Comments (2)
njtierney
commented on June 12, 2024
Thanks for posting this - this is a new error introduced in the latest release, I confirm that I get the same error:
# Library for dealing with missing values
library(naniar)
# Load `oceanbuoys` data
data("oceanbuoys")
# Impute the mean value and track the imputations
ocean_imp_mean <- oceanbuoys |>
naniar::nabular(only_miss = TRUE) |>
naniar::impute_mean_all() |>
naniar::add_label_shadow()
# Gather the imputed data: Throws an error
ocean_imp_mean |>
naniar::shadow_long(humidity, air_temp_c)
#> Error in `tidyr::pivot_longer()`:
#> ! Can't combine `year` <double> and `any_missing` <character>.
#> Backtrace:
#> ▆
#> 1. ├─naniar::shadow_long(ocean_imp_mean, humidity, air_temp_c)
#> 2. │ ├─tidyr::pivot_longer(...)
#> 3. │ └─tidyr:::pivot_longer.data.frame(...)
#> 4. │ └─tidyr::pivot_longer_spec(...)
#> 5. │ └─vctrs::vec_ptype_common(...)
#> 6. └─vctrs (local) `<fn>`()
#> 7. └─vctrs::vec_default_ptype2(...)
#> 8. ├─base::withRestarts(...)
#> 9. │ └─base (local) withOneRestart(expr, restarts[[1L]])
#> 10. │ └─base (local) doWithOneRestart(return(expr), restart)
#> 11. └─vctrs::stop_incompatible_type(...)
#> 12. └─vctrs:::stop_incompatible(...)
#> 13. └─vctrs:::stop_vctrs(...)
#> 14. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = vctrs_error_call(call))Created on 2023-03-30 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 (2022-10-31)
#> os macOS Ventura 13.2
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Australia/Hobart
#> date 2023-03-30
#> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.6.0 2023-01-09 [1] CRAN (R 4.2.0)
#> colorspace 2.1-0 2023-01-23 [1] CRAN (R 4.2.0)
#> digest 0.6.31 2022-12-11 [1] CRAN (R 4.2.0)
#> dplyr 1.1.0 2023-01-29 [1] CRAN (R 4.2.1)
#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.2.0)
#> fansi 1.0.4 2023-01-22 [1] CRAN (R 4.2.0)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
#> fs 1.6.1 2023-02-06 [1] CRAN (R 4.2.0)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
#> ggplot2 3.4.1 2023-02-10 [1] CRAN (R 4.2.0)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
#> gtable 0.3.1 2022-09-01 [1] CRAN (R 4.2.0)
#> htmltools 0.5.4 2022-12-07 [1] CRAN (R 4.2.0)
#> knitr 1.42 2023-01-25 [1] CRAN (R 4.2.0)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
#> naniar * 1.0.0 2023-02-02 [1] CRAN (R 4.2.0)
#> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
#> purrr 1.0.1 2023-01-10 [1] CRAN (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.2 2022-11-11 [1] CRAN (R 4.2.0)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.0)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.0)
#> rmarkdown 2.20 2023-01-19 [1] CRAN (R 4.2.0)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.0)
#> scales 1.2.1 2022-08-20 [1] CRAN (R 4.2.0)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
#> styler 1.9.0 2023-01-15 [1] CRAN (R 4.2.0)
#> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0)
#> tidyr 1.3.0 2023-01-24 [1] CRAN (R 4.2.0)
#> tidyselect 1.2.0 2022-10-10 [1] CRAN (R 4.2.0)
#> utf8 1.2.3 2023-01-31 [1] CRAN (R 4.2.0)
#> vctrs 0.5.2 2023-01-23 [1] CRAN (R 4.2.0)
#> visdat 0.6.0 2023-02-02 [1] local
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
#> xfun 0.37 2023-01-31 [1] CRAN (R 4.2.0)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.2.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────Thanks again for posting this, this will be fixed in an upcoming release.
from naniar.
njtierney
commented on June 12, 2024
Thank you again for this @siavash-babaei !
