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RTF Examples for Tables with Sublineby, Pageby, and Groupby Features

Source: vignettes/example-sublineby-pageby-groupby.Rmd
example-sublineby-pageby-groupby.Rmd

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 "-----".

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())
## `summarise()` has grouped output by 'TRT01P'. You can override using the
## `.groups` argument.
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))
pagebyvar DCREASCD Xanomeline High Dose Xanomeline Low Dose Placebo
—– Participants randomized 84 84 86
—– Participants treated 84 84 86
—– Participants completed 27 25 58
—– Participants discontinued 57 59 28
Discontinued reason Adverse Event 40 44 8
Discontinued reason Death 0 1 2

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.

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))
AEDECOD 0 54 81 AEBODSYS
Participants in population 86 84 84 a
with one or more severe AE 7 16 8 a
with no severe AE 79 68 76 a
NA NA NA NA a
cardiac disorders 3 0 1 cardiac disorders
atrial fibrillation 0 0 1 cardiac disorders

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.

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))
USUBJID ASTDY AEDECD1 DUR AESEV AESER AEREL AEACN AEOUT TRTA SUBJLINE SUBLINEBY
200 01-701-1360 3 APPLICATION SITE PRURITUS NA MODERATE N PROBABLE NOT RECOVERED/NOT RESOLVED Xanomeline High Dose Subject ID = 01-701-1360, Gender = M, Race = WHITE, AGE = 67 Years, TRT = Xanomeline High Dose Trial Number: CDISCPILOT01, Site Number: 701
201 01-701-1360 6 APPLICATION SITE VESICLES NA MODERATE N PROBABLE NOT RECOVERED/NOT RESOLVED Xanomeline High Dose Subject ID = 01-701-1360, Gender = M, Race = WHITE, AGE = 67 Years, TRT = Xanomeline High Dose Trial Number: CDISCPILOT01, Site Number: 701

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")