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

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  freq(
    colvar = "TRT01PN",
    rowvar = "ITTFL",
    statlist = statlist("n"),
    subset = ITTFL == "Y",
    rowtext = "Analysis set: ITT"
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  freq(
    colvar = "TRT01PN",
    rowvar = "SEX",
    statlist = statlist(c("N", "n (x.x%)")),
    row_header = "Sex"
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  mutate(
    SEX = factor(SEX, levels = c("M", "F"), labels = c("Male", "Female"))
  ) %>%
  freq(
    colvar = "TRT01PN",
    rowvar = "SEX",
    statlist = statlist(c("N", "n (x.x%)")),
    row_header = "Sex"
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  mutate(SEX = factor(
    SEX,
    levels = c("M", "F"), labels = c("Male", "Female")
  )) %>%
  freq(
    colvar = "TRT01PN",
    rowvar = "SEX",
    statlist = statlist("n/N (x.x%)"),
    row_header = "Sex"
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  mutate(SEX = factor(
    SEX,
    levels = c("M", "F"), labels = c("Male", "Female")
  )) %>%
  freq(
    colvar = "TRT01PN",
    rowbyvar = "SEX",
    rowvar = "AGEGR1",
    statlist = statlist(c("N", "n (x.x%)"), denoms_by = c("SEX", "TRT01PN")),
    row_header = "Age group"
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  freq(
    colvar = "TRT01PN",
    rowbyvar = "ETHNIC",
    rowvar = "RACE",
    statlist = statlist(c("N", "n (x.x%)")),
    row_header = "Race"
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- cdisc_adsl %>%
  freq(
    colvar = "TRT01PN",
    rowbyvar = "ETHNIC",
    rowvar = "RACE",
    statlist = statlist(c("N", "n (x.x%)")),
    row_header = "Race",
    pad = FALSE
  )

knitr::kable(tbl)

## -----------------------------------------------------------------------------
adae <- cdisc_adae %>%
  rename(TRT01AN = TRTAN)

tbl <- adae %>%
  freq(
    denom_df = cdisc_adsl,
    colvar = "TRT01AN",
    rowvar = "AEDECOD",
    descending_by = "81"
  )

knitr::kable(head(tbl, 10))

## -----------------------------------------------------------------------------
tbl <- adae %>%
  freq(
    denom_df = cdisc_adsl,
    colvar = "TRT01AN",
    rowvar = "AEDECOD",
    rowbyvar = "AESEV",
    statlist = statlist(c("n (x.x)"), denoms_by = "TRT01AN")
  )

knitr::kable(head(tbl, 10))

## ----message=FALSE------------------------------------------------------------
adae <- cdisc_adae %>%
  filter(SAFFL == "Y", TRTEMFL == "Y") %>%
  filter(AEBODSYS %in% c(
    "GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS",
    "SKIN AND SUBCUTANEOUS TISSUE DISORDERS"
  )) %>%
  rename(TRT01AN = TRTAN)

adsl <- cdisc_adsl %>%
  filter(SAFFL == "Y")

## -----------------------------------------------------------------------------
tbl <- nested_freq(adae,
  denom_df = adsl,
  colvar = "TRT01AN",
  rowvar = "AEBODSYS*AEDECOD",
  statlist = statlist("n (x.x%)"),
  descending_by = "81",
  row_header = "System organ class \\\n Preferred term"
)

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- nested_freq(adae,
  denom_df = adsl,
  colvar = "TRT01AN",
  rowvar = "AEBODSYS*AEDECOD",
  statlist = statlist("n (x.x%)"),
  descending_by = "81",
  cutoff = 2,
  cutoff_stat = "n",
  row_header = "System organ class \\\n Preferred term"
)

knitr::kable(tbl)

## -----------------------------------------------------------------------------
tbl <- nested_freq(adae,
  denom_df = adsl,
  colvar = "TRT01AN",
  rowvar = "AEBODSYS*AEDECOD",
  statlist = statlist("n (x.x%)"),
  descending_by = "81",
  cutoff = "81 >= 2",
  cutoff_stat = "n",
  row_header = "System organ class \\\n Preferred term"
)

knitr::kable(tbl)