## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", echo = TRUE, eval = TRUE, warning=FALSE, fig.height = 6, fig.width = 9, fig.align='center' ) ## ----color-function, echo = FALSE--------------------------------------------- colorize <- function(text, color) { if (knitr::is_latex_output()) { sprintf("\\textcolor{%s}{%s}", color, text) } else if (knitr::is_html_output()) { sprintf("%s", color, text) } else text } ## ----setup, echo = FALSE, message = FALSE, warning = FALSE-------------------- library(dplyr) library(tidyverse) library(gtsummary) library(summarySCI) library(flextable) ## ----message = FALSE---------------------------------------------------------- library(survival) data(cancer, package="survival") colon1 <- colon %>% group_by(id) %>% slice(1) %>% # Select the first row within each id group ungroup() ## ----echo = FALSE------------------------------------------------------------- n_patients <- nrow(colon) ## ----------------------------------------------------------------------------- set.seed(123) colon2 <- colon1 %>% select(rx, sex, age, extent) %>% filter(rx != "Lev") %>% mutate(rx = if_else(rx == "Obs", "Control", rx), extent = if_else(row_number() %in% sample(row_number(), size = round(0.1 * n())), NA, extent)) %>% rename(Male = sex) %>% mutate(extent = as.factor(extent)) ## ----------------------------------------------------------------------------- head(colon2) ## ----------------------------------------------------------------------------- summaryTable(data = colon2) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, vars = c("Male", "age", "extent"), group = "rx") ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", labels = list(age = "Age", extent = "Extent")) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", labels = list(rx = "Arm", age = "Age", extent = "Extent"), add_n = FALSE) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", overall = TRUE, labels = list(age = "Age", extent = "Extent")) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", vars = "Male", labels = list(age = "Age"), dichotomous_as = "dichotomous", value = list(Male ~ "1"), missing = FALSE) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", stat_cont = "median_IQR", stat_cat = "n_N", labels = list(age = "Age", sex = "Sex", extent = "Extent")) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", vars = c("age", "extent"), stat_cont = "mean_sd", test = TRUE, ci = TRUE, labels = list(age = "Age", extent = "Extent") ) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", vars = "extent", test = TRUE, ci = TRUE, missing_percent = FALSE, labels = list(extent = "Extent") ) summaryTable(data = colon2, group = "rx", vars = "extent", test = TRUE, ci = TRUE, missing_percent = TRUE, labels = list(extent = "Extent") ) ## ----------------------------------------------------------------------------- summaryTable(data = colon2, group = "rx", vars = "extent", missing_percent = "both", test = TRUE, labels = list(extent = "Extent") )