## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----eval=FALSE---------------------------------------------------------------
# install.packages("finalfit")

## ----warning=FALSE, message=FALSE---------------------------------------------
library(finalfit)
library(dplyr)

dependent = "differ.factor"

# Specify explanatory variables of interest
explanatory = c("age", "sex.factor", 
  "extent.factor", "obstruct.factor", 
  "nodes")

## ----warning=FALSE, message=FALSE---------------------------------------------
colon_s %>% 
  select(age, sex.factor, extent.factor, obstruct.factor, nodes) %>% 
  names() -> explanatory

## ----warning=FALSE, message=FALSE---------------------------------------------
colon_s %>% 
  ff_glimpse(dependent, explanatory)

## ----eval=FALSE---------------------------------------------------------------
# colon_s %>%
#   summary_factorlist(dependent, explanatory,
#   p=TRUE, na_include=TRUE)

## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
colon_s %>% 
  summary_factorlist(dependent, explanatory, 
  p=TRUE, na_include=TRUE) %>% 
  knitr::kable(row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))

## ----eval=FALSE---------------------------------------------------------------
# explanatory = c("age", "sex.factor",
#   "extent.factor", "nodes")
# 
# colon_s %>%
# 	mutate(
# 		nodes = ff_label(nodes, "Lymph nodes involved")
# 	) %>%
#   summary_factorlist(dependent, explanatory,
#     p=TRUE, na_include=TRUE,
#     add_dependent_label=TRUE) -> table 1
# table1

## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
explanatory = c("age", "sex.factor", 
  "extent.factor", "nodes")

colon_s %>% 
  mutate(
    nodes = ff_label(nodes, "Lymph nodes involved")) %>% 
  summary_factorlist(dependent, explanatory, 
    p=TRUE, na_include=TRUE, 
    add_dependent_label=TRUE) %>% 
	knitr::kable(row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))

## ----eval=FALSE---------------------------------------------------------------
# explanatory = c("age", "sex.factor",
#   "extent.factor", "nodes", "differ.factor")
# dependent = "mort_5yr"
# colon_s %>%
#   finalfit(dependent, explanatory,
#   dependent_label_prefix = "") -> table2
# table2

## ----warning=FALSE, message=FALSE, echo=FALSE---------------------------------
explanatory = c("age", "sex.factor", 
  "extent.factor", "nodes", "differ.factor")
dependent = "mort_5yr"
colon_s %>% 
  finalfit(dependent, explanatory, 
  dependent_label_prefix = "") %>% 
	knitr::kable(row.names=FALSE, align=c("l", "l", "r", "r", "r", "r"))

## ----warning=FALSE, message=FALSE, eval=FALSE---------------------------------
# colon_s %>%
#   or_plot(dependent, explanatory,
#   breaks = c(0.5, 1, 5, 10, 20, 30))

## ----eval=FALSE---------------------------------------------------------------
# # Save objects for knitr/markdown
# save(table1, table2, dependent, explanatory, file = "out.rda")