Error: Internal renaming led to duplicated names

[bhara033]

Please note:

The brms issue tracker is reserved for bug reports and feature requests. brms-related questions should rather be asked on https://discourse.mc-stan.org/ in order to reach a wider community.

Hello Paul,

Hope you are doing well. I am fairly new to using "brms" but wanted to report, what I consider, a bug.
When I tried to run the model below, I got the following error:

Error: Internal renaming led to duplicated names.
Occured for: 'var21', 'var22', 'var23', 'var24', 'var25', 'var26', 'var27', 'var28', 'var29', 'var21', 'var22', 'var23', 'var24', 'var25', 'var26', 'var27', 'var28', 'var29'

I checked to make sure that my column names were, in fact, not duplicated. The error seems to be strange because I am able to run several other models using the same dataset without any issues.

I would be grateful if you could help me understand what's going on here.

My model:

result <- brm(
  bf(
    mvbind(var9, var10, var15, var16) ~ var2 + var13 + var14 + var19 + var21 + var22 + var23 + var24 + var25 + var26 + var27 + var28 + var29 + var30 + var34 + var48 + var49 + var53 + var54 + var55 + var58 + var61 + var63 + var64 + var89 + var90 + var91 + var92 + var93 + var94,
           zi ~ var2 + var5 + var114,
		   autocor = ~ar(time = var2, gr = var4:var3:var1)
    ),
  data = y,
  family = zero_inflated_negbinomial(),
  iter = 2000, # default 2000
  warmup = 1000, # default iter/2
  chains = 4, # default 4
  cores = 32,
  backend = "rstan",
  open_progress = TRUE,
  save_pars = save_pars(all = TRUE))
  )

Another issue I wanted to bring to your attention is that currently I am unable to use the option "backend = "cmdstanr"." The reason I wish to use this feature is to leverage parallel computing in "brms" (I am unsure if using the backend = "rstan" also achieves the same thing). Initially, I got an error saying I needed to install this additional R package called "cmdstanr." When I attempted to install it, the installer terminated with the following warning:

Warning in install.packages :
package ‘cmdstanr’ is not available for this version of R

Could you please help me in addressing this issue? Thank you!

Regards,

Suhas

[paul-buerkner]

thanks. can you please provide a full minimal reprex for the error (duplicated names) you encountered? bhara033 ***@***.***> schrieb am Mi., 17. Apr. 2024, 18:14:

…

Please note: The brms issue tracker is reserved for bug reports and feature requests. brms-related questions should rather be asked on https://discourse.mc-stan.org/ in order to reach a wider community. Hello Paul, Hope you are doing well. I am fairly new to using "brms" but wanted to report, what I consider, a bug. When I tried to run the model below, I got the following error: *Error: Internal renaming led to duplicated names. Occured for: 'var21', 'var22', 'var23', 'var24', 'var25', 'var26', 'var27', 'var28', 'var29', 'var21', 'var22', 'var23', 'var24', 'var25', 'var26', 'var27', 'var28', 'var29'* I checked to make sure that my column names were, in fact, not duplicated. The error seems to be strange because I am able to run several other models using the same dataset without any issues. I would be grateful if you could help me understand what's going on here. My model: result <- brm( bf( mvbind(var9, var10, var15, var16) ~ var2 + var13 + var14 + var19 + var21 + var22 + var23 + var24 + var25 + var26 + var27 + var28 + var29 + var30 + var34 + var48 + var49 + var53 + var54 + var55 + var58 + var61 + var63 + var64 + var89 + var90 + var91 + var92 + var93 + var94, zi ~ var2 + var5 + var114, autocor = ~ar(time = var2, gr = var4:var3:var1) ), data = y, family = zero_inflated_negbinomial(), iter = 2000, # default 2000 warmup = 1000, # default iter/2 chains = 4, # default 4 cores = 32, backend = "rstan", open_progress = TRUE, save_pars = save_pars(all = TRUE)) ) Another issue I wanted to bring to your attention is that currently I am unable to use the option "*backend = "cmdstanr"*." The reason I wish to use this feature is to leverage parallel computing in "brms" (I am unsure if using the backend = "rstan" also achieves the same thing). Initially, I got an error saying I needed to install this additional R package called "cmdstanr." When I attempted to install it, the installed terminated with the following warning: *Warning in install.packages : package ‘cmdstanr’ is not available for this version of R* Could you please help me in addressing this issue? Thank you! Regards, Suhas — Reply to this email directly, view it on GitHub <#1648>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCW2AATJHJZFWN4KQGUQW3Y52NX7AVCNFSM6AAAAABGLUJE4GVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2DQNRZGMZTGMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[paul-buerkner]

