagnik raises the question as to why the psych package does not offer the ‘equamax’ rotation. It is because all rotations are handled through the GPArotation package which does not offer equamax. Sagnik also points out that if the requested rotation is not available, fa defaults to rotate=“none” without any warning. I have fixed that for the next release (1.4.4). (1.4.4 also will fix a bug in corr.test introduced into 1.4.3). The question about why printing just the loadings matrix leaves blank cells? That is because the loadings matrix of class “loadings” which the default print function prints with a cut = .3. Using the example from Sagnik, print(efa_pa$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 kri...@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.st...@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$loadings, the matrix shown has many blank cells whereas the final result showing the loadings doesn't have so* !! *Loadings:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 0.123 0.170 * - Could you please explain* what the com column means* in the output:? * PA1 PA3 PA2 PA4 h2 u2 com* *Var1 0.44 0.14 -0.03 -0.10 0.22665 0.773 1.3* *Var2 0.08 0.11 0.02 0.78 0.62951 0.370 1.1* *Var3 0.62 0.12 0.15 0.14 0.43578 0.564 1.3* - Request you to add option for *equamax rotation* also if possible. I have come across the above issues until now. Please do correct me if I am
Re: [R] Issues with fa() function in psych
Sagnik raises the question as to why the psych package does not offer the ‘equamax’ rotation. It is because all rotations are handled through the GPArotation package which does not offer equamax. Sagnik also points out that if the requested rotation is not available, fa defaults to rotate=“none” without any warning. I have fixed that for the next release (1.4.4). (1.4.4 also will fix a bug in corr.test introduced into 1.4.3). The question about why printing just the loadings matrix leaves blank cells? That is because the loadings matrix of class “loadings” which the default print function prints with a cut = .3. Using the example from Sagnik, print(efa_pa$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 kri...@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.st...@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:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 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.st...@gmail.com sagnik@gmail.com [[alternative HTML version deleted]] __ R-help@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
[R] Issues with fa() function in psych
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:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 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.st...@gmail.com sagnik@gmail.com [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Issues with fa() function in psych
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.st...@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:* * PA1PA2PA3PA4 * *Var10.401 -0.243* *Var20.336 -0.1040.710* *Var30.624 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.st...@gmail.com sagnik@gmail.com [[alternative HTML version deleted]] __ R-help@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@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.
