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report.lm: "Warning: Using $ in model formulas can produce unexpected results", but doing so errors #379

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rempsyc opened this issue Jul 1, 2023 · 3 comments
Open

report.lm: "Warning: Using $ in model formulas can produce unexpected results", but doing so errors #379

rempsyc opened this issue Jul 1, 2023 · 3 comments

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@rempsyc
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rempsyc commented Jul 1, 2023

It would be nice to get rid of the several warnings in R CMD check, but the proposed fix leads to an error:

library(report)

data(sleep)
d <- datawizard::data_modify(sleep, group = as.integer(group) - 1L)
d_wide <<- datawizard::data_to_wide(
  d,
  names_from = "group",
  values_from = "extra",
  names_prefix = "group"
)

model_io <- lm(d_wide$group0 - d_wide$group1 ~ 1)
out <- report(model_io)
#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

model_io <- lm(group0 - group1 ~ 1, data = d_wide)
out <- report(model_io)
#> Error in eval(predvars, data, env): object 'group0' not found
#> Error: Unable to refit the model with standardized data.
#>   Try instead to standardize the data (standardize(data)) and refit the
#>   model manually.

Created on 2023-07-01 with reprex v2.0.2

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.0 (2023-04-21 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language (EN)
#>  collate  English_Canada.utf8
#>  ctype    English_Canada.utf8
#>  tz       America/Toronto
#>  date     2023-07-01
#>  pandoc   3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package      * version  date (UTC) lib source
#>  bayestestR     0.13.1.2 2023-07-01 [1] https://easystats.r-universe.dev (R 4.3.1)
#>  cli            3.6.1    2023-03-23 [1] CRAN (R 4.3.0)
#>  coda           0.19-4   2020-09-30 [1] CRAN (R 4.3.0)
#>  codetools      0.2-19   2023-02-01 [2] CRAN (R 4.3.0)
#>  datawizard     0.8.0.4  2023-06-28 [1] https://easystats.r-universe.dev (R 4.3.1)
#>  digest         0.6.31   2022-12-11 [1] CRAN (R 4.3.0)
#>  effectsize     0.8.3.11 2023-06-30 [1] https://easystats.r-universe.dev (R 4.3.1)
#>  emmeans        1.8.6    2023-05-11 [1] CRAN (R 4.3.0)
#>  estimability   1.4.1    2022-08-05 [1] CRAN (R 4.3.0)
#>  evaluate       0.21     2023-05-05 [1] CRAN (R 4.3.0)
#>  fastmap        1.1.1    2023-02-24 [1] CRAN (R 4.3.0)
#>  fs             1.6.2    2023-04-25 [1] CRAN (R 4.3.0)
#>  glue           1.6.2    2022-02-24 [1] CRAN (R 4.3.0)
#>  highr          0.10     2022-12-22 [1] CRAN (R 4.3.0)
#>  htmltools      0.5.5    2023-03-23 [1] CRAN (R 4.3.0)
#>  insight        0.19.3   2023-06-29 [1] https://easystats.r-universe.dev (R 4.3.1)
#>  knitr          1.40     2022-08-24 [1] CRAN (R 4.3.0)
#>  lattice        0.21-8   2023-04-05 [2] CRAN (R 4.3.0)
#>  lifecycle      1.0.3    2022-10-07 [1] CRAN (R 4.3.0)
#>  magrittr       2.0.3    2022-03-30 [1] CRAN (R 4.3.0)
#>  MASS           7.3-58.4 2023-03-07 [2] CRAN (R 4.3.0)
#>  Matrix         1.5-4    2023-04-04 [2] CRAN (R 4.3.0)
#>  multcomp       1.4-23   2023-03-09 [1] CRAN (R 4.3.0)
#>  mvtnorm        1.2-2    2023-06-08 [1] CRAN (R 4.3.0)
#>  parameters     0.21.1.2 2023-06-28 [1] https://easystats.r-universe.dev (R 4.3.1)
#>  performance    0.10.4.1 2023-06-22 [1] https://easystats.r-universe.dev (R 4.3.1)
#>  purrr          1.0.1    2023-01-10 [1] CRAN (R 4.3.0)
#>  R.cache        0.16.0   2022-07-21 [1] CRAN (R 4.3.0)
#>  R.methodsS3    1.8.2    2022-06-13 [1] CRAN (R 4.3.0)
#>  R.oo           1.25.0   2022-06-12 [1] CRAN (R 4.3.0)
#>  R.utils        2.12.2   2022-11-11 [1] CRAN (R 4.3.0)
#>  report       * 0.5.7.4  2023-05-20 [1] local
#>  reprex         2.0.2    2022-08-17 [1] CRAN (R 4.3.0)
#>  rlang          1.1.1    2023-04-28 [1] CRAN (R 4.3.0)
#>  rmarkdown      2.22     2023-06-01 [1] CRAN (R 4.3.0)
#>  rstudioapi     0.14     2022-08-22 [1] CRAN (R 4.3.0)
#>  sandwich       3.0-2    2022-06-15 [1] CRAN (R 4.3.0)
#>  sessioninfo    1.2.2    2021-12-06 [1] CRAN (R 4.3.0)
#>  stringi        1.7.12   2023-01-11 [1] CRAN (R 4.3.0)
#>  stringr        1.5.0    2022-12-02 [1] CRAN (R 4.3.0)
#>  styler         1.9.1    2023-03-04 [1] CRAN (R 4.3.0)
#>  survival       3.5-5    2023-03-12 [2] CRAN (R 4.3.0)
#>  TH.data        1.1-2    2023-04-17 [1] CRAN (R 4.3.0)
#>  vctrs          0.6.3    2023-06-14 [1] CRAN (R 4.3.0)
#>  withr          2.5.0    2022-03-03 [1] CRAN (R 4.3.0)
#>  xfun           0.39     2023-04-20 [1] CRAN (R 4.3.0)
#>  xtable         1.8-4    2019-04-21 [1] CRAN (R 4.3.0)
#>  yaml           2.3.7    2023-01-23 [1] CRAN (R 4.3.0)
#>  zoo            1.8-12   2023-04-13 [1] CRAN (R 4.3.0)
#> 
#>  [1] C:/Users/there/AppData/Local/R/win-library/4.3
#>  [2] C:/Program Files/R/R-4.3.0/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
@rempsyc
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rempsyc commented Jul 1, 2023

