inst/doc/tidytlg.R

In tidytlg: Create TLGs using the 'tidyverse'

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "figures"
)

working_dir <- tempdir()

## ----echo=FALSE, out.width = "600px"------------------------------------------
knitr::include_graphics("titles.PNG")

## ----echo=FALSE, out.width = "500px"------------------------------------------
knitr::include_graphics("column_metadata.PNG")

## ----echo=FALSE, out.width = "600px", out.height = "60px"---------------------
knitr::include_graphics("column_header.PNG")

## ----message=FALSE------------------------------------------------------------
# Prep Environment -------------------------------------------------------------------------------------
library(dplyr)
library(haven)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata, "adsl.xpt")))

## ----message=FALSE------------------------------------------------------------
# Process Data -----------------------------------------------------------------------------------------
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  mutate(SEX = factor(SEX, levels = c("M", "F", "U"), labels = c("Male", "Female", "Unknown"))) %>%
  tlgsetup(
    var = "TRT01PN",
    column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
    tbltype = "type3"
  )

## ----message=FALSE------------------------------------------------------------
# Generate Results -------------------------------------------------------------------------------------

## Analysis set row
t1 <- adsl %>%
  freq(
    colvar = "colnbr",
    rowvar = "ITTFL",
    statlist = statlist("n"),
    subset = ITTFL == "Y",
    rowtext = "Analysis set: ITT"
  )

## Univariate summary for AGE
t2 <- adsl %>%
  univar(
    colvar = "colnbr",
    rowvar = "AGE",
    statlist = statlist(c("N", "MEANSD", "MEDIAN", "RANGE", "IQRANGE")),
    decimal = 0,
    row_header = "Age, years"
  )

## Count (percentages) for SEX
t3 <- adsl %>%
  freq(
    colvar = "colnbr",
    rowvar = "SEX",
    statlist = statlist(c("N", "n (x.x%)")),
    row_header = "Gender"
  )

## -----------------------------------------------------------------------------
# Format Results ---------------------------------------------------------------------------------------

tbl <- bind_table(t1, t2, t3,
  column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
  tbltype = "type3"
)

## -----------------------------------------------------------------------------
knitr::kable(tbl)

## -----------------------------------------------------------------------------
tblid <- "Table01"

gentlg(
  huxme = tbl,
  opath = file.path(working_dir),
  file = tblid,
  orientation = "landscape",
  title_file = system.file("extdata/titles.xls", package = "tidytlg")
)[[1]]

## -----------------------------------------------------------------------------
gentlg(
  huxme = tbl,
  format = "HTML",
  print.hux = FALSE,
  file = tblid,
  orientation = "landscape",
  title_file = system.file("extdata/titles.xls", package = "tidytlg")
)[[1]]

## -----------------------------------------------------------------------------
# Prep Environment ---------------------------------------------------------------------------------------
library(dplyr)
library(haven)
library(tidytlg)

adsl <- cdisc_adsl
adae <- cdisc_adae

# Process Data --------------------------------------------------------------------------------------------
adsl <- adsl %>%
  filter(SAFFL == "Y") %>%
  select(USUBJID, SAFFL, TRT01AN, TRT01A)

adae <- adae %>%
  filter(SAFFL == "Y" & TRTEMFL == "Y") %>%
  mutate(
    BSPT = paste(AEBODSYS, "[", AEDECOD, "]"),
    SAEFL = if_else(AESER == "Y", "Yes", "No"),
    DTHFL = if_else(AEOUT == "FATAL", "Yes", "No")
  ) %>%
  select(USUBJID, ASTDY, TRTA, BSPT, AETERM, SAEFL, DTHFL)

tbl <- inner_join(adsl, adae, by = "USUBJID") %>%
  arrange(TRT01AN, USUBJID, ASTDY) %>%
  select(TRT01A, USUBJID, ASTDY, TRTA, BSPT, AETERM, SAEFL, DTHFL) %>%
  filter(USUBJID %in% c("01-701-1015", "01-701-1023"))

# Output Results ------------------------------------------------------------------------------------------
gentlg(
  huxme = tbl,
  tlf = "l",
  format = "HTML",
  print.hux = FALSE,
  orientation = "landscape",
  file = "Listing01",
  title = "Listing of Adverse Events",
  idvars = c("TRT01A", "USUBJID"),
  wcol = 0.15,
  colheader = c(
    "Treatment Group",
    "Subject ID",
    "Study Day of AE",
    "Treatment Period",
    "Body System [Preferred Term]",
    "Verbatim Term",
    "Serious",
    "Fatal"
  )
)[[1]]

