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paul-buerkner / brms

brms R package for Bayesian generalized multivariate non-linear multilevel models using Stan
https://paul-buerkner.github.io/brms/
GNU General Public License v2.0
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Warning message when running models with `mi()` syntax? #1685

Closed maxdrohde closed 1 month ago

maxdrohde commented 1 month ago

When I ran the "Imputation during model fitting" model from the missing data vignette, I got the following warnings:

Warning messages:
1: In subset.data.frame(x$frame$re, resp = x$resp) :
 extra argument ‘resp’ will be disregarded 
2: In subset.data.frame(x$frame$re, resp = x$resp) :
 extra argument ‘resp’ will be disregarded 
3: In subset.data.frame(x$frame$re, resp = x$resp) :
 extra argument ‘resp’ will be disregarded 
4: In subset.data.frame(x$frame$re, resp = x$resp) :
 extra argument ‘resp’ will be disregarded

Is this a bug, or a normal warning?

Reproducible Example

library(brms)

data("nhanes", package = "mice")

bform <- bf(bmi | mi() ~ age * mi(chl)) +
    bf(chl | mi() ~ age) + set_rescor(FALSE)
fit_imp2 <- brm(bform, data = nhanes)

System Info

> devtools::session_info()
─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.0 (2024-04-24)
 os       macOS Sonoma 14.6.1
 system   x86_64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Chicago
 date     2024-09-06
 rstudio  2024.04.2+764 Chocolate Cosmos (desktop)
 pandoc   3.3 @ /usr/local/bin/pandoc

