inst/doc/exploratory_analysis.R

In rtables: Reporting Tables

## ---- echo=FALSE--------------------------------------------------------------
knitr::opts_chunk$set(comment = "#")

## ---- message=FALSE-----------------------------------------------------------
library(rtables)
library(dplyr)

## -----------------------------------------------------------------------------
table(ex_adsl$ARM)
table(ex_adsl$SEX, ex_adsl$ARM)

## -----------------------------------------------------------------------------
qtable(ex_adsl, col_vars = "ARM")
qtable(ex_adsl, col_vars = "ARM", row_vars = "SEX")

## -----------------------------------------------------------------------------
qtable(ex_adsl, "ARM", show_colcounts = FALSE)

## ---- eval = FALSE------------------------------------------------------------
#  tmp_adsl <- ex_adsl
#  tmp_adsl$new <- rep_len(c("","A", "B"), nrow(tmp_adsl))
#  
#  qtable(tmp_adsl, row_vars = "new")

## -----------------------------------------------------------------------------
qtable(ex_adsl, row_vars = c("SEX", "STRATA1"), col_vars = c("ARM", "STRATA2"))

## -----------------------------------------------------------------------------
qtable(ex_adsl, 
       row_vars = c("SEX", "STRATA1"), 
       col_vars = c("ARM", "STRATA2"), 
       drop_levels = FALSE)

## -----------------------------------------------------------------------------
table(ex_adsl$SEX, ex_adsl$STRATA1, ex_adsl$ARM, ex_adsl$STRATA2) 

## -----------------------------------------------------------------------------
t1 <- ftable(ex_adsl[, c("SEX", "STRATA1", "ARM", "STRATA2")]) 
ftable(t1, row.vars = c("SEX", "STRATA1"))

## -----------------------------------------------------------------------------
tmp_adsl <- ex_adsl
tmp_adsl[[1]] <- NA_character_

qtable(tmp_adsl, row_vars = "ARM", col_vars = "SEX")

## -----------------------------------------------------------------------------
# Recode NA values
tmp_adsl[[1]] <- addNA(tmp_adsl[[1]])

qtable(tmp_adsl, row_vars = "ARM", col_vars = "SEX")

## -----------------------------------------------------------------------------
tmp_adsl$new1 <- factor(NA_character_, levels = c("X", "Y", "Z"))
qtable(tmp_adsl, row_vars = "ARM", col_vars = "new1")

## -----------------------------------------------------------------------------
tmp_adsl$new2 <- addNA(tmp_adsl$new1)
levels(tmp_adsl$new2)[4] <- "<NA>" # NA needs to be a recognizible string
qtable(tmp_adsl, row_vars = "ARM", col_vars = "new2")

## -----------------------------------------------------------------------------
qtable(ex_adsl, row_vars = "STRATA2", col_vars = "ARM", avar = "AGE", afun = mean)

## -----------------------------------------------------------------------------
qtable(ex_adsl, row_vars = "STRATA2", col_vars = "ARM", avar = "AGE", afun = range)

## -----------------------------------------------------------------------------
fivenum2 <- function(x) {
    setNames(as.list(fivenum(x)), c("min","Q1","MED","Q3","max"))
}
qtable(ex_adsl, row_vars = "STRATA2", col_vars = "ARM", avar = "AGE", afun = fivenum2)

## -----------------------------------------------------------------------------
meansd_range = function(x) {
    in_rows(
        "Mean (sd)" = rcell(c(mean(x), sd(x)), format = "xx.xx (xx.xx)"),
        "Range" = rcell(range(x), format = "xx - xx")
    )
}

qtable(ex_adsl, row_vars = "STRATA2", col_vars = "ARM", avar = "AGE", afun = meansd_range)

## -----------------------------------------------------------------------------
qtable(ex_adsl, row_vars = c("STRATA1", "STRATA2"), col_vars = "ARM",
      avar = "AGE", afun = mean)

qtable(ex_adsl, row_vars = c("STRATA1", "STRATA2"), col_vars = "ARM",
       summarize_groups = TRUE, avar = "AGE", afun = mean)

## -----------------------------------------------------------------------------
qtable(ex_adsl, row_vars = "STRATA2", col_vars = "ARM",
       title = "Strata 2 Summary", 
       subtitle = paste0("STUDY ", ex_adsl$STUDYID[1]), 
       main_footer = paste0("Date: ", as.character(Sys.Date())))