[Bug]: Mixed models bayesian LMM failed

CherylPain commented 3 months ago

JASP Version

0.19.0

Commit ID

No response

JASP Module

Mixed Models

What analysis are you seeing the problem on?

Bayesian Linear Mixed Models

What OS are you seeing the problem on?

Windows 11

Bug Description

I have entered the same variables as attempted in the classical version of LMM, however, the analysis isn't running, and gives me the following output: This analysis terminated unexpectedly.

Error in ref_grid(object = NULL, data = structure(list(PreAcc = c(2, : Can't handle an object of class 'NULL' Use help('models', package = 'emmeans') for information on supported models.

Stack trace tryCatchOne(expr, names, parentenv, handlers[[1]])

doTryCatch(return(expr), name, parentenv, handler)

withCallingHandlers(expr = analysis(jaspResults = jaspResults, dataset = dataset, options = options), error = .addStackTrace)

analysis(jaspResults = jaspResults, dataset = dataset, options = options)

.mmRunAnalysis(jaspResults, dataset, options, 'BLMM')

.mmTrends(jaspResults, dataset, options, type)

emmeans::emtrends(object = trendsModel, data = trendsDataset, specs = unlist(options$trendsVariables), var = unlist(options$trendsTrendVariable), at = trendsAt, options = list(level = trendsCI), lmer.df = if (trendsType = 'LMM') trendsDf)

do.call('ref_grid', c(rgargs))

ref_grid(object = NULL, data = list(PreAcc = c(2, 4, 2, -20, -25, 2, -30, -9, -3, 9, -5, -3, 41, -36, 3, 17, 22, -15, -55, 5, -5, 15, -8, -6, -3, -3, -3, 6, 0, 0, -70, 35, -15, -83, 14, 25, -11, -24, 30, 15, 3, -22, 25, -13, -36, 25, 25, -30, 0, -12, 5, 5, 50, -55, -40, -73, 15, -11, -7, -2, -60, 3, -10, 20, -10, -20, 8, -6, -10, -3, -5, 6, 10, 11, 7, -45, 0, -10, 22, -18, 13, -6, -22, 2, -26, 29, -2, -35, -5, 0), Expectation = c(0, 0, 0, 110, 95, 57, 40, 11, 3, 10, 17, 10, 66, 108, 73, 80, 90, 110, 70, 20, 25, 20, 15, 10, 10, 7, 3, 14, 14, 14, 100, 50, 50, 107, 30, 46, 155, 154, 115, 10, 20, 22, 55, 65, 71, 35, 50, 95, 60, 50, 10, 35, 50, 80, 105, 120, 30, 70, 65, 71, 120, 17, 20, 40, 50, 70, 70, 76, 65, 126, 36, 26, 10, 12, 10, 125, 60, 60, 86, 107, 89, 25, 25, 10, 69, 48, 74, 90, 60, 45), PARTICIPANT = c(2, 2, 2, 5, 5, 5, 10, 10, 10, 13, 13, 13, 15, 15, 15, 19, 19, 19, 20, 20, 20, 23, 23, 23, 25, 25, 25, 28, 28, 28, 1, 1, 1, 3, 3, 3, 6, 6, 6, 8, 8, 8, 11, 11, 11, 14, 14, 14, 17, 17, 17, 21, 21, 21, 26, 26, 26, 27, 27, 27, 4, 4, 4, 7, 7, 7, 9, 9, 9, 12, 12, 12, 16, 16, 16, 18, 18, 18, 22, 22, 22, 24, 24, 24, 29, 29, 29, 30, 30, 30), TRIAL = c(1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3), PRIME = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3)), at = list(Expectation = c(14.5625687591264, 53.3222222222222, 92.081875685318)), options = list(level = 0.95, just.data = TRUE), lmer.df = NULL)

stop(data)

To receive assistance with this problem, please report the message above at: https://jasp-stats.org/bug-reports

Expected Behaviour

The analysis should have run

Steps to Reproduce

1.Bayesian Linear Mixed Model

Enter PreAcc as DV 3.Fixed effects: Expectation, Trial, Prime
Random effects as participant
Interactions added between expectation trial, expectation prime, trial * prime
I added contrasts, although removed them and the same error occurred.
Analysis just doesn't run.

Log (if any)

I have emailed this to you as I can't seem to upload it. My email is cheryl.williams@port.ac.uk. Thank you.

More Debug Information

This analysis terminated unexpectedly.

Error in ref_grid(object = NULL, data = structure(list(PreAcc = c(2, : Can't handle an object of class 'NULL' Use help('models', package = 'emmeans') for information on supported models.

Stack trace tryCatchOne(expr, names, parentenv, handlers[[1]])

doTryCatch(return(expr), name, parentenv, handler)

withCallingHandlers(expr = analysis(jaspResults = jaspResults, dataset = dataset, options = options), error = .addStackTrace)

analysis(jaspResults = jaspResults, dataset = dataset, options = options)

.mmRunAnalysis(jaspResults, dataset, options, 'BLMM')

