In Merck/r2rtf: Easily Create Production-Ready Rich Text Format (RTF) Table and Figure

knitr::opts_chunk$set(echo = TRUE)

library(r2rtf)
library(dplyr)
library(tidyr)

Overview

In rtf_body(), r2rtf provided three advanced arguments to customize table layout.

• page_by: The variable is used as section header.
• group_by: The variable only display when it is first appeared.
• subline_by: The variable is used as page subline header.

If one or more of the arguments are used, they need to be properly ordered in subline_by, page_by and group_by.

For page_by, the argument new_page and pageby_header and pageby_row further customize the table layout. Details can be found in the rtf_body() documentation.

We provided three examples below to illustrate the idea.

Example 1: Pageby

We used page_by variable to illustrate how to create a simple disposition table.

Note: This example also illustrate how to avoid row header by setting corresponding value in page_by variable to "-----".

knitr::include_graphics("pdf/pageby-disposition.pdf")

Step 1: Create data for RTF table

data(r2rtf_adsl)
adsl <- r2rtf_adsl

# randomized
row1 <- adsl %>%
  subset(ITTFL == "Y") %>%
  group_by(TRT01P) %>%
  count()

# treated
row2 <- adsl %>%
  subset(SAFFL == "Y") %>%
  group_by(TRT01P) %>%
  summarise(trtn = n())

# completed study
row3 <- adsl %>%
  subset(SAFFL == "Y" & DCREASCD == "Completed") %>%
  group_by(TRT01P) %>%
  summarise(cmpln = n())

# discontinued study
row4 <- adsl %>%
  subset(SAFFL == "Y" & DCREASCD != "Completed") %>%
  group_by(TRT01P) %>%
  summarise(dcn = n())

# discontinuation reason
reas <- adsl %>%
  subset(SAFFL == "Y" & DCREASCD != "Completed") %>%
  group_by(TRT01P, DCREASCD) %>%
  summarise(reasn = n())

ds <- rbind(
  row1 %>% merge(row2, by = "TRT01P") %>%
    merge(row3, by = "TRT01P") %>%
    merge(row4, by = "TRT01P") %>%
    pivot_longer(2:5, names_to = "DCREASCD", values_to = "n") %>%
    pivot_wider(names_from = TRT01P, values_from = "n"),
  reas %>% pivot_wider(names_from = TRT01P, values_from = c("reasn"))
) %>%
  mutate(
    DCREASCD = ifelse(DCREASCD == "n", "Participants randomized",
      ifelse(DCREASCD == "trtn", "Participants treated",
        ifelse(DCREASCD == "cmpln", "Participants completed",
          ifelse(DCREASCD == "dcn", "Participants discontinued", paste0("   ", DCREASCD))
        )
      )
    ),
    pagebyvar = ifelse(substr(DCREASCD, 1, 5) == "Parti", "-----", "Discontinued reason")
  ) %>%
  # pagebyvar will be assigned to page_by argument in rtf_body function later.
  # then table will be grouped by single cell row with pagebyvar's value in it.
  # if pagebyvar's value is "-----", the single cell row will be removed from table.

  select(pagebyvar, DCREASCD, "Xanomeline High Dose", "Xanomeline Low Dose", Placebo)

ds[is.na(ds)] <- 0

knitr::kable(head(ds))

Step 2: Define table format

ds_tbl <- ds %>%
  rtf_title("Disposition of Participants", "(ITT Population)") %>%
  rtf_colheader(" | Xanomeline High Dose |Xanomeline Low Dose | Placebo",
    col_rel_width = c(3, 2, 2, 2)
  ) %>%
  rtf_colheader(" | n | n | n ",
    border_top = c("", rep("single", 3)),
    col_rel_width = c(3, rep(2, 3))
  ) %>%
  # the table will be grouped by single cell row with pagebyvar's value in it.
  # if pagebyvar's value is "-----", the single cell row will be removed from table.
  rtf_body(
    page_by = "pagebyvar",
    col_rel_width = c(1, 3, 2, 2, 2),
    text_justification = c("l", "l", rep("c", 3)),
    text_format = c("b", rep("", 4)),
    border_top = c("single", rep("", 4)),
    border_bottom = c("single", rep("", 4)),
  ) %>%
  rtf_footnote(c("This is footnote")) %>%
  rtf_source("Source:  [Study MK9999P001: adam-adsl]")