## -----------------------------------------------------------------------------
# Prep Environment ---------------------------------------------------------------------------------------
library(dplyr)
library(haven)
library(ggplot2)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata, "adsl.xpt")))

tblid <- "Graph01"

# Process Data --------------------------------------------------------------------------------------------
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  select(USUBJID, ITTFL, TRT01PN, TRT01P, AGE, SEX, HEIGHTBL, WEIGHTBL) %>%
  mutate(SEX = factor(SEX, levels = c("M", "F"), labels = c("Male", "Female")))

# Generate Results ----------------------------------------------------------------------------------------

plot <- ggplot(data = adsl, aes(x = HEIGHTBL, y = WEIGHTBL)) +
  geom_point() +
  labs(
    x = "Baseline Height (cm)",
    y = "Baseline Weight (kg)"
  ) +
  facet_wrap(~SEX, nrow = 1)

# create png file
png(file.path(working_dir, paste0(tblid, ".png")), width = 2800, height = 1300, res = 300, type = "cairo")

plot

dev.off()

# Output Results ------------------------------------------------------------------------------------------

gentlg(
  tlf = "g",
  plotnames = file.path(system.file("extdata", package = "tidytlg"), paste0(tblid, ".png")),
  plotwidth = 10,
  plotheight = 5,
  orientation = "landscape",
  opath = file.path(working_dir), ,
  file = tblid,
  title_file = system.file("extdata/titles.xls", package = "tidytlg")
)

## ----echo=FALSE, out.width = "750px"------------------------------------------
knitr::include_graphics("graph01.PNG")

## -----------------------------------------------------------------------------
library(dplyr)
library(haven)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata, "adsl.xpt")))

# Process data
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  mutate(SEX = factor(SEX, levels = c("M", "F", "U"), labels = c("Male", "Female", "Unknown")))

# define table metadata
table_metadata <- tibble::tribble(
  ~func, ~df, ~rowvar, ~decimal, ~rowtext, ~row_header, ~statlist, ~subset,
  "freq", "adsl", "ITTFL", NA, "Analysis set: ITT", NA, statlist("n"), "ITTFL == 'Y'",
  "univar", "adsl", "AGE", 0, NA, "Age (Years)", NA, NA,
  "freq", "adsl", "SEX", NA, NA, "Gender", statlist(c("N", "n (x.x%)")), NA
) %>%
  mutate(colvar = "TRT01PN")

# Generate results
tbl <- generate_results(table_metadata,
  column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
  tbltype = "type3"
)

# Output results
tblid <- "Table01"

gentlg(
  huxme = tbl,
  format = "HTML",
  print.hux = FALSE,
  file = tblid,
  orientation = "landscape",
  title_file = system.file("extdata/titles.xls", package = "tidytlg")
)[[1]]

## ----message=FALSE------------------------------------------------------------
library(dplyr)
library(haven)
library(tidytlg)

# read adsl from PhUSE test data factory
testdata <- "https://github.com/phuse-org/TestDataFactory/raw/main/Updated/TDF_ADaM/"
adsl <- read_xpt(url(paste0(testdata, "adsl.xpt")))

# Process data
adsl <- adsl %>%
  filter(ITTFL == "Y") %>%
  mutate(SEX = factor(SEX, levels = c("M", "F"), labels = c("Male", "Female")))

# define table metadata
table_metadata <- tibble::tribble(
  ~func, ~df, ~rowvar, ~decimal, ~rowtext, ~row_header, ~statlist, ~subset, ~tablebyvar,
  "univar", "adsl", "AGE", 0, NA, "Age (Years)", NA, NA, "SEX",
  "freq", "adsl", "RACE", NA, NA, "Race", statlist(c("N", "n (x.x%)")), NA, "SEX"
) %>%
  mutate(colvar = "TRT01PN")

# Generate results
tbl <- generate_results(table_metadata,
  column_metadata_file = system.file("extdata/column_metadata.xlsx", package = "tidytlg"),
  tbltype = "type3"
)

# Output results
tblid <- "Table01"

gentlg(
  huxme = tbl,
  format = "HTML",
  print.hux = FALSE,
  file = tblid,
  orientation = "landscape",
  title_file = system.file("extdata/titles.xls", package = "tidytlg")
)[[1]]