This now works, but by default changes value to character, as that is the safest way to have this always succeed. Otherwise you can specify your own coercion function to transform value values. Here's an example:
library(naniar)
aq_shadow <- nabular(airquality)
shadow_long(aq_shadow)
#> # A tibble: 918 × 4
#> variable value variable_NA value_NA
#> <chr> <chr> <chr> <fct>
#> 1 Ozone 41 Ozone_NA !NA
#> 2 Solar.R 190 Solar.R_NA !NA
#> 3 Wind 7.4 Wind_NA !NA
#> 4 Temp 67 Temp_NA !NA
#> 5 Month 5 Month_NA !NA
#> 6 Day 1 Day_NA !NA
#> 7 Ozone 36 Ozone_NA !NA
#> 8 Solar.R 118 Solar.R_NA !NA
#> 9 Wind 8 Wind_NA !NA
#> 10 Temp 72 Temp_NA !NA
#> # ℹ 908 more rows
# then filter only on Ozone and Solar.R
shadow_long(aq_shadow, Ozone, Solar.R)
#> # A tibble: 306 × 4
#> variable value variable_NA value_NA
#> <chr> <chr> <chr> <fct>
#> 1 Ozone 41 Ozone_NA !NA
#> 2 Solar.R 190 Solar.R_NA !NA
#> 3 Ozone 36 Ozone_NA !NA
#> 4 Solar.R 118 Solar.R_NA !NA
#> 5 Ozone 12 Ozone_NA !NA
#> 6 Solar.R 149 Solar.R_NA !NA
#> 7 Ozone 18 Ozone_NA !NA
#> 8 Solar.R 313 Solar.R_NA !NA
#> 9 Ozone <NA> Ozone_NA NA
#> 10 Solar.R <NA> Solar.R_NA NA
#> # ℹ 296 more rows
# ensure `value` is numeric
shadow_long(aq_shadow, fn_value_transform = as.numeric)
#> # A tibble: 918 × 4
#> variable value variable_NA value_NA
#> <chr> <dbl> <chr> <fct>
#> 1 Ozone 41 Ozone_NA !NA
#> 2 Solar.R 190 Solar.R_NA !NA
#> 3 Wind 7.4 Wind_NA !NA
#> 4 Temp 67 Temp_NA !NA
#> 5 Month 5 Month_NA !NA
#> 6 Day 1 Day_NA !NA
#> 7 Ozone 36 Ozone_NA !NA
#> 8 Solar.R 118 Solar.R_NA !NA
#> 9 Wind 8 Wind_NA !NA
#> 10 Temp 72 Temp_NA !NA
#> # ℹ 908 more rows
shadow_long(aq_shadow, Ozone, Solar.R, fn_value_transform = as.numeric)
#> # A tibble: 306 × 4
#> variable value variable_NA value_NA
#> <chr> <dbl> <chr> <fct>
#> 1 Ozone 41 Ozone_NA !NA
#> 2 Solar.R 190 Solar.R_NA !NA
#> 3 Ozone 36 Ozone_NA !NA
#> 4 Solar.R 118 Solar.R_NA !NA
#> 5 Ozone 12 Ozone_NA !NA
#> 6 Solar.R 149 Solar.R_NA !NA
#> 7 Ozone 18 Ozone_NA !NA
#> 8 Solar.R 313 Solar.R_NA !NA
#> 9 Ozone NA Ozone_NA NA
#> 10 Solar.R NA Solar.R_NA NA
#> # ℹ 296 more rowsCreated on 2023-05-01 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.0 (2023-04-21)
#> os macOS Ventura 13.2
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2023-05-01
#> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/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)
#> digest 0.6.31 2022-12-11 [1] CRAN (R 4.3.0)
#> dplyr 1.1.2 2023-04-20 [1] CRAN (R 4.3.0)
#> evaluate 0.20 2023-01-17 [1] CRAN (R 4.3.0)
#> fansi 1.0.4 2023-01-22 [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)
#> 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)
#> gtable 0.3.3 2023-03-21 [1] CRAN (R 4.3.0)
#> htmltools 0.5.5 2023-03-23 [1] CRAN (R 4.3.0)
#> knitr 1.42 2023-01-25 [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)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
#> naniar * 1.0.0.9000 2023-05-01 [1] 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 1.0.1 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)
#> 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 1.1.0 2023-03-14 [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 4.3.0)
#> styler 1.9.1 2023-03-04 [1] CRAN (R 4.3.0)
#> 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)
#> visdat 0.6.0 2023-02-02 [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)
#> yaml 2.3.7 2023-01-23 [1] CRAN (R 4.3.0)
#>
#> [1] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library
#>
#> ──────────────────────────────────────────────────────────────────────────────from naniar.
Related Issues (20)
- update pkgdown to bootstrap 3
- Gives a warning message saying "The `guide` argument in `scale_*()` cannot be `FALSE`" HOT 2
- Cannot modify ggplot theme for `gg_miss_upset`. HOT 2
- Improve `miss_summary` by providing a nice print method HOT 1
- Helpers to identify which rows and variables have over a certain % or number of missingns
- consider deprecating `cast_shadow` and friends
- use across with scoped variants with replace_with_na (e.g., _if _at _all)
- use cli for error and warning messages, and expect_snapshot for capturing errors HOT 1
- Implement new `gg_miss_upset()` function
- impute_mean_all throws an error when working with dataset containing categorical variables HOT 2
- Imputation of categorical data HOT 2
- Error running MCAR_TEST: Error in test_if_dataframe(data) : could not find function "test_if_dataframe" HOT 1
- Fix package alias issue
- Defining the range of % Miss in gg_miss_var HOT 1
- recode_shadow() special missings are not accounted for by summary functions HOT 1
- miss_scan_count should contain percentage information and default to descending order
- gg_miss_fct() is using a deprecated function from forcats package HOT 3
- Release naniar 1.1.0
- `imputed` as a basic method
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from naniar.