Step 3: Output

# Output .rtf file
ds_tbl %>%
  rtf_encode() %>%
  write_rtf("rtf/pageby-disposition.rtf")

Example 2: Pageby with pageby_row = "first_row"

We used page_by variable and pageby_row = "first_row" to illustrate how to create a simple adverse events table.

knitr::include_graphics("pdf/pageby-firstrow-ae.pdf")

Step 1: Create data for RTF table

# Read in and merge r2rtf_adsl and r2rtf_adae data
data(r2rtf_adsl)
data(r2rtf_adae)

ana <- r2rtf_adsl %>%
  subset(SAFFL == "Y") %>%
  select(USUBJID, TRT01AN, TRT01A)

# inner join adsl to bring in TRT01AN
aedata <- inner_join(ana, r2rtf_adae, by = "USUBJID") %>%
  filter(AEDECOD != "" & SAFFL == "Y" & AESEV == "SEVERE") %>%
  mutate(
    AEDECOD = tolower(AEDECOD),
    AEBODSYS = tolower(AEBODSYS)
  )

# participants part
overall <- ana %>%
  group_by(TRT01AN) %>%
  summarise(n = n_distinct(USUBJID)) %>%
  mutate(AEDECOD = "Participants in population")

withAE <- aedata %>%
  group_by(TRT01AN) %>%
  summarise(withAE = n_distinct(USUBJID)) %>%
  mutate(AEDECOD = "  with one or more severe AE") %>%
  rename(n = withAE)

woAE <- left_join(overall, withAE, by = "TRT01AN", suffix = c(".x", ".y")) %>%
  mutate(
    woAE = n.x - n.y,
    AEDECOD = "  with no severe AE"
  ) %>%
  select(TRT01AN, AEDECOD, woAE) %>%
  rename(n = woAE)

part1 <- bind_rows(overall, withAE, woAE) %>%
  pivot_wider(names_from = TRT01AN, values_from = n) %>%
  mutate(AEBODSYS = "  a")

# AE part
bodsys <- aedata %>%
  group_by(TRT01AN, AEBODSYS) %>%
  summarise(n = n_distinct(USUBJID))

decod <- aedata %>%
  group_by(TRT01AN, AEBODSYS, AEDECOD) %>%
  summarise(n = n_distinct(USUBJID)) %>%
  arrange(AEBODSYS, AEDECOD)

part2 <- bind_rows(bodsys, decod) %>%
  pivot_wider(names_from = TRT01AN, values_from = n, values_fill = 0) %>%
  arrange(AEBODSYS, !is.na(AEDECOD)) %>%
  mutate(AEDECOD = ifelse(is.na(AEDECOD), AEBODSYS, paste("  ", AEDECOD)))

blank <- tibble(AEBODSYS = "  a")

apr0ae <- bind_rows(part1, blank, part2)

knitr::kable(head(apr0ae))

