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:muscle: Models' quality and performance metrics (R2, ICC, LOO, AIC, BF, ...)
https://easystats.github.io/performance/
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`check_model` not working for `brms::brm` with `Beta()` family #737

Closed roaldarbol closed 2 months ago

roaldarbol commented 3 months ago

I'm attempting to run check_model() on a model specified with brms() and get the following error:

bayes_ratio_state <- brms::brm(activity_ratio ~ trial + (1 | animal_id),
                        data = df_ratio_state,
                        family = Beta()
                        )
> check_model(bayes_ratio_state)
Error in get(family$family)(link = family$link) : 
  unused argument (link = family$link)

If I run the same model, but with family=gaussian() it works.

strengejacke commented 3 months ago

Do you have a reproducible example?

roaldarbol commented 3 months ago

Sure thing:

library(tibble)
library(brms)
#> Loading required package: Rcpp
#> Loading 'brms' package (version 2.21.0). Useful instructions
#> can be found by typing help('brms'). A more detailed introduction
#> to the package is available through vignette('brms_overview').
#> 
#> Attaching package: 'brms'
#> The following object is masked from 'package:stats':
#> 
#>     ar
library(performance)
df_ratio_episode <- tibble::tibble(
  animal_id = factor(
    rep(
      c(
        "208", "209", "210", "214", "223", "228", "211", "213", "217", "222", "234",
        "241", "216", "230", "231", "240", "242", "244", "218", "220", "225", "237",
        "239", "219", "251", "252", "253", "254"
      ),
      each = 2L
    ),
    levels = c(
      "200", "204", "205", "206", "215", "224", "208", "209", "210", "214", "223",
      "228", "211", "213", "217", "222", "234", "241", "216", "230", "231", "240",
      "242", "244", "218", "220", "225", "237", "239", "245", "219", "236", "251",
      "252", "253", "254"
    )
  ),
  trial = rep(c(1, 2), 28),
  activity_ratio = c(
    0.1313027016689785, 0.08387917431645128, 0.1395420340967623,
    0.09844057594710427, 0.19414443290359096, 0.16304581176275632,
    0.17274983272168504, 0.17357956037939837, 0.09729583968716982,
    0.05138063319955499, 0.14298075594540044, 0.10179701101266003,
    0.09168390375802275, 0.11591243874797318, 0.2521345405747349,
    0.16335726666875724, 0.13436311090275369, 0.12012636336085161,
    0.13868852567209072, 0.12008249718946021, 0.27708418835127824,
    0.22042035159734397, 0.2649703945513039, 0.22158610629846917,
    0.2001770607989554, 0.2238562351804714, 0.1105503693420828,
    0.08255349183783911, 0.21927303214082697, 0.22211274055043914,
    0.10446530203550744, 0.11336175801811256, 0.0826812722435201,
    0.09328851878674252, 0.13701773797551595, 0.1297098120849381,
    0.05986226055235673, 0.14423247009476106, 0.19474645802355026,
    0.1713563584485577, 0.25663498351317365, 0.30249307043720924,
    0.09082761877930186, 0.10402396536249521, 0.21941679494558652,
    0.28459112981037343, 0.11218161441362348, 0.12449715062493952,
    0.18427917423975973, 0.14845015830783756, 0.19444224064643065,
    0.13471565660441723, 0.11247341287367296, 0.08660523675310272,
    0.1763980204528711, 0.1049572229068965
  ),
) |>
  dplyr::group_by(animal_id)

