Hello I use R 4.4.1 on Debian testing with pandoc 3.1.3 and quarto 1

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Header formatting issue with quarto about gtsummary HOT 7 CLOSED

philippemichel commented on August 28, 2024

Header formatting issue with quarto

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Comments (7)

philippemichel commented on August 28, 2024 1

The result is quite correct with the following code (gtsummary v2.0) :

---
title: "TEST"
format: pdf
---

```{r}
library(gtsummary)

trial |>
  tbl_summary(
    by = trt
  ) |>
  as_kable()
```z

("z" is here for not close the block code with the triple`, to clear)

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Melkiades commented on August 28, 2024

{gtsummary} does not show any issue in your reprex. It regards your quarto code or system env. Please also consider reading again the guidelines for posting issues, thanks!!

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philippemichel commented on August 28, 2024


---
title: "test"
format: pdf
---

```{r}
library(gtsummary)

trial %>%
  select(age, grade, trt) %>%
 tbl_summary(by = trt)


The last line was missing.

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DanChaltiel commented on August 28, 2024

I have the same bug on Windows 10.

I cannot use reprex with Quarto so I'm not sure how to share a reproducible example.

Therefore, here is the output as an image, see that the header is misconstructed:

And here are my versions:

packageVersion("gt")
#> [1] '0.11.0'
packageVersion("gtsummary")
#> [1] '2.0.0'
quarto::quarto_version()
#> [1] '1.5.56'

^{Created on 2024-08-09 with reprex v2.1.0}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.3 (2024-02-29 ucrt)
#>  os       Windows 10 x64 (build 19045)
#>  system   x86_64, mingw32
#>  ui       RTerm
#>  language en
#>  collate  French_France.utf8
#>  ctype    French_France.utf8
#>  tz       Europe/Paris
#>  date     2024-08-09
#>  pandoc   3.1.11 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.6.2   2023-12-11 [1] CRAN (R 4.3.3)
#>  digest        0.6.35  2024-03-11 [1] CRAN (R 4.3.3)
#>  evaluate      0.23    2023-11-01 [1] CRAN (R 4.3.2)
#>  fastmap       1.1.1   2023-02-24 [1] CRAN (R 4.3.2)
#>  fs            1.6.3   2023-07-20 [1] CRAN (R 4.3.2)
#>  glue          1.7.0   2024-01-09 [1] CRAN (R 4.3.3)
#>  htmltools     0.5.7   2023-11-03 [1] CRAN (R 4.3.2)
#>  jsonlite      1.8.7   2023-06-29 [1] CRAN (R 4.3.2)
#>  knitr         1.46    2024-04-06 [1] CRAN (R 4.3.3)
#>  later         1.3.1   2023-05-02 [1] CRAN (R 4.3.2)
#>  lifecycle     1.0.4   2023-11-07 [1] CRAN (R 4.3.2)
#>  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.3.2)
#>  processx      3.8.2   2023-06-30 [1] CRAN (R 4.3.2)
#>  ps            1.7.5   2023-04-18 [1] CRAN (R 4.3.2)
#>  purrr         1.0.2   2023-08-10 [1] CRAN (R 4.3.2)
#>  quarto        1.4     2024-03-06 [1] CRAN (R 4.3.3)
#>  R.cache       0.16.0  2022-07-21 [1] CRAN (R 4.3.2)
#>  R.methodsS3   1.8.2   2022-06-13 [1] CRAN (R 4.3.1)
#>  R.oo          1.25.0  2022-06-12 [1] CRAN (R 4.3.1)
#>  R.utils       2.12.3  2023-11-18 [1] CRAN (R 4.3.3)
#>  Rcpp          1.0.12  2024-01-09 [1] CRAN (R 4.3.3)
#>  reprex        2.1.0   2024-01-11 [1] CRAN (R 4.3.3)
#>  rlang         1.1.3   2024-01-10 [1] CRAN (R 4.3.3)
#>  rmarkdown     2.27    2024-05-17 [1] CRAN (R 4.3.3)
#>  rstudioapi    0.15.0  2023-07-07 [1] CRAN (R 4.3.2)
#>  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.3.2)
#>  styler        1.10.3  2024-04-07 [1] CRAN (R 4.3.3)
#>  vctrs         0.6.5   2023-12-01 [1] CRAN (R 4.3.3)
#>  withr         3.0.0   2024-01-16 [1] CRAN (R 4.3.3)
#>  xfun          0.43    2024-03-25 [1] CRAN (R 4.3.3)
#>  yaml          2.3.8   2023-12-11 [1] CRAN (R 4.3.2)
#> 
#>  [1] C:/Users/Dan/AppData/Local/R/win-library/4.3
#>  [2] C:/Program Files/R/R-4.3.3/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

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ddsjoberg commented on August 28, 2024

Can you install gt v0.10.1 and see if you get the same result? I think this looks like a gt+Quarto issue perhaps?

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DanChaltiel commented on August 28, 2024

Same result with gt v0.10.1.
However, the problem disappears with gtsummary v1.7.2.
The fact that it used kable instead of gt might be an important hint. Maybe we can use that in v2?

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ddsjoberg commented on August 28, 2024

Thanks @Melkiades for investigating!

I would check two things:

Is it the introduction on the line break in the header that is causing the formatting issue.
If not, check the result using gt 0.10.1 and again with gtsummary 1.7.2. When testing the older gtsummary, ensure you force the drawing of the table with gt (rather than the default kable printer)

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Header formatting issue with quarto about gtsummary HOT 7 CLOSED

Comments (7)

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