The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

Themes

library(sumExtras)
library(gtsummary)
library(gt)

use_jama_theme()

use_jama_theme() sets the {gtsummary} theme to JAMA compact styling for the rest of your session. It reduces padding, tightens font sizes, and produces tables suited for publication or reports.

use_jama_theme()

trial |>
  tbl_summary(by = trt) |>
  extras()
Overall
N = 2001		 Drug A
N = 981		 Drug B
N = 1021		 p-value2
Age 47 (38, 57) 46 (37, 60) 48 (39, 56) 0.718
    Unknown 11 7 4
Marker Level (ng/mL) 0.64 (0.22, 1.41) 0.84 (0.23, 1.60) 0.52 (0.18, 1.21) 0.085
    Unknown 10 6 4
T Stage


0.866
    T1 53 (27%) 28 (29%) 25 (25%)
    T2 54 (27%) 25 (26%) 29 (28%)
    T3 43 (22%) 22 (22%) 21 (21%)
    T4 50 (25%) 23 (23%) 27 (26%)
Grade


0.871
    I 68 (34%) 35 (36%) 33 (32%)
    II 68 (34%) 32 (33%) 36 (35%)
    III 64 (32%) 31 (32%) 33 (32%)
Tumor Response 61 (32%) 28 (29%) 33 (34%) 0.530
    Unknown 7 3 4
Patient Died 112 (56%) 52 (53%) 60 (59%) 0.412
Months to Death/Censor 22.4 (15.9, 24.0) 23.5 (17.4, 24.0) 21.2 (14.5, 24.0) 0.145
1 Median (Q1, Q3); n (%)
2 Wilcoxon rank sum test; Pearson’s Chi-squared test

This is equivalent to calling gtsummary::set_gtsummary_theme(gtsummary::theme_gtsummary_compact("jama")) but shorter to type.

To reset back to the default {gtsummary} theme:

gtsummary::reset_gtsummary_theme()

theme_gt_compact()

When you mix {gtsummary} tables with plain {gt} tables in the same document, the styling mismatch is noticeable. theme_gt_compact() applies the same JAMA compact look to {gt} tables.

Default gt

trial |>
  select(trt, age, grade) |>
  head(10) |>
  gt::gt()

With theme_gt_compact()

trial |>
  select(trt, age, grade) |>
  head(10) |>
  gt::gt() |>
  theme_gt_compact()
Chemotherapy Treatment Age Grade
Drug A 23 II
Drug B 9 I
Drug A 31 II
Drug A NA III
Drug A 51 III
Drug B 39 I
Drug A 37 II
Drug A 32 I
Drug A 31 II
Drug B 34 I
Chemotherapy Treatment Age Grade
Drug A 23 II
Drug B 9 I
Drug A 31 II
Drug A NA III
Drug A 51 III
Drug B 39 I
Drug A 37 II
Drug A 32 I
Drug A 31 II
Drug B 34 I

You can layer additional {gt} styling on top:

trial |>
  dplyr::select(trt, age, grade, marker) |>
  head(8) |>
  gt::gt() |>
  theme_gt_compact() |>
  gt::tab_header(
    title = "Trial Patient Sample",
    subtitle = "First 8 patients"
  )
Trial Patient Sample
First 8 patients
Chemotherapy Treatment Age Grade Marker Level (ng/mL)
Drug A 23 II 0.160
Drug B 9 I 1.107
Drug A 31 II 0.277
Drug A NA III 2.067
Drug A 51 III 2.767
Drug B 39 I 0.613
Drug A 37 II 0.354
Drug A 32 I 1.739

More Vignettes

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.