Some additional info:

Warnings come from: parameters::model_parameters() and insight::get_data()

library(report)
data(sleep)
d <- datawizard::data_modify(sleep, group = as.integer(group) - 1L)
d_wide <<- datawizard::data_to_wide(
  d,
  names_from = "group",
  values_from = "extra",
  names_prefix = "group"
)
x <- lm(d_wide$group0 - d_wide$group1 ~ 1)
params <- parameters::model_parameters(x, ci_random = FALSE)
#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =
out <- insight::get_data(x)
#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =
#> Warning: Could not recover model data from environment. Please make sure your
#>   data is available in your workspace.
#>   Trying to retrieve data from the model frame now.

Created on 2023-07-01 with reprex v2.0.2

Error comes from: report_effectsize()

library(report)
data(sleep)
d <- datawizard::data_modify(sleep, group = as.integer(group) - 1L)
d_wide <<- datawizard::data_to_wide(
  d,
  names_from = "group",
  values_from = "extra",
  names_prefix = "group"
)
x <- lm(group0 - group1 ~ 1, data = d_wide)
params <- parameters::model_parameters(x, ci_random = FALSE)
effsize <- report_effectsize(x)
#> Error in eval(predvars, data, env): object 'group0' not found
#> Error: Unable to refit the model with standardized data.
#>   Try instead to standardize the data (standardize(data)) and refit the
#>   model manually.

Created on 2023-07-01 with reprex v2.0.2

@etiennebacher do you think these are coming from datawizard or insight::get_data() somehow? Do you have a suggestion to where to start looking to fix this issue?

@etiennebacher
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Looks like it comes from datawizard::standardize(), I'll open an issue:

library(report)
library(datawizard)

data(sleep)
d <- data_modify(sleep, group = as.integer(group) - 1L)
d_wide <- data_to_wide(
  d,
  names_from = "group",
  values_from = "extra",
  names_prefix = "group"
)

model1 <- lm(d_wide$group0 - d_wide$group1 ~ 1)
standardize(model1)
#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =

#> Warning: Using `$` in model formulas can produce unexpected results. Specify your
#>   model using the `data` argument instead.
#>   Try: group0 - group1 ~ 1,
#>   data =
#> 
#> Call:
#> lm(formula = d_wide$group0 - d_wide$group1 ~ 1, data = data_std)
#> 
#> Coefficients:
#> (Intercept)  
#>       -1.58

model1 <- lm(group0 - group1 ~ 1, data = d_wide)
standardize(model1)
#> Error in eval(predvars, data, env): objet 'group0' introuvable
#> Error: Unable to refit the model with standardized data.
#>   Try instead to standardize the data (standardize(data)) and refit the
#>   model manually.

Created on 2023-07-01 with reprex v2.0.2

@etiennebacher etiennebacher mentioned this issue Jul 1, 2023
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@mattansb
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mattansb commented Jul 2, 2023

Note that standardizing the components of a composite variable will probably lead to nonsense results.

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@rempsyc @mattansb @etiennebacher