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package        * version     date (UTC) lib source
 abind            1.4-5       2016-07-21 [1] CRAN (R 4.4.0)
 backports        1.5.0       2024-05-23 [1] CRAN (R 4.4.0)
 bayesplot        1.11.1.9000 2024-08-02 [1] https://stan-dev.r-universe.dev (R 4.4.0)
 bridgesampling   1.1-2       2021-04-16 [1] CRAN (R 4.4.0)
 brms           * 2.21.6      2024-09-06 [1] Github (paul-buerkner/brms@ddd34fc)
 Brobdingnag      1.2-9       2022-10-19 [1] CRAN (R 4.4.0)
 cachem           1.1.0       2024-05-16 [1] CRAN (R 4.4.0)
 callr            3.7.6       2024-03-25 [1] CRAN (R 4.4.0)
 checkmate        2.3.2       2024-07-29 [1] CRAN (R 4.4.0)
 cli              3.6.3       2024-06-21 [1] CRAN (R 4.4.0)
 coda             0.19-4.1    2024-01-31 [1] CRAN (R 4.4.0)
 codetools        0.2-20      2024-03-31 [1] CRAN (R 4.4.0)
 colorspace       2.1-1       2024-07-26 [1] CRAN (R 4.4.0)
 curl             5.2.2       2024-08-26 [1] CRAN (R 4.4.1)
 devtools       * 2.4.5       2022-10-11 [1] CRAN (R 4.4.0)
 digest           0.6.37      2024-08-19 [1] CRAN (R 4.4.1)
 distributional   0.4.0       2024-02-07 [1] CRAN (R 4.4.0)
 dplyr            1.1.4       2023-11-17 [1] CRAN (R 4.4.0)
 ellipsis         0.3.2       2021-04-29 [1] CRAN (R 4.4.0)
 fansi            1.0.6       2023-12-08 [1] CRAN (R 4.4.0)
 fastmap          1.2.0       2024-05-15 [1] CRAN (R 4.4.0)
 fs               1.6.4       2024-04-25 [1] CRAN (R 4.4.0)
 generics         0.1.3       2022-07-05 [1] CRAN (R 4.4.0)
 ggplot2          3.5.1       2024-04-23 [1] CRAN (R 4.4.0)
 glue             1.7.0       2024-01-09 [1] CRAN (R 4.4.0)
 gridExtra        2.3         2017-09-09 [1] CRAN (R 4.4.0)
 gtable           0.3.5       2024-04-22 [1] CRAN (R 4.4.0)
 htmltools        0.5.8.1     2024-04-04 [1] CRAN (R 4.4.0)
 htmlwidgets      1.6.4       2023-12-06 [1] CRAN (R 4.4.0)
 httpuv           1.6.15      2024-03-26 [1] CRAN (R 4.4.0)
 inline           0.3.19      2021-05-31 [1] CRAN (R 4.4.0)
 jsonlite         1.8.8       2023-12-04 [1] CRAN (R 4.4.0)
 later            1.3.2       2023-12-06 [1] CRAN (R 4.4.0)
 lattice          0.22-6      2024-03-20 [1] CRAN (R 4.4.0)
 lifecycle        1.0.4       2023-11-07 [1] CRAN (R 4.4.0)
 loo              2.8.0.9000  2024-08-05 [1] https://stan-dev.r-universe.dev (R 4.4.0)
 magrittr         2.0.3       2022-03-30 [1] CRAN (R 4.4.0)
 Matrix           1.7-0       2024-03-22 [1] CRAN (R 4.4.0)
 matrixStats      1.4.0       2024-09-04 [1] CRAN (R 4.4.1)
 memoise          2.0.1       2021-11-26 [1] CRAN (R 4.4.0)
 mime             0.12        2021-09-28 [1] CRAN (R 4.4.0)
 miniUI           0.1.1.1     2018-05-18 [1] CRAN (R 4.4.0)
 munsell          0.5.1       2024-04-01 [1] CRAN (R 4.4.0)
 mvtnorm          1.3-1       2024-09-03 [1] CRAN (R 4.4.1)
 nlme             3.1-166     2024-08-14 [1] CRAN (R 4.4.1)
 pillar           1.9.0       2023-03-22 [1] CRAN (R 4.4.0)
 pkgbuild         1.4.4       2024-03-17 [1] CRAN (R 4.4.0)
 pkgconfig        2.0.3       2019-09-22 [1] CRAN (R 4.4.0)
 pkgload          1.4.0       2024-06-28 [1] CRAN (R 4.4.0)
 posterior        1.6.0       2024-07-03 [1] CRAN (R 4.4.0)
 processx         3.8.4       2024-03-16 [1] CRAN (R 4.4.0)
 profvis          0.3.8       2023-05-02 [1] CRAN (R 4.4.0)
 promises         1.3.0       2024-04-05 [1] CRAN (R 4.4.0)
 ps               1.7.7       2024-07-02 [1] CRAN (R 4.4.0)
 purrr            1.0.2       2023-08-10 [1] CRAN (R 4.4.0)
 QuickJSR         1.3.1       2024-07-14 [1] CRAN (R 4.4.0)
 R6               2.5.1       2021-08-19 [1] CRAN (R 4.4.0)
 Rcpp           * 1.0.13      2024-07-17 [1] CRAN (R 4.4.0)
 RcppParallel     5.1.9       2024-08-19 [1] CRAN (R 4.4.1)
 remotes          2.5.0       2024-03-17 [1] CRAN (R 4.4.0)
 rlang            1.1.4       2024-06-04 [1] CRAN (R 4.4.0)
 rstan            2.35.0.9000 2024-06-29 [1] https://stan-dev.r-universe.dev (R 4.4.0)
 rstantools       2.4.0.9000  2024-07-19 [1] https://stan-dev.r-universe.dev (R 4.4.0)
 rstudioapi       0.16.0      2024-03-24 [1] CRAN (R 4.4.0)
 scales           1.3.0       2023-11-28 [1] CRAN (R 4.4.0)
 sessioninfo      1.2.2       2021-12-06 [1] CRAN (R 4.4.0)
 shiny            1.9.1       2024-08-01 [1] CRAN (R 4.4.0)
 StanHeaders      2.35.0.9000 2024-06-25 [1] https://stan-dev.r-universe.dev (R 4.4.0)
 stringi          1.8.4       2024-05-06 [1] CRAN (R 4.4.0)
 stringr          1.5.1       2023-11-14 [1] CRAN (R 4.4.0)
 tensorA          0.36.2.1    2023-12-13 [1] CRAN (R 4.4.0)
 tibble           3.2.1       2023-03-20 [1] CRAN (R 4.4.0)
 tidyselect       1.2.1       2024-03-11 [1] CRAN (R 4.4.0)
 urlchecker       1.0.1       2021-11-30 [1] CRAN (R 4.4.0)
 usethis        * 3.0.0       2024-07-29 [1] CRAN (R 4.4.0)
 utf8             1.2.4       2023-10-22 [1] CRAN (R 4.4.0)
 V8               5.0.0       2024-08-16 [1] CRAN (R 4.4.1)
 vctrs            0.6.5       2023-12-01 [1] CRAN (R 4.4.0)
 xtable           1.8-4       2019-04-21 [1] CRAN (R 4.4.0)

 [1] /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library
paul-buerkner commented 1 month ago

Thanks! This was caused by a typo which is now fixed :-)