Customize, Merge, and Export

Make the output look like it belongs in the final report. Rename labels, merge tables, and save tables or plots.

library(gtregression)
library(dplyr)

data("data_birthwt", package = "gtregression")

birthwt_data <- data_birthwt |>
  mutate(
    race = factor(race, levels = c(1, 2, 3),
                  labels = c("White", "Black", "Other")),
    smoke = factor(smoke, levels = c(0, 1), labels = c("No", "Yes")),
    ht = factor(ht, levels = c(0, 1), labels = c("No", "Yes")),
    ui = factor(ui, levels = c(0, 1), labels = c("No", "Yes")),
    low = factor(low, levels = c(0, 1), labels = c("Normal BW", "Low BW"))
  )

birthwt_desc <- descriptive_table(
  birthwt_data,
  exposures = c("age", "lwt", "race", "smoke", "ht", "ui"),
  by = "low"
)
birthwt_uni <- uni_reg(
  birthwt_data,
  outcome = "low",
  exposures = c("age", "lwt", "race", "smoke", "ht", "ui"),
  approach = "logit"
)
birthwt_multi <- multi_reg(
  birthwt_data,
  outcome = "low",
  exposures = c("smoke", "ht", "ui"),
  adjust_for = c("age", "lwt", "race"),
  approach = "logit"
)

Customize Labels

birthwt_custom <- modify_table(
  birthwt_multi,
  variable_labels = c(
    smoke = "Smoking during pregnancy",
    ht = "Hypertension",
    ui = "Uterine irritability"
  ),
  header_labels = c(estimate = "Adjusted OR", p.value = "P"),
  caption = "Adjusted regression for low birth weight"
)

birthwt_custom$table

Adjusted regression for low birth weight
Characteristic	Adjusted OR	P
Hypertension
No	—
Yes	5.99 (1.51–23.79)	0.011
Smoking during pregnancy
No	—
Yes	2.87 (1.36–6.04)	0.006
Uterine irritability
No	—
Yes	2.27 (0.98–5.24)	0.055
Abbreviations: OR = Odds Ratio; CI = Confidence Interval.

Merge Tables

birthwt_merged <- merge_tables(
  birthwt_desc,
  birthwt_uni,
  birthwt_multi,
  spanners = c("Descriptive", "Crude", "Adjusted")
)

birthwt_merged$table

	Descriptive		Crude			Adjusted
Characteristic	Normal BW	Low BW	N	OR (95% CI)	p-value	Adjusted OR (95% CI)	p-value
age	23.0 (19.0-28.0)	22.0 (19.5-25.0)	189	0.95 (0.89-1.01)	0.105
ht			189
No	125 (96.2%)	52 (88.1%)		--
Yes	5 (3.8%)	7 (11.9%)		3.37 (1.02-11.09)	0.046
lwt	123.5 (113.0-147.0)	120.0 (104.0-130.0)	189	0.99 (0.97-1.00)	0.023
race			189
White	73 (56.2%)	23 (39.0%)		--
Black	15 (11.5%)	11 (18.6%)		2.33 (0.94-5.77)	0.068	—
Other	42 (32.3%)	25 (42.4%)		1.89 (0.96-3.74)	0.067	5.99 (1.51–23.79)	0.011
smoke			189
No	86 (66.2%)	29 (49.2%)		--		—
Yes	44 (33.8%)	30 (50.8%)		2.02 (1.08-3.78)	0.028	2.87 (1.36–6.04)	0.006
ui			189
No	116 (89.2%)	45 (76.3%)		--		—
Yes	14 (10.8%)	14 (23.7%)		2.58 (1.14-5.83)	0.023	2.27 (0.98–5.24)	0.055
Categorical variables shown as n (%); percentages are by column.
Continuous variables shown as Median (IQR).
Abbreviations: OR = Odds Ratio; CI = Confidence Interval.
Adjusted for age, lwt, and race

Save Outputs

When no destination is supplied, save helpers use a temporary folder.

save_table(birthwt_merged, filename = "birthwt-table", format = "html")

birthwt_plot <- plot_reg(
  birthwt_multi,
  title = "Adjusted Regression for Low Birth Weight"
)

save_plot(birthwt_plot, filename = "birthwt-forest", format = "png")

Word Reports

Use format = "flextable" when the destination is Word.

birthwt_multi_ft <- multi_reg(
  birthwt_data,
  outcome = "low",
  exposures = c("smoke", "ht", "ui"),
  adjust_for = c("age", "lwt", "race"),
  approach = "logit",
  format = "flextable"
)

save_docx(
  tables = list(birthwt_multi_ft),
  filename = "birthwt-report",
  titles = "Adjusted Regression"
)

What To Inspect

modify_table(): changed labels, caption, and caveat.
merge_tables(): $table, $table_display, and $footnotes.
save_table(), save_plot(), save_docx(): returned file paths.

- Customize, Merge, and Export