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Problem in "tssem1"

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Eleanor's picture
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Joined: 09/12/2017 - 03:41
Problem in "tssem1"

Hi Mike and all,

I'm a new learner of meta-analysis and just try to use metaSEM.

My dataset comprises 90 sets of 19*19 correlation matrix and every one contains some missing values. I'm trying to estimate a TSSEM model but encounter a problem in the first stage.

After loading all the 90 matrices, I use "is.pd" to check if they are positive definite, and the results are all "TRUE". When I use "tssem1(my.R, n, method="FEM"), it returns an error message saying that "Error in eigen(if (doDykstra) R else Y, symmetric = TRUE) : infinite or missing values in 'x'". Then I try to apply a random effect model by "tssem1(my.R, n, method="REM", RE.type="Diag", acov="weighted")", but no result has come out.

Is it due to the missing value, or any other issues that I have mistakenly ignored? how should I do to resolve the problem? Sincerely appreciate if you could help, thanks!

Best regards,

Eleanor

Mike Cheung's picture
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Joined: 10/08/2009 - 22:37
Hi Eleanor,

Hi Eleanor,

Could you please provide the data and R code so that I can check it?

Best,
Mike

Eleanor's picture
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Joined: 09/12/2017 - 03:41
Hi Mike,

Hi Mike,

Here are the R code and data FYI., thank you!

Cheers,
Eleanor

Mike Cheung's picture
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Joined: 10/08/2009 - 22:37
Dear Eleanor,

Dear Eleanor,

There in no data in many of the correlation coefficients. It is normal that the program does not work.

Regards,
Mike

> pattern.na(My.R,show.na=FALSE)
x1 x2 x3 x4 x5 x6 x7 x8 x9 x10 x11 x12 x13 x14 x15 x16 x17 x18 x19
x1 49 35 0 32 9 18 9 23 3 1 22 12 9 2 3 4 2 2 12
x2 35 38 0 24 5 11 6 19 3 1 15 7 6 1 4 3 3 2 6
x3 0 0 12 2 1 0 0 1 0 7 1 0 1 4 1 0 0 0 2
x4 32 24 2 41 3 14 6 18 1 0 17 8 8 2 3 4 1 1 8
x5 9 5 1 3 11 4 4 5 1 0 7 3 6 0 1 0 1 0 3
x6 18 11 0 14 4 18 5 10 0 0 10 6 3 0 0 2 0 0 3
x7 9 6 0 6 4 5 10 5 2 0 4 5 5 1 0 0 0 0 1
x8 23 19 1 18 5 10 5 27 0 0 16 4 6 1 3 4 2 1 8
x9 3 3 0 1 1 0 2 0 4 0 0 2 2 0 2 0 2 2 0
x10 1 1 7 0 0 0 0 0 0 8 0 0 0 1 0 0 0 0 1
x11 22 15 1 17 7 10 4 16 0 0 27 2 7 0 2 1 1 0 9
x12 12 7 0 8 3 6 5 4 2 0 2 14 6 0 0 1 0 0 2
x13 9 6 1 8 6 3 5 6 2 0 7 6 13 0 0 1 0 0 5
x14 2 1 4 2 0 0 1 1 0 1 0 0 0 6 1 0 0 0 0
x15 3 4 1 3 1 0 0 3 2 0 2 0 0 1 11 0 4 3 1
x16 4 3 0 4 0 2 0 4 0 0 1 1 1 0 0 7 0 0 0
x17 2 3 0 1 1 0 0 2 2 0 1 0 0 0 4 0 4 3 0
x18 2 2 0 1 0 0 0 1 2 0 0 0 0 0 3 0 3 3 0
x19 12 6 2 8 3 3 1 8 0 1 9 2 5 0 1 0 0 0 20

Eleanor's picture
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Joined: 09/12/2017 - 03:41
Dear Mike,

Dear Mike,

Thanks for pointing out the problem.
Following your comments, I consolidated my data into 64 matrices with 10 variables to eliminate missing data. When running "pattern.na(My.R,show.na=FALSE)", the result is as follows:

> pattern.na(My.R,show.na=FALSE)
x1 x2 x3 x4 x5 x6 x7 x8 x9 x10
x1 46 33 31 9 17 9 23 21 12 9
x2 33 36 23 5 10 6 19 14 7 6
x3 31 23 40 3 13 6 18 16 8 8
x4 9 5 3 11 4 4 5 7 3 6
x5 17 10 13 4 17 5 10 9 6 3
x6 9 6 6 4 5 10 5 4 5 5
x7 23 19 18 5 10 5 27 16 4 6
x8 21 14 16 7 9 4 16 26 2 7
x9 12 7 8 3 6 5 4 2 14 6
x10 9 6 8 6 3 5 6 7 6 13

Then I tried to fit my data into FEM and REM respectively, but still not results have popped out. The error notice I've got are "Error in cov2cor(sampleS) : 'V' is not a square numeric matrix", and "Error: Argument 'backtransf' must be a logical."

Thank you very much if you could help to check again and advise what issues I should pay attention to.

Cheers,
Eleanor

Mike Cheung's picture
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Joined: 10/08/2009 - 22:37
Hi Eleanor,

Hi Eleanor,

The fixed-effects model does not work because of the missing data. The random-effects model works but it may take a while to run.

random2<-tssem1 (My.R, Myn, method = "REM", RE.type = "Diag", acov = "weighted")
random2 <- rerun(random2)
summary(random2)

Best,
Mike

Eleanor's picture
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Joined: 09/12/2017 - 03:41
Hi Mike,

Hi Mike,
Following your advice, I have got the results of the random-effect model, after running the program for quite a while. Seems I need a bit more patience with my computer :-)
Thank you very much for your time and kind help!

Cheers,
Eleanor

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