merck/boxly

Interactive box plot for clinical trial analysis

boxly's Issues

Repo description

I think this description would be a bit better:

Create interactive box plots with ease, ideal for visualizing data from lab tests, vital signs, electrocardiograms, and more.

compared to the current

Create interactive box plot for lab test, vital signs, electrocardiogram etc.

The reasoning:

1. Not limiting to visualizing only the listed types of data.
2. Consistent usage of plurals.
3. Avoids using "etc."

Reduce declare of global variables

Why would we have so many global variables? Better to check what is absolutely required.

utils::globalVariables(c(
  "ANL01FL", "boxly_adlb", "CHG", "Freq", "group", "label", "outdata", "outlier",
  "param", "PARAMCD", "text", "TRT01A", "TRTA", "x", "AVISITN"
))

Using DT vs. reactable

Why would we choice DT instead of reactable?

https://github.com/Merck/boxly/blob/main/R/boxly.R#L188

Fix example code in vignette

In vignettes/boxly-cran.Rmd, you have:

library("boxploy")

meta_boxly(
  boxly_adsl,
  boxly_adlb,
  population_term = "apat",
  observation_term = "wk12",
  observation_subset = AVISITN <= 12 & !is.na(CHG)
) |>
  prepare_boxly() |>
  boxply()

This does not actually work because there is no package called "boxploy" and there is no function called boxply().

output doesn't look well when click box on the plot

Here is what output looks like when click the box by accident.

Create vignettes for boxly

Try to use boxly for ADLB, ADVS and ADEG

Replace exclamation points with full stop in messages

In prepare_boxly(), there are a few message() calls with exclamation points (!) at the end of the message.

• From the tidyverse style guide, error messages should end in a full stop (.).

• Also, from the Google developer documentation style guide:

Don't use exclamation points in text except when they're part of a code example. Rather than using exclamation points to call attention to an important point, consider using notices such as Note or Caution.

format summary statistics

Format statistics display as hover label on the box.

Enable codecov badge

The current badge in README did not display code coverage number.

Option to show only error bar on output

https://chart-studio.plotly.com/create/?fid=chelsea_lyn:155#/

README: add a GIF/video to show use cases.

Please include a GIF/video in the README file to illustrate the package.

Do we need boxly_adeg and boxly_advs?

I did not see the two datasets are used.

• boxly_adeg
• boxly_advs

Release boxly 0.1.0

Prepare for release

• Check current CRAN check results
• Check licensing of included files
• Review pkgdown reference index for, e.g., missing topics
• Bump version
• Update cran-comments.md (optional)
• Update NEWS.md
• Review pkgdown website
• urlchecker::url_check()
• Check with local machine
• Check with GitHub Actions
• Check with win-builder

Submit to CRAN

• Draft GitHub release
• Submit to CRAN via web form
• Approve emails

Wait for CRAN

• Accepted 🎉
• Post on r-packages mailing list
• Tweet

Remove r2rtf dependency

It seems you only need a dataset from r2rtf::r2rtf_adsl. Better to create an independent dataset boxly::boxly_adsl to remove the dependency.

Remove metalite.ae dependency

Update document to avoid

@inheritParams metalite.ae::prepare_ae_specific

Handle situation with 0 rows

Seems we have bug when a PARAM has 0 rows after we adding more parameters using change in #18

Example code

meta <- meta_boxly(
  boxly_adsl,
  boxly_adlb,
  population_term = "apat",
  observation_term = "wk12",
  observation_subset = ANL01FL == "Y" & AVISITN <= 12 & !is.na(CHG)
  )

outdata <- prepare_boxly(meta,
  population = "apat",
  observation = "wk12",
  parameter = meta$plan$parameter,
  analysis = "boxly"
)

Message

Warning: In observation level data, the facet variable 'PARAM' is automatically transformed into a factor!
Warning: In observation level data, the group variable 'AVISITN' is automatically transformed into a factor!
Error in `$<-.data.frame`(`*tmp*`, outlier, value = NA) : 
  replacement has 1 row, data has 0

Improve meta_boxly

We need to improve meta_boxly API like we did in meta_forestly.

output shown not well on the knitted output when multiple box plot

When trying multiple box plots in one RMD file, the output display blank.

Enable user to customize hover label variables for outliers

For now, the outlier's hover label is fixed. They are participant ID and parameter value.