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.by argument works incorrectly for factor level groups. #140

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jgaeb opened this issue Mar 6, 2024 · 0 comments
Open

.by argument works incorrectly for factor level groups. #140

jgaeb opened this issue Mar 6, 2024 · 0 comments

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@jgaeb
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jgaeb commented Mar 6, 2024

The problem

Calibrating by group errors when the group is a factor, since no data is passed to the calibration model. The problem appears to be with how split_dplyr_groups() works.

Reproducible example

library(probably)
#> 
#> Attaching package: 'probably'
#> The following objects are masked from 'package:base':
#> 
#>     as.factor, as.ordered
library(tidymodels)
library(tidyverse)

df <- tibble(
  p = runif(100),
  y = factor(runif(100) <= log(p / (1 - p)), levels = c(TRUE, FALSE)),
  z = factor(sample(letters[1:3], 100, replace = TRUE))
)

m <- logistic_reg() %>%
  set_engine("glm") %>%
  set_mode("classification") %>%
  fit(y ~ p, data = df)

# This works
m_calib <- m %>%
  predict(new_data = df, type = "prob") %>%
  bind_cols(df) %>%
  mutate(z = as.character(z)) %>%
  cal_estimate_logistic(truth = y, .by = z)

# This errors
m_calib <- m %>%
  predict(new_data = df, type = "prob") %>%
  bind_cols(df) %>%
  cal_estimate_logistic(truth = y, .by = z)
#> Error in mgcv::gam(f_model, data = .data, family = "binomial", ...): Not enough (non-NA) data to do anything meaningful