bayes_ratio_episode <- brms::brm(activity_ratio ~ trial + (1 | animal_id),
                                 data = df_ratio_episode,
                                 family = brms::Beta())
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/bin/R \
#>   CMD SHLIB foo.c
#> using C compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
#> using SDK: ‘’
#> clang -arch x86_64 -I"/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/include" -DNDEBUG   -I"/Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/Rcpp/1.0.12/5ea2700d21e038ace58269ecdbeb9ec0/Rcpp/include/"  -I"/Volumes/ResearchSSD/002-Tracking-1Day/.renv/library/R-4.4/x86_64-apple-darwin20/RcppEigen/include/"  -I"/Volumes/ResearchSSD/002-Tracking-1Day/.renv/library/R-4.4/x86_64-apple-darwin20/RcppEigen/include/unsupported"  -I"/Volumes/ResearchSSD/002-Tracking-1Day/.renv/library/R-4.4/x86_64-apple-darwin20/BH/include" -I"/Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/StanHeaders/2.32.7/3e1bf18c6ab1dc0a4a139bf566f78bbe/StanHeaders/include/src/"  -I"/Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/StanHeaders/2.32.7/3e1bf18c6ab1dc0a4a139bf566f78bbe/StanHeaders/include/"  -I"/Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/RcppParallel/5.1.7/a45594a00f5dbb073d5ec9f48592a08a/RcppParallel/include/"  -I"/Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/rstan/2.32.6/8a5b5978f888a3477c116e0395d006f8/rstan/include" -DEIGEN_NO_DEBUG  -DBOOST_DISABLE_ASSERTS  -DBOOST_PENDING_INTEGER_LOG2_HPP  -DSTAN_THREADS  -DUSE_STANC3 -DSTRICT_R_HEADERS  -DBOOST_PHOENIX_NO_VARIADIC_EXPRESSION  -D_HAS_AUTO_PTR_ETC=0  -include '/Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/StanHeaders/2.32.7/3e1bf18c6ab1dc0a4a139bf566f78bbe/StanHeaders/include/stan/math/prim/fun/Eigen.hpp'  -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/roaldarbol/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.4/x86_64-apple-darwin20/StanHeaders/2.32.7/3e1bf18c6ab1dc0a4a139bf566f78bbe/StanHeaders/include/stan/math/prim/fun/Eigen.hpp:22:
#> In file included from /Volumes/ResearchSSD/002-Tracking-1Day/.renv/library/R-4.4/x86_64-apple-darwin20/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Volumes/ResearchSSD/002-Tracking-1Day/.renv/library/R-4.4/x86_64-apple-darwin20/RcppEigen/include/Eigen/Core:19:
#> /Volumes/ResearchSSD/002-Tracking-1Day/.renv/library/R-4.4/x86_64-apple-darwin20/RcppEigen/include/Eigen/src/Core/util/Macros.h:679:10: fatal error: 'cmath' file not found
#> #include <cmath>
#>          ^~~~~~~
#> 1 error generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 8.2e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.82 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1: 
#> Chain 1: 
#> Chain 1: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 1: Iteration:  200 / 2000 [ 10%]  (Warmup)
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#> Chain 1: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 1: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 1: 
#> Chain 1:  Elapsed Time: 0.381 seconds (Warm-up)
#> Chain 1:                0.287 seconds (Sampling)
#> Chain 1:                0.668 seconds (Total)
#> Chain 1: 
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 2).
#> Chain 2: 
#> Chain 2: Gradient evaluation took 2.6e-05 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2: 
#> Chain 2: 
#> Chain 2: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 2: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 2: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 2: Iteration:  600 / 2000 [ 30%]  (Warmup)
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#> Chain 2: Iteration: 1000 / 2000 [ 50%]  (Warmup)
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#> Chain 2: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 2: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 2: 
#> Chain 2:  Elapsed Time: 0.43 seconds (Warm-up)
#> Chain 2:                0.283 seconds (Sampling)
#> Chain 2:                0.713 seconds (Total)
#> Chain 2: 
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 3).
#> Chain 3: 
#> Chain 3: Gradient evaluation took 2.7e-05 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
#> Chain 3: Adjust your expectations accordingly!
#> Chain 3: 
#> Chain 3: 
#> Chain 3: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 3: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 3: Iteration:  400 / 2000 [ 20%]  (Warmup)
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#> Chain 3: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 3: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 3: 
#> Chain 3:  Elapsed Time: 0.361 seconds (Warm-up)
#> Chain 3:                0.269 seconds (Sampling)
#> Chain 3:                0.63 seconds (Total)
#> Chain 3: 
#> 
#> SAMPLING FOR MODEL 'anon_model' NOW (CHAIN 4).
#> Chain 4: 
#> Chain 4: Gradient evaluation took 2.7e-05 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4: 
#> Chain 4: 
#> Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
#> Chain 4: Iteration:  200 / 2000 [ 10%]  (Warmup)
#> Chain 4: Iteration:  400 / 2000 [ 20%]  (Warmup)
#> Chain 4: Iteration:  600 / 2000 [ 30%]  (Warmup)
#> Chain 4: Iteration:  800 / 2000 [ 40%]  (Warmup)
#> Chain 4: Iteration: 1000 / 2000 [ 50%]  (Warmup)
#> Chain 4: Iteration: 1001 / 2000 [ 50%]  (Sampling)
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#> Chain 4: Iteration: 1800 / 2000 [ 90%]  (Sampling)
#> Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
#> Chain 4: 
#> Chain 4:  Elapsed Time: 0.383 seconds (Warm-up)
#> Chain 4:                0.296 seconds (Sampling)
#> Chain 4:                0.679 seconds (Total)
#> Chain 4:

performance::check_model(bayes_ratio_episode)
#> Error in get(family$family)(link = family$link): unused argument (link = family$link)

Created on 2024-07-05 with reprex v2.1.0

strengejacke commented 2 months ago

Should be fixed in bayestestR now.