## ----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---------------------------------------------------------- data<- as.data.frame(cbind(c(1:10), c("A","A","A","A","A","B","B","B","B","B"), c("absent","present","absent","present","absent","absent","present","absent","present","absent"), c("absent","absent","present","absent","absent","absent","absent","absent","absent","absent"), c("present","absent","present","present","present","present","present","present","present","present"))) names(data)<-c("upn", "arm", "liver", "lung", "brain") ## ----------------------------------------------------------------------------- summarySCI::summaryLevels(data=data, vars = c("liver", "lung", "brain"), label = "Site of progression", levels= "present",) ## ----------------------------------------------------------------------------- summarySCI::summaryLevels(data=data, vars = c("liver", "lung", "brain"), group = "arm", label = "Site of progression", levels= "present") ## ----------------------------------------------------------------------------- summarySCI::summaryLevels(data=data, vars = c("liver", "lung", "brain"), group = "arm", label = "Site of progression", levels= "present", overall = TRUE) ## ----------------------------------------------------------------------------- summarySCI::summaryLevels(data=data, vars = c("liver", "lung", "brain"), group = "arm", label = "Site of progression", test = TRUE,, levels= "present") ## ----------------------------------------------------------------------------- summarySCI::summaryLevels(data=data, vars = c("liver", "lung", "brain"), group = "arm", levels= "present", label = "Site of progression", test = TRUE, test_cat = "chisq.test") ## ----------------------------------------------------------------------------- summarySCI::summaryLevels(data=data, vars = c("liver", "lung", "brain"), group = "arm", label = "Site of progression", levels= "present", test = TRUE, test_cat = "fisher.test", ci=TRUE, conf_level = 0.9, overall = FALSE)