Created on 2024-03-06 with reprex v2.0.2

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.2 (2023-10-31)
#>  os       macOS Sonoma 14.2.1
#>  system   aarch64, darwin23.0.0
#>  ui       unknown
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2024-03-06
#>  pandoc   3.1.11.1 @ /opt/homebrew/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package      * version    date (UTC) lib source
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#>  broom        * 1.0.5      2023-06-09 [1] CRAN (R 4.3.1)
#>  butcher        0.3.3      2023-08-23 [1] CRAN (R 4.3.1)
#>  class          7.3-22     2023-05-03 [1] CRAN (R 4.3.1)
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#>  dials        * 1.2.0      2023-04-03 [1] CRAN (R 4.3.0)
#>  DiceDesign     1.9        2021-02-13 [1] CRAN (R 4.3.0)
#>  digest         0.6.34     2024-01-11 [1] CRAN (R 4.3.1)
#>  dplyr        * 1.1.4      2023-11-17 [1] CRAN (R 4.3.1)
#>  evaluate       0.23       2023-11-01 [1] CRAN (R 4.3.1)
#>  fansi          1.0.6      2023-12-08 [1] CRAN (R 4.3.1)
#>  fastmap        1.1.1      2023-02-24 [1] CRAN (R 4.3.1)
#>  forcats      * 1.0.0      2023-01-29 [1] CRAN (R 4.3.1)
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#>  fs             1.6.3      2023-07-20 [1] CRAN (R 4.3.1)
#>  furrr          0.3.1      2022-08-15 [1] CRAN (R 4.3.1)
#>  future         1.33.0     2023-07-01 [1] CRAN (R 4.3.1)
#>  future.apply   1.11.0     2023-05-21 [1] CRAN (R 4.3.1)
#>  generics       0.1.3      2022-07-05 [1] CRAN (R 4.3.1)
#>  ggplot2      * 3.4.2      2023-04-03 [1] CRAN (R 4.3.1)
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#>  glue           1.7.0      2024-01-09 [1] CRAN (R 4.3.1)
#>  gower          1.0.1      2022-12-22 [1] CRAN (R 4.3.0)
#>  GPfit          1.0-8      2019-02-08 [1] CRAN (R 4.3.0)
#>  gtable         0.3.3      2023-03-21 [1] CRAN (R 4.3.1)
#>  hardhat        1.3.0      2023-03-30 [1] CRAN (R 4.3.0)
#>  hms            1.1.3      2023-03-21 [1] CRAN (R 4.3.1)
#>  htmltools      0.5.5      2023-03-23 [1] CRAN (R 4.3.1)
#>  infer        * 1.0.4      2022-12-02 [1] CRAN (R 4.3.0)
#>  ipred          0.9-14     2023-03-09 [1] CRAN (R 4.3.0)
#>  iterators      1.0.14     2022-02-05 [1] CRAN (R 4.3.0)
#>  knitr          1.43       2023-05-25 [1] CRAN (R 4.3.1)
#>  lattice        0.21-8     2023-04-05 [1] CRAN (R 4.3.1)
#>  lava           1.7.2.1    2023-02-27 [1] CRAN (R 4.3.0)
#>  lhs            1.1.6      2022-12-17 [1] CRAN (R 4.3.0)
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#>  listenv        0.9.0      2022-12-16 [1] CRAN (R 4.3.1)
#>  lubridate    * 1.9.2      2023-02-10 [1] CRAN (R 4.3.1)
#>  magrittr       2.0.3      2022-03-30 [1] CRAN (R 4.3.1)
#>  MASS           7.3-60     2023-05-04 [1] CRAN (R 4.3.1)
#>  Matrix         1.6-0      2023-07-08 [1] CRAN (R 4.3.1)
#>  mgcv           1.9-0      2023-07-11 [1] CRAN (R 4.3.1)
#>  modeldata    * 1.2.0      2023-08-09 [1] CRAN (R 4.3.1)
#>  munsell        0.5.0      2018-06-12 [1] CRAN (R 4.3.1)
#>  nlme           3.1-162    2023-01-31 [1] CRAN (R 4.3.1)
#>  nnet           7.3-19     2023-05-03 [2] CRAN (R 4.3.2)
#>  parallelly     1.36.0     2023-05-26 [1] CRAN (R 4.3.1)
#>  parsnip      * 1.1.1      2023-08-17 [1] CRAN (R 4.3.1)
#>  pillar         1.9.0      2023-03-22 [1] CRAN (R 4.3.1)
#>  pkgconfig      2.0.3      2019-09-22 [1] CRAN (R 4.3.1)
#>  probably     * 1.0.2      2023-06-29 [1] CRAN (R 4.3.1)
#>  prodlim        2023.03.31 2023-04-02 [1] CRAN (R 4.3.0)
#>  purrr        * 1.0.2      2023-08-10 [1] CRAN (R 4.3.1)
#>  R.cache        0.16.0     2022-07-21 [1] CRAN (R 4.3.1)
#>  R.methodsS3    1.8.2      2022-06-13 [1] CRAN (R 4.3.1)
#>  R.oo           1.25.0     2022-06-12 [1] CRAN (R 4.3.1)
#>  R.utils        2.12.2     2022-11-11 [1] CRAN (R 4.3.1)
#>  R6             2.5.1      2021-08-19 [1] CRAN (R 4.3.1)
#>  Rcpp           1.0.10     2023-01-22 [1] CRAN (R 4.3.1)
#>  readr        * 2.1.4      2023-02-10 [1] CRAN (R 4.3.1)
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#>  rmarkdown      2.23       2023-07-01 [1] CRAN (R 4.3.1)
#>  rpart          4.1.21     2023-10-09 [2] CRAN (R 4.3.2)
#>  rsample      * 1.1.1      2022-12-07 [1] CRAN (R 4.3.0)
#>  scales       * 1.2.1      2022-08-20 [1] CRAN (R 4.3.1)
#>  sessioninfo    1.2.2      2021-12-06 [1] CRAN (R 4.3.1)
#>  stringi        1.8.3      2023-12-11 [1] CRAN (R 4.3.1)
#>  stringr      * 1.5.1      2023-11-14 [1] CRAN (R 4.3.1)
#>  styler         1.10.1     2023-06-05 [1] CRAN (R 4.3.1)
#>  survival       3.5-7      2023-08-14 [2] CRAN (R 4.3.2)
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#>  tidymodels   * 1.1.0      2023-05-01 [1] CRAN (R 4.3.0)
#>  tidyr        * 1.3.0      2023-01-24 [1] CRAN (R 4.3.1)
#>  tidyselect     1.2.0      2022-10-10 [1] CRAN (R 4.3.1)
#>  tidyverse    * 2.0.0      2023-02-22 [1] CRAN (R 4.3.1)
#>  timechange     0.2.0      2023-01-11 [1] CRAN (R 4.3.1)
#>  timeDate       4022.108   2023-01-07 [1] CRAN (R 4.3.0)
#>  tune         * 1.1.1      2023-04-11 [1] CRAN (R 4.3.0)
#>  tzdb           0.4.0      2023-05-12 [1] CRAN (R 4.3.1)
#>  utf8           1.2.4      2023-10-22 [1] CRAN (R 4.3.1)
#>  vctrs          0.6.5      2023-12-01 [1] CRAN (R 4.3.1)
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#>  workflows    * 1.1.3      2023-02-22 [1] CRAN (R 4.3.0)
#>  workflowsets * 1.0.1      2023-04-06 [1] CRAN (R 4.3.0)
#>  xfun           0.39       2023-04-20 [1] CRAN (R 4.3.1)
#>  yaml           2.3.7      2023-01-23 [1] CRAN (R 4.3.1)
#>  yardstick    * 1.2.0      2023-04-21 [1] CRAN (R 4.3.0)
#> 
#>  [1] /opt/homebrew/lib/R/4.3/site-library
#>  [2] /opt/homebrew/Cellar/r/4.3.2/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
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@jgaeb