Hi,
I am trying to reproduce the example on how to use varsel and cv_varsel(), and it does not seem to work on my end. I was not sure if this was a bug or I am missing something, so I am posting here before creating an issue on Github. Thank you for your input!
I used the following example in my Rconsole (Projection Predictive Variable Selection — varsel.brmsfit • brms) but the I got the following error message.
fit <- brm(count ~ zAge + zBase * Trt,
data = epilepsy, family = poisson())
summary(fit)
# perform variable selection without cross-validation
vs <- varsel(fit)
summary(vs)
plot(vs)
# perform variable selection with cross-validation
cv_vs <- cv_varsel(fit)
summary(cv_vs)
plot(cv_vs)
Error in init_refmodel(object = object, formula = formula, family = family, :
argument "formula" is missing, with no default
6.
stopifnot(inherits(formula, "formula"))
5.
init_refmodel(object = object, formula = formula, family = family,
extract_model_data = extract_model_data, ...)
4.
get_refmodel.default(object, ...)
3.
get_refmodel(object, ...)
2.
varsel.default(fit)
1.
varsel(fit)
I tried to supply formula, data, and other things, but it keeps me asking more things that I do not know where it comes from.
session info
> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.2
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] projpred_2.4.0 broom.mixed_0.2.9.4 ggbeeswarm_0.7.1 gghalves_0.1.3 ggokabeito_0.1.0 patchwork_1.1.2
[7] tidybayes_3.0.3 bayesplot_1.10.0 brms_2.18.1 Rcpp_1.0.9 lmerTest_3.1-3 lme4_1.1-30
[13] Matrix_1.5-1 ggrain_0.0.2 GGally_2.1.2 psych_2.2.9 here_1.0.1 forcats_0.5.2
[19] stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1 readr_2.1.3 tidyr_1.3.0 tibble_3.1.8
[25] ggplot2_3.4.1 tidyverse_1.3.2
loaded via a namespace (and not attached):
[1] utf8_1.2.3 tidyselect_1.2.0 htmlwidgets_1.5.4 grid_4.1.2 munsell_0.5.0
[6] codetools_0.2-18 effectsize_0.7.0.5 DT_0.25 future_1.28.0 miniUI_0.1.1.1
[11] withr_2.5.0 Brobdingnag_1.2-9 colorspace_2.1-0 knitr_1.40 rstudioapi_0.14
[16] stats4_4.1.2 listenv_0.8.0 labeling_0.4.2 emmeans_1.8.1-1 rstan_2.26.13
[21] mnormt_2.1.1 bit64_4.0.5 farver_2.1.1 datawizard_0.6.1 bridgesampling_1.1-2
[26] rprojroot_2.0.3 parallelly_1.32.1 coda_0.19-4 vctrs_0.5.2 generics_0.1.3
[31] TH.data_1.1-1 xfun_0.33 R6_2.5.1 markdown_1.1 gamm4_0.2-6
[36] reshape_0.8.9 assertthat_0.2.1 vroom_1.6.0 promises_1.2.0.1 scales_1.2.1
[41] multcomp_1.4-20 googlesheets4_1.0.1 beeswarm_0.4.0 gtable_0.3.1 globals_0.16.1
[46] processx_3.7.0 sandwich_3.0-2 rlang_1.0.6 zeallot_0.1.0 sjPlot_2.8.12
[51] splines_4.1.2 gargle_1.2.1 broom_1.0.1 checkmate_2.1.0 inline_0.3.19
[56] yaml_2.3.6 reshape2_1.4.4 abind_1.4-5 modelr_0.1.9 threejs_0.3.3
[61] crosstalk_1.2.0 backports_1.4.1 httpuv_1.6.6 tensorA_0.36.2 tools_4.1.2
[66] ICC_2.4.0 ellipsis_0.3.2 posterior_1.3.1 RColorBrewer_1.1-3 plyr_1.8.7
[71] base64enc_0.1-3 ps_1.7.1 prettyunits_1.1.1 correlation_0.8.2 zoo_1.8-11
[76] haven_2.5.1 fs_1.5.2 furrr_0.3.1 magrittr_2.0.3 data.table_1.14.4
[81] ggdist_3.2.0 colourpicker_1.1.1 reprex_2.0.2 googledrive_2.0.0 mvtnorm_1.1-3
[86] sjmisc_2.8.9 matrixStats_0.62.0 hms_1.1.2 shinyjs_2.1.0 mime_0.12
[91] evaluate_0.16 arrayhelpers_1.1-0 xtable_1.8-4 shinystan_2.6.0 sjstats_0.18.1
[96] readxl_1.4.1 gridExtra_2.3 ggeffects_1.1.3 rstantools_2.2.0 compiler_4.1.2
[101] ggstatsplot_0.9.4 V8_4.2.1 crayon_1.5.2 minqa_1.2.4 StanHeaders_2.26.13
[106] htmltools_0.5.3 mgcv_1.8-40 later_1.3.0 tzdb_0.3.0 RcppParallel_5.1.5
[111] lubridate_1.8.0 DBI_1.1.3 sjlabelled_1.2.0 dbplyr_2.2.1 MASS_7.3-58.1
[116] boot_1.3-28 cli_3.6.0 parallel_4.1.2 insight_0.19.0 igraph_1.3.5
[121] pkgconfig_2.0.3 statsExpressions_1.3.3 numDeriv_2016.8-1.1 xml2_1.3.3 paletteer_1.4.1
[126] svUnit_1.0.6 dygraphs_1.1.1.6 vipor_0.4.5 estimability_1.4.1 ggpp_0.5.1
[131] rvest_1.0.3 distributional_0.3.1 callr_3.7.2 digest_0.6.30 parameters_0.18.2
[136] rmarkdown_2.16 cellranger_1.1.0 curl_4.3.3 shiny_1.7.2 gtools_3.9.3
[141] nloptr_2.0.3 lifecycle_1.0.3.9000 nlme_3.1-159 jsonlite_1.8.2 cmdstanr_0.5.3
[146] fansi_1.0.4 pillar_1.8.1 lattice_0.20-45 loo_2.5.1 fastmap_1.1.0
[151] httr_1.4.4 pkgbuild_1.3.1 survival_3.4-0 glue_1.6.2 xts_0.12.2
[156] bayestestR_0.13.0 shinythemes_1.2.0 bit_4.0.4 stringi_1.7.12 performance_0.9.2
[161] rematch2_2.1.2