atorus-research / pharmartf Goto Github PK

Hello,

Thank you for the great package. I have been using it to generate my RTF documents. In the reference manual, it says the future plans include colors. Do you have a timeline for that? I would like to put in a request for text color. Thank you!

Copying issue text from here

@NNaikp could you share your output on timestamp and R language setting? Thanks!

Github doesn't support .rtf so I have attached the file here (tlf-primary.docx) as .docx. Here is also a screenshot from the .rtf file:

My default language in Word is UK english.

When I did the review I set Sys.setenv(LANG = "en") as it was showing me error messages in danish. But after some googling I can see that the locale is still Danish, also if I set the language to English:

> Sys.setenv(LANG = "en")
> Sys.getlocale()
[1] "LC_COLLATE=Danish_Denmark.1252;LC_CTYPE=Danish_Denmark.1252;LC_MONETARY=Danish_Denmark.1252;LC_NUMERIC=C;LC_TIME=Danish_Denmark.1252"

After running Sys.setlocale(locale = "English") I see

> Sys.setlocale(locale = "English")
[1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"

Which yields:

Maybe pharmaRTF::write_rtf needs to check the locale before sinking the file? I can see from the documentation of Sys.setlocale() that it is OS dependent. The one above is Windows (my local). This one is from a linux server:

> Sys.getlocale()
[1] "LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C"

Hi guys,

I've been running reverse dependency checks on huxtable dependencies. pharmaRTF currently gets a couple of errors in running examples:

*   checking examples ... ERROR
  
    > library(huxtable)
    
 ...
    > ht <- huxtable(
    +   column1 = 1:5,
    +   column2 = letters[1:5]
    + )
    > rtf <- rtf_doc(ht, list(hf_line("aTitle")))
    > 
    > header_rows(rtf)
    Error in UseMethod("header_rows") : 
      no applicable method for 'header_rows' applied to an object of class "rtf_doc"
    Calls: header_rows
    Execution halted

I guess header_rows is a pharmaRTF method that is now getting interfered with by the new huxtable generic and function, of the same name.

I also get some testing failures:

      [ OK: 212 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 5 ]
      1. Error: insert_buffer adds a blank column correctly (@test_helpers.r#37) 
      2. Failure: hf_string orderes lines properly (@test_rtf-code-generators.r#24) 
      3. Failure: header_string lines populates correctly (@test_rtf-code-generators.r#123) 
      4. Failure: header_string lines populates correctly (@test_rtf-code-generators.r#124) 
      5. Failure: rtf_doc returns a list with a table, title, and footnotes (@test_rtf_doc.r#14) 

You can test the latest version of huxtable with

remotes::install_github("hughjonesd/huxtable")

The master branch is now in bugfix-only mode.

Hi Eli,

This is a really great package!
However, my company standards dictate that

outputs must not include any text in the header or footer, as they are reserved for regulatory publishing.

Is is possible to do this with pharmaRTF now? Or could it be sometime in the future?

Thanks!

Hi,

The pharmaRTF package is so good to creat RTF file, but I have a query that what's the reason put the column names in header. According to RTF in clinical trials, we usually put the whole table including column names in the RTF body part, certainly I'm not familiar with RTF.

I'm looking for some solutions to creat RTF instead of SAS in R

Thanks!

Is it possible to use this package to generate a word report which has proper table formatting as shown in this package but also with proper table numbering and referencing?

@millera minor fix to improve riskmetric score:

Add to DESCRIPTION file URL: https://atorus-research.github.io/pharmaRTF/, https://github.com/atorus-research/pharmaRTF

Thanks to @DawnYe for this report in atorus-research/CDISC_pilot_replication#7.

With tibble 3.1.0 even my_tibble[FALSE, "notAColumn"] <- 1 will result in a new column being created. This is intended behavior for tibble now. This breaks fill_missing_data() which is an unexported function in read_hf.R. This is the offending line:

 .data[is.na(.data[var]), var] <- correct_defaults(var)

correct_defaults returns NULL when var is 'type'. This would never happen in an actual hf_file but even if it returns null, tibble is trying to add a new column and failing because its not a vector, a bare list, a data frame or a matrix.

Thankfully this is an easy fix. Either add type as a option in the correct_defaults as a blank matrix, or add an if statement like the following:

if(any(is.na(.data[[var]]))
          .data[is.na(.data[[var]]), var] <- correct_defaults(var)

Hi,

Thanks for creating this. One thing that I have noticed is that the generated RTF files look different in LibreOffice Writer compared to how they look in Microsoft Word. In LibreOffice, there is an extra gap between the column heading and the table body that is not present in Word. While it looks as if things are being rendered differently, it this something that can be addressed?

Many thanks,

John