Replace table by plot on tm_missing_data

[llrs-roche]

Pull Request

Fixes #495

Replaces the table by a plot on "By Variables Levels" tab.
The colors match those in the other plots of the module.
It also required to add a "new" dependency, formatters, which is a dependency of tern, rlistings, rtable. I added it on Suggests.

There is an extra commit to update the lintr names

data <- within(teal_data(), {
  ADSL <- rADSL
  ADRS <- rADRS
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

init(
  data = data,
  modules = modules(tm_missing_data())
) |> runApp()

[github-actions]

Code Coverage Summary

Filename                      Stmts    Miss  Cover    Missing
--------------------------  -------  ------  -------  -------------------------------------------
R/tm_a_pca.R                    864     864  0.00%    141-1132
R/tm_a_regression.R             751     751  0.00%    180-1027
R/tm_data_table.R               200     200  0.00%    100-348
R/tm_file_viewer.R              172     172  0.00%    50-257
R/tm_front_page.R               143     132  7.69%    77-246
R/tm_g_association.R            320     320  0.00%    161-547
R/tm_g_bivariate.R              664     406  38.86%   332-786, 827, 932, 949, 967, 978-1000
R/tm_g_distribution.R          1106    1106  0.00%    156-1404
R/tm_g_response.R               345     345  0.00%    179-594
R/tm_g_scatterplot.R            709     709  0.00%    261-1065
R/tm_g_scatterplotmatrix.R      272     253  6.99%    200-501, 562, 576
R/tm_missing_data.R            1172    1172  0.00%    126-1475
R/tm_outliers.R                1029    1029  0.00%    162-1341
R/tm_rmarkdown.R                154      68  55.84%   144-196, 225-240, 284-285, 345-368
R/tm_t_crosstable.R             263     263  0.00%    177-482
R/tm_variable_browser.R         887     881  0.68%    89-1113, 1164-1347
R/utils.R                       185     120  35.14%   87-250, 279-305, 317-326, 331, 345-364, 453
R/zzz.R                           2       2  0.00%    2-3
TOTAL                          9238    8793  4.82%

Diff against main

Filename               Stmts    Miss  Cover
-------------------  -------  ------  --------
R/tm_missing_data.R      +92     +92  +100.00%
TOTAL                    +92     +92  -0.05%

Results for commit: 01d9758

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

[github-actions]

Unit Tests Summary

  1 files   24 suites   15m 45s ⏱️
157 tests 152 ✅ 5 💤 0 ❌
479 runs  474 ✅ 5 💤 0 ❌

Results for commit 01d9758.

♻️ This comment has been updated with latest results.

[llrs-roche]

PR updated, now showing the plot:

there was some issues with the required input being linked to an empty string

[llrs-roche]

There are differences when tested with ADSL +ADRS data and when using just other data. The problem was mainly with the iris+mtcars used on the tests that require some more relaxed req() calls

App with iris+mtcars (like tests)

dev_mode()
devtools::install()
library("teal.modules.general")

source("tests/testthat/helper-TealAppDriver.R", echo = FALSE)

datat <- within(simple_teal_data(), {
  set.seed(123)
  
  add_nas <- function(x) {
    x[sample(seq_along(x), floor(length(x) * runif(1, .05, .17)))] <- NA
    x
  }
  
  iris[] <- lapply(iris, add_nas)
  mtcars[] <- lapply(mtcars, add_nas)
  mtcars[["cyl"]] <- as.factor(mtcars[["cyl"]])
  mtcars[["gear"]] <- as.factor(mtcars[["gear"]])
})

teal::init(
  data = datat,
  modules = modules(tm_missing_data())
)|> runApp()

[averissimo]

It seems ready to be merged.

I have 1 final question regarding borders to further separate the tiles.

Other comments are just technical details

[llrs-roche]

Thanks for the feedback. Applying the changes and suggesting news ones to keep the module coherent.

[kumamiao]

Thanks @llrs-roche and @averissimo for working on this PR. It looks good to me and I agree with replacing the table with the plot. Agree with Andre to display counts when counts is selected.

[llrs-roche]

Thanks for the patch André:

[averissimo]

Awesome work @llrs-roche !! 💯