search

njtierney / naniar

Tidy data structures, summaries, and visualisations for missing data
http://naniar.njtierney.com/
Other
649 stars 54 forks source link

gg_miss_fct() is using a deprecated function from forcats package #342

Closed szimmer closed 4 months ago

szimmer commented 5 months ago

When using gg_miss_fct, a warning is displayed that a deprecated function from forcats is being used.

library(naniar)
#> Warning: package 'naniar' was built under R version 4.3.2

gg_miss_fct(x = riskfactors, fct = marital)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `marital = (function (x) ...`.
#> Caused by warning:
#> ! `fct_explicit_na()` was deprecated in forcats 1.0.0.
#> ℹ Please use `fct_na_value_to_level()` instead.
#> ℹ The deprecated feature was likely used in the naniar package.
#>   Please report the issue at <https://github.com/njtierney/naniar/issues>.

Created on 2024-03-01 with reprex v2.0.2

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.1 (2023-06-16 ucrt) #> os Windows 11 x64 (build 22631) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.utf8 #> ctype English_United States.utf8 #> tz America/New_York #> date 2024-03-01 #> pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.1 2023-03-23 [1] CRAN (R 4.3.0) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) #> curl 5.0.0 2023-01-12 [1] CRAN (R 4.3.0) #> digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0) #> dplyr 1.1.3 2023-09-03 [1] CRAN (R 4.3.1) #> evaluate 0.21 2023-05-05 [1] CRAN (R 4.3.0) #> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.3.0) #> farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> forcats 1.0.0 2023-01-29 [1] CRAN (R 4.3.0) #> fs 1.6.2 2023-04-25 [1] CRAN (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) #> ggplot2 3.4.2 2023-04-03 [1] CRAN (R 4.3.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.3.0) #> gridExtra 2.3 2017-09-09 [1] CRAN (R 4.3.2) #> gtable 0.3.3 2023-03-21 [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) #> httr 1.4.6 2023-05-08 [1] CRAN (R 4.3.0) #> knitr 1.42 2023-01-25 [1] CRAN (R 4.3.0) #> labeling 0.4.2 2020-10-20 [1] 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) #> mime 0.12 2021-09-28 [1] CRAN (R 4.3.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) #> naniar * 1.0.0 2023-02-02 [1] CRAN (R 4.3.2) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> purrr 1.0.1 2023-01-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.1) #> 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 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> 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 2.21 2023-03-26 [1] CRAN (R 4.3.0) #> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.3.0) #> scales 1.2.1 2022-08-20 [1] CRAN (R 4.3.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.1) #> styler 1.10.1 2023-06-05 [1] CRAN (R 4.3.1) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) #> tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.3.0) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) #> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.3.0) #> vctrs 0.6.2 2023-04-19 [1] CRAN (R 4.3.0) #> viridis 0.6.4 2023-07-22 [1] CRAN (R 4.3.2) #> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0) #> visdat 0.6.0 2023-02-02 [1] CRAN (R 4.3.2) #> 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) #> xml2 1.3.4 2023-04-27 [1] CRAN (R 4.3.0) #> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0) #> #> [1] C:/Users/steph/AppData/Local/R/win-library/4.3 #> [2] C:/Program Files/R/R-4.3.1/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
njtierney commented 4 months ago

Thanks for this @szimmer !

njtierney commented 4 months ago

I can't seem to replicate this?

library(naniar)

gg_miss_fct(x = riskfactors, fct = marital)