Step 2: Define table format

apr0ae_rtf <- apr0ae %>%
  rtf_page(orientation = "landscape") %>%
  rtf_title(c("Participants with Severe Adverse Events", "(Incidence \\geq 0% in One or More Treatment Groups)"), "(ASaT Population)") %>%
  rtf_colheader(" | Placebo | Xanomeline Low Dose| Xanomeline High Dose  ",
    col_rel_width = c(5, 2, 2, 2),
    border_bottom = c("", rep("single", 3))
  ) %>%
  rtf_colheader(" | n |  n  | n  ",
    border_top    = c("", rep("single", 3)),
    border_bottom = "single",
    col_rel_width = c(5, rep(2, 3)),
  ) %>%
  rtf_body(
    col_rel_width = c(5, rep(2, 3), 1),
    text_justification = c("l", "c", "c", "c", "l"),
    border_first = "",
    page_by = "AEBODSYS",
    pageby_row = "first_row",
  ) %>%
  rtf_footnote(c("This is footnote")) %>%
  rtf_source("Source:  [Study MK9999P001: adam-adae]")

Step 3: Output

# Output .rtf file
apr0ae_rtf %>%
  rtf_encode() %>%
  write_rtf("rtf/pageby-firstrow-ae.rtf")

Example 3: sublineby, pageby, and groupby features

We used page_by, subline_by and group_by to illustrate how to create a simple adverse events listing.

knitr::include_graphics("pdf/pageby-ae-listing.pdf")

Step 1: Create data for RTF table

data(r2rtf_adae)

ae_t1 <- r2rtf_adae[200:260, ] %>%
  mutate(
    SUBLINEBY = paste0(
      "Trial Number: ", STUDYID,
      ", Site Number: ", SITEID
    ),
    SUBJLINE = paste0(
      "Subject ID = ", USUBJID,
      ", Gender = ", SEX,
      ", Race = ", RACE,
      ", AGE = ", AGE, " Years",
      ", TRT = ", TRTA
    ),
    # create a subject line with participant's demographic information.
    # this is for page_by argument in rtf_body function
    AEDECD1 = tools::toTitleCase(AEDECOD), # propcase the AEDECOD
    DUR = paste(ADURN, ADURU, sep = " ")
  ) %>% # AE duration with unit
  select(USUBJID, ASTDY, AEDECD1, DUR, AESEV, AESER, AEREL, AEACN, AEOUT, TRTA, SUBJLINE, SUBLINEBY) # display variable using this order

knitr::kable(head(ae_t1, 2))

Step 2: Define table format

ae_tbl <- ae_t1 %>%
  # It is important to order variable properly.
  arrange(SUBLINEBY, TRTA, SUBJLINE, USUBJID, ASTDY) %>%
  rtf_page(orientation = "landscape", col_width = 9) %>%
  rtf_page_header() %>%
  rtf_page_footer(text = "CONFIDENTIAL") %>%
  rtf_title(
    "Listing of Subjects With Serious Adverse Events",
    "ASaT"
  ) %>%
  rtf_colheader("Subject| Rel Day | Adverse | | | | |Action| |",
    col_rel_width = c(2.5, 2, 4, 2, 3, 2, 3, 2, 5)
  ) %>%
  rtf_colheader("ID| of Onset | Event | Duration | Intensity | Serious |
                Related | Taken| Outcome",
    border_top = "",
    col_rel_width = c(2.5, 2, 4, 2, 3, 2, 3, 2, 5)
  ) %>%
  rtf_body(
    col_rel_width = c(2.5, 2, 4, 2, 3, 2, 3, 2, 5, 1, 1, 1),
    text_justification = c("l", rep("c", 8), "l", "l", "l"),
    text_format = c(rep("", 9), "b", "", "b"),
    border_top = c(rep("", 9), "single", "single", "single"),
    border_bottom = c(rep("", 9), "single", "single", "single"),
    subline_by = "SUBLINEBY",
    page_by = c("TRTA", "SUBJLINE"),
    group_by = c("USUBJID", "ASTDY")
  ) %>%
  rtf_footnote(c("This is footnote 1")) %>%
  rtf_source("Source:  [Study MK9999P001: adam-adae]")

Step 3: Output

# Output .rtf file
ae_tbl %>%
  rtf_encode() %>%
  write_rtf("rtf/pageby-ae-listing.rtf")

Merck/r2rtf documentation built on April 18, 2024, 11:51 a.m.