I suspect your questions may actually be better suited for the Stan discourse forums Paul Buerkner ***@***.***> schrieb am Mi., 17. Apr. 2024, 18:17:

…

thanks. can you please provide a full minimal reprex for the error (duplicated names) you encountered? bhara033 ***@***.***> schrieb am Mi., 17. Apr. 2024, 18:14: > Please note: > > The brms issue tracker is reserved for bug reports and feature requests. > brms-related questions should rather be asked on > https://discourse.mc-stan.org/ in order to reach a wider community. > > Hello Paul, > > Hope you are doing well. I am fairly new to using "brms" but wanted to > report, what I consider, a bug. > When I tried to run the model below, I got the following error: > > > *Error: Internal renaming led to duplicated names. Occured for: 'var21', > 'var22', 'var23', 'var24', 'var25', 'var26', 'var27', 'var28', 'var29', > 'var21', 'var22', 'var23', 'var24', 'var25', 'var26', 'var27', 'var28', > 'var29'* > > I checked to make sure that my column names were, in fact, not > duplicated. The error seems to be strange because I am able to run several > other models using the same dataset without any issues. > > I would be grateful if you could help me understand what's going on here. > > My model: > > result <- brm( > bf( > mvbind(var9, var10, var15, var16) ~ var2 + var13 + var14 + var19 + var21 + var22 + var23 + var24 + var25 + var26 + var27 + var28 + var29 + var30 + var34 + var48 + var49 + var53 + var54 + var55 + var58 + var61 + var63 + var64 + var89 + var90 + var91 + var92 + var93 + var94, > zi ~ var2 + var5 + var114, > autocor = ~ar(time = var2, gr = var4:var3:var1) > ), > data = y, > family = zero_inflated_negbinomial(), > iter = 2000, # default 2000 > warmup = 1000, # default iter/2 > chains = 4, # default 4 > cores = 32, > backend = "rstan", > open_progress = TRUE, > save_pars = save_pars(all = TRUE)) > ) > > Another issue I wanted to bring to your attention is that currently I am > unable to use the option "*backend = "cmdstanr"*." The reason I wish to > use this feature is to leverage parallel computing in "brms" (I am unsure > if using the backend = "rstan" also achieves the same thing). Initially, I > got an error saying I needed to install this additional R package called > "cmdstanr." When I attempted to install it, the installed terminated with > the following warning: > > > *Warning in install.packages : package ‘cmdstanr’ is not available for > this version of R* > > Could you please help me in addressing this issue? Thank you! > > Regards, > > Suhas > > — > Reply to this email directly, view it on GitHub > <#1648>, or unsubscribe > <https://github.com/notifications/unsubscribe-auth/ADCW2AATJHJZFWN4KQGUQW3Y52NX7AVCNFSM6AAAAABGLUJE4GVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2DQNRZGMZTGMY> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> >

[bhara033]

Sure, Paul! I will share a full reprex for the error with you soon. Thank you!

[bhara033]

I have invited you to collaborate on the "test" repository on GitHub. Thank you!

[paul-buerkner]

can you perhaps just post a minimal reproducible example here in this issue? bhara033 ***@***.***> schrieb am Mi., 17. Apr. 2024, 20:51:

…

I have invited you to collaborate on the "test" repository on GitHub. Thank you! — Reply to this email directly, view it on GitHub <#1648 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADCW2ACP5IX2CBVNCK57EZ3Y53ACXAVCNFSM6AAAAABGLUJE4GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANRRHE4DSOJZGY> . You are receiving this because you commented.Message ID: ***@***.***>

[bmfazio]

Hi, here's a minimal reprex. The error happens because var2 is a factor, so the coefficient for level "2" clashes for the slope on var22. Should be solvable from the user side by renaming but a more informative error message may be useful.

library(brms)
y = data.frame(
  var1 = 0,
  var2 = as.factor(1:3),
  var22 = 0
)
get_prior(bf(var1 ~ var2 + var22), data = y)

[bhara033]

Thank you, @bmfazio! Renaming var2 fixed the issue for me. Sorry for deleting the text file containing R code I posted earlier. I found some issues that needed to be fixed. I can repost it if needed. Thank you!