Created on 2024-03-04 with reprex v2.1.0

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.2 (2023-10-31) #> os macOS Sonoma 14.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Melbourne #> date 2024-03-04 #> pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) #> curl 5.2.0 2023-12-08 [1] CRAN (R 4.3.1) #> 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) #> farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> forcats 1.0.0 2023-01-29 [1] CRAN (R 4.3.0) #> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) #> ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.3.1) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) #> gridExtra 2.3 2017-09-09 [2] CRAN (R 4.3.0) #> gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0) #> highr 0.10 2022-12-22 [1] CRAN (R 4.3.0) #> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) #> naniar * 1.0.0.9000 2024-01-12 [2] local #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [2] CRAN (R 4.3.0) #> R.methodsS3 1.8.2 2022-06-13 [2] CRAN (R 4.3.0) #> R.oo 1.26.0 2024-01-24 [2] CRAN (R 4.3.1) #> R.utils 2.12.3 2023-11-18 [2] CRAN (R 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> reprex 2.1.0 2024-01-11 [2] CRAN (R 4.3.1) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) #> rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1) #> rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1) #> sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.3.0) #> styler 1.10.2 2023-08-29 [2] CRAN (R 4.3.0) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) #> tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.1) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) #> 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) #> viridis 0.6.5 2024-01-29 [1] CRAN (R 4.3.1) #> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0) #> visdat 0.6.0 2023-02-02 [2] CRAN (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) #> xfun 0.42 2024-02-08 [1] CRAN (R 4.3.1) #> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) #> #> [1] /Users/nick/Library/R/arm64/4.3/library #> [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```
njtierney commented 4 months ago

Ah using CRAN naniar gives me this error:

library(naniar)

gg_miss_fct(x = riskfactors, fct = marital)
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `marital = (function (x) ...`.
#> Caused by warning:
#> ! `fct_explicit_na()` was deprecated in forcats 1.0.0.
#> ℹ Please use `fct_na_value_to_level()` instead.
#> ℹ The deprecated feature was likely used in the naniar package.
#>   Please report the issue at <https://github.com/njtierney/naniar/issues>.

Created on 2024-03-04 with reprex v2.1.0

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.2 (2023-10-31) #> os macOS Sonoma 14.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Melbourne #> date 2024-03-04 #> pandoc 3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) #> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.3.0) #> curl 5.2.0 2023-12-08 [1] CRAN (R 4.3.1) #> 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) #> farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> forcats 1.0.0 2023-01-29 [1] CRAN (R 4.3.0) #> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0) #> ggplot2 3.5.0 2024-02-23 [1] CRAN (R 4.3.1) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) #> gridExtra 2.3 2017-09-09 [2] CRAN (R 4.3.0) #> gtable 0.3.4 2023-08-21 [1] CRAN (R 4.3.0) #> highr 0.10 2022-12-22 [1] CRAN (R 4.3.0) #> htmltools 0.5.7 2023-11-03 [1] CRAN (R 4.3.1) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> labeling 0.4.3 2023-08-29 [1] CRAN (R 4.3.0) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0) #> naniar * 1.0.0 2023-02-02 [1] CRAN (R 4.3.0) #> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [2] CRAN (R 4.3.0) #> R.methodsS3 1.8.2 2022-06-13 [2] CRAN (R 4.3.0) #> R.oo 1.26.0 2024-01-24 [2] CRAN (R 4.3.1) #> R.utils 2.12.3 2023-11-18 [2] CRAN (R 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> reprex 2.1.0 2024-01-11 [2] CRAN (R 4.3.1) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) #> rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1) #> rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.0) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.3.1) #> sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.3.0) #> styler 1.10.2 2023-08-29 [2] CRAN (R 4.3.0) #> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0) #> tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.1) #> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.3.0) #> 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) #> viridis 0.6.5 2024-01-29 [1] CRAN (R 4.3.1) #> viridisLite 0.4.2 2023-05-02 [1] CRAN (R 4.3.0) #> visdat 0.6.0 2023-02-02 [2] CRAN (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) #> xfun 0.42 2024-02-08 [1] CRAN (R 4.3.1) #> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.3.1) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) #> #> [1] /Users/nick/Library/R/arm64/4.3/library #> [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library #> #> ────────────────────────────────────────────────────────────────────────────── ```

This has been solved in naniar devel on github, so I'll close this and it will be pushed in the next release of naniar