Error: column(s) not found: [L_1[1,1], L_1[2,1], L_1[1,2], L_1[2,2]]

[joshua-zh]

When I reran the example to get the AMEs and marginal coefficients on the page, I encountered an error like this:

Error: column(s) not found: [L_1[1,1], L_1[2,1], L_1[1,2], L_1[2,2]]

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] data.table_1.14.9 brmsmargins_0.2.0 brms_2.20.6 Rcpp_1.0.11

[JWiley]

You either need to save all parameters in your brms model. See: https://paul-buerkner.github.io/brms/reference/save_pars.html Or use the cmdstanr backend. I forget which off hand and am away from my computer atm.

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On Sun, Nov 19, 2023 at 03:40 jzh ***@***.***> wrote: When I reran the example to get the AMEs and marginal coefficients on the page , <https://joshuawiley.com/brmsmargins/articles/mixed-effects-marginaleffects.html> I encountered an error like this: Error: column(s) not found: [L_1[1,1], L_1[2,1], L_1[1,2], L_1[2,2]] attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] data.table_1.14.9 brmsmargins_0.2.0 brms_2.20.6 Rcpp_1.0.11 — Reply to this email directly, view it on GitHub <#10>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACOZHG34QIUN4YTMOVMG5LYFDQJPAVCNFSM6AAAAAA7RCTMZWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYDANBZGI2DIOA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[joshua-zh]

Thank you for your response. I am afraid the error is still present. When I set effect = “fixedonly” or “includeRE”, everything was ok; however, when setting effect = “integrateoutRE”, this error popped up.

[JWiley]

Can you please give me a reproducible example?

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On Sun, 19 Nov 2023 at 22:40, jzh ***@***.***> wrote: Thank you for your response. I am afraid the error is still present. When I set effect = “fixedonly” or “includeRE”, everything was ok; however, when setting effect = “integrateoutRE”, this error popped up. — Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACOZHAXU24FGR5V7MLF34DYFHV4VAVCNFSM6AAAAAA7RCTMZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJXHAZDQNZWGU> . You are receiving this because you commented.Message ID: ***@***.***>

[joshua-zh]

I just copied the codes for the logistic regression on this page and executed them in Rstudio.

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] data.table_1.14.9 brmsmargins_0.2.0 brms_2.20.6 Rcpp_1.0.11

[JWiley]

Just tested again. It works for me when adding: save_pars = save_pars(all=TRUE) to the brm() model paired with the cmdstanr backends as in the vignette. I believe the change is that brms defaults no longer includes some of the needed parameters so need to explicitly ask for those to be saved.

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On Mon, Nov 20, 2023 at 12:49 jzh ***@***.***> wrote: I just copied the codes for the logistic regression on this page <https://joshuawiley.com/brmsmargins/articles/mixed-effects-marginaleffects.html> and executed them in Rstudio. attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] data.table_1.14.9 brmsmargins_0.2.0 brms_2.20.6 Rcpp_1.0.11 — Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACOZHHW5JXC42HMGDRYAKTYFKZJBAVCNFSM6AAAAAA7RCTMZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJYGA4DMOJRGU> . You are receiving this because you commented.Message ID: ***@***.***>

[joshua-zh]

Thank you for your patience and understanding. This setup works. Previously, I only set save_pars = save_pars() 😅. BTW, the rstan backends also work fine.

[JWiley]

Oh good to know about rstan backend. That one crashes a lot for whatever reason on my computer so I have trouble testing it. I'll try to get the vignettes and examples all updated.

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On Mon, 20 Nov 2023 at 18:59, jzh ***@***.***> wrote: Thank you for your patience and understanding. This setup works. Previously, I only set save_pars = save_pars() 😅. BTW, the rstan backends also work fine. — Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACOZHF7O7MA6E7SYVMLOI3YFMEUXAVCNFSM6AAAAAA7RCTMZWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJYGQYDOOJRHA> . You are receiving this because you commented.Message ID: ***@***.***>