.mmTrends(jaspResults, dataset, options, type)

emmeans::emtrends(object = trendsModel, data = trendsDataset, specs = unlist(options$trendsVariables), var = unlist(options$trendsTrendVariable), at = trendsAt, options = list(level = trendsCI), lmer.df = if (trendsType = 'LMM') trendsDf)

do.call('ref_grid', c(rgargs))

ref_grid(object = NULL, data = list(PreAcc = c(2, 4, 2, -20, -25, 2, -30, -9, -3, 9, -5, -3, 41, -36, 3, 17, 22, -15, -55, 5, -5, 15, -8, -6, -3, -3, -3, 6, 0, 0, -70, 35, -15, -83, 14, 25, -11, -24, 30, 15, 3, -22, 25, -13, -36, 25, 25, -30, 0, -12, 5, 5, 50, -55, -40, -73, 15, -11, -7, -2, -60, 3, -10, 20, -10, -20, 8, -6, -10, -3, -5, 6, 10, 11, 7, -45, 0, -10, 22, -18, 13, -6, -22, 2, -26, 29, -2, -35, -5, 0), Expectation = c(0, 0, 0, 110, 95, 57, 40, 11, 3, 10, 17, 10, 66, 108, 73, 80, 90, 110, 70, 20, 25, 20, 15, 10, 10, 7, 3, 14, 14, 14, 100, 50, 50, 107, 30, 46, 155, 154, 115, 10, 20, 22, 55, 65, 71, 35, 50, 95, 60, 50, 10, 35, 50, 80, 105, 120, 30, 70, 65, 71, 120, 17, 20, 40, 50, 70, 70, 76, 65, 126, 36, 26, 10, 12, 10, 125, 60, 60, 86, 107, 89, 25, 25, 10, 69, 48, 74, 90, 60, 45), PARTICIPANT = c(2, 2, 2, 5, 5, 5, 10, 10, 10, 13, 13, 13, 15, 15, 15, 19, 19, 19, 20, 20, 20, 23, 23, 23, 25, 25, 25, 28, 28, 28, 1, 1, 1, 3, 3, 3, 6, 6, 6, 8, 8, 8, 11, 11, 11, 14, 14, 14, 17, 17, 17, 21, 21, 21, 26, 26, 26, 27, 27, 27, 4, 4, 4, 7, 7, 7, 9, 9, 9, 12, 12, 12, 16, 16, 16, 18, 18, 18, 22, 22, 22, 24, 24, 24, 29, 29, 29, 30, 30, 30), TRIAL = c(1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3), PRIME = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3)), at = list(Expectation = c(14.5625687591264, 53.3222222222222, 92.081875685318)), options = list(level = 0.95, just.data = TRUE), lmer.df = NULL)

stop(data)

To receive assistance with this problem, please report the message above at: https://jasp-stats.org/bug-reports

Final Checklist

[X] I have included a screenshot showcasing the issue, if possible.
[X] I have included a JASP file (zipped) or data file that causes the crash/bug, if applicable.
[X] I have accurately described the bug, and steps to reproduce it.

tomtomme commented 3 months ago

To reproduce and understand this error: Could you share your .jasp-file by renaming to .zip and drag and dropping it here? thx

I am from the issue-collaborator team, but without access to the eMail you send the file to.

CherylPain commented 2 months ago

Hi sorry for the delay, I have just handed in my masters dissertation (yesterday), so have lost track of emails. I'm not sure which file it was now, and can't find a trace of the email I sent you, Maybe thats because it was through the website, I'm not sure. I'm also not sure if the issue was resolved when I updated the software, or how I got around it. From the name of this file I just found, I think it may be this one.

Thank you.

Cheryl LMM data - sent to JASP.zip https://drive.google.com/file/d/1XmOqV51XqNmD2NvVl29QJgtJsdQKAbuQ/view?usp=drive_web

On Mon, Sep 2, 2024 at 10:09 AM Thomas Langkamp @.***> wrote:

To reproduce and understand this error: Could you share your .jasp-file by renaming to .zip and drag and dropping it here? thx

I am from the issue-collaborator team, but without access to the eMail you send the file to.

— Reply to this email directly, view it on GitHub https://github.com/jasp-stats/jasp-issues/issues/2869#issuecomment-2324220010, or unsubscribe https://github.com/notifications/unsubscribe-auth/BKODL3IAMGOMVTJS7MNRXTLZUQTNVAVCNFSM6AAAAABMJVSDHCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRUGIZDAMBRGA . You are receiving this because you authored the thread.Message ID: @.***>

tomtomme commented 1 month ago

@CherylPain I tried downloading the file but have not sufficient rights to do so... so I asked for those rights via gdrive.

CherylPain commented 1 month ago

I’ve granted them to you now.

On Wed, 23 Oct 2024 at 15:15, Thomas Langkamp @.***> wrote:

@CherylPain https://github.com/CherylPain I tried downloading the file but have not sufficient rights to do so... so I asked for those rights via gdrive.

— Reply to this email directly, view it on GitHub https://github.com/jasp-stats/jasp-issues/issues/2869#issuecomment-2432353820, or unsubscribe https://github.com/notifications/unsubscribe-auth/BKODL3KL3EYEEUEXOTEDHYDZ46VOPAVCNFSM6AAAAABMJVSDHCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMZSGM2TGOBSGA . You are receiving this because you were mentioned.Message ID: @.***>

tomtomme commented 1 month ago

Thx. So I waited for half an hour and the LMM finished just fine. I removed all other analysis to keep the file size in check, but still - its a big computation and a 15MB file. Check it out here: LMM data - sent to JASPx.zip

also as a screenshot: Bildschirmfoto_20241023_171415

All OTHER analysis finished within seconds and were fine but it is still to big to upload (>25MB). So tell me what you need. I may have to split it into more files.

Maybe you just did not wait long enough. I have a pretty beefy machine, so on yours this could take much longer than 30 minutes or even do not finish at all if you do not have sufficient RAM free.

Whatever. If this is still not solved on your side, it might be win11 specific (I run linux) or because I used 0.19.2 beta which will be released in some weeks as final.

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