CODEWITHSUNDEEP
rgtsummary
devster
devster

Reputation: 159

gtsummary add units to variable labels in tbl_summary

I'm trying to customize the labels of a gtsummary::tbl_summary() and I'm having some trouble adding units to variables which do have this information.

Below the code I'm using:

set.seed(123)
library(tidyverse)
library(gtsummary)
d <- tidyr::tibble(
    id = c(1,2,3,4,5,6,7,8,9,10),
    inf_1 = structure(sample(rnorm(100, mean=42, sd=14), size = 10), label = "Age", units = "years"),
    inf_2 = structure(factor(sample(seq(0,1), size = 10, replace = TRUE), levels = c(0,1), labels = c("Unchecked", "Checked")), label = "BSI"),
)

d %>%
    gtsummary::tbl_summary(
        data = .,
        include = -id,
        label = ~ ifelse(
            "units" %in% names(attributes(.)),
            toString(attr(., "label"), attr(., "units")),
            toString(attr(., "label"))
        ),
        type = list(all_continuous() ~ "continuous2"),
        statistic = list(
            all_continuous() ~ c(
                "{median} ({p25}, {p75})",
                "{min}, {max}"
            ),
            all_categorical() ~ "{n} / {N} ({p}%)"
        )
    ) %>%
    gtsummary::as_gt()

And the output:

output_table

Created on 2024-12-25 with reprex v2.1.1

I believe this is because the "label" attribute is empty but this seems to be what the package uses by default according to documentation. Commenting out the label argument gives a standard output.

Any suggestions on how to do this?

Thank you.

Upvotes: 1

Views: 69

Answers (1)

Tim G
Tim G

Reputation: 4182

this works:

d %>%
  gtsummary::tbl_summary(
    data = .,
    include = -id,
    label = list(
      inf_1 ~ paste(attr(d$inf_1, "label"), paste0("(", attr(d$inf_1, "units"), ")")),
      inf_2 ~ attr(d$inf_2, "label")
    ),
    type = list(all_continuous() ~ "continuous2"),
    statistic = list(
      all_continuous() ~ c("{median} ({p25}, {p75})", "{min}, {max}"),
      all_categorical() ~ "{n} / {N} ({p}%)"
    )
  ) %>%
  gtsummary::as_gt()

out

Or to automatically use the label and units (if present) we can do:

build_labels <- function(data) {
  lapply(data, function(x) {
    label <- attr(x, "label")
    units <- attr(x, "units")
    if (!is.null(units)) {
      paste(label, paste0("(", units, ")"))
    } else {
      label
    }
  })
}

e <- tidyr::tibble(
  id = c(1,2,3,4,5,6,7,8,9,10),
  inf_1 = structure(sample(rnorm(100, mean=42, sd=14), size = 10), label = "Age", units = "years"),
  inf_2 = structure(factor(sample(seq(0,1), size = 10, replace = TRUE), levels = c(0,1), labels = c("Unchecked", "Checked")), label = "BSI"),
  inf_3 = structure(sample(rnorm(50, mean=12, sd=3), size = 10), label = "Footsize", units = "cm"),
)

# Usage in tbl_summary
e %>%
  gtsummary::tbl_summary(
    data = .,
    include = -id,
    label = build_labels(e),
    type = list(all_continuous() ~ "continuous2"),
    statistic = list(
      all_continuous() ~ c("{median} ({p25}, {p75})", "{min}, {max}"),
      all_categorical() ~ "{n} / {N} ({p}%)"
    )
  ) %>%
  gtsummary::as_gt()

out2

Upvotes: 3

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