End-to-End Example

library(clinify)
library(Tplyr)
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

tplyr_adsl <- tplyr_adsl |>
  mutate(
    SEX = recode(SEX, M = "Male", F = "Female"),
    RACE = factor(
      RACE,
      c(
        "AMERICAN INDIAN OR ALASKA NATIVE",
        "ASIAN",
        "BLACK OR AFRICAN AMERICAN",
        "NATIVE HAWAIIN OR OTHER PACIFIC ISLANDER",
        "WHITE",
        "MULTIPLE"
      )
    )
  )

t <- tplyr_table(tplyr_adsl, TRT01P) |>
  add_layer(
    group_count(SEX, by = "Sex n (%)") |>
      set_missing_count(f_str("xx", n), Missing = NA, denom_ignore = TRUE)
  ) |>
  add_layer(
    group_desc(AGE, by = "Age (Years)")
  ) |>
  add_layer(
    group_count(AGEGR1, by = "Age Categories n (%)") |>
      set_missing_count(f_str("xx", n), Missing = NA, denom_ignore = TRUE)
  ) |>
  add_layer(
    group_count(RACE, by = "Race n (%)") |>
      set_missing_count(f_str("xx", n), Missing = NA, denom_ignore = TRUE) |>
      set_order_count_method("byfactor")
  ) |>
  add_layer(
    group_count(ETHNIC, by = "Ethnicity n (%)") |>
      set_missing_count(f_str("xx", n), Missing = NA, denom_ignore = TRUE)
  ) |>
  add_layer(
    group_desc(HEIGHTBL, by = "Height at Baseline")
  ) |>
  add_layer(
    group_desc(WEIGHTBL, by = "Weight at Baseline")
  )

# Apply some conditional formatting for blanking out 0's.
dat <- build(t) |>
  mutate(
    across(
      starts_with("var"),
      ~ if_else(
        ord_layer_index %in% c(1, 3:5),
        apply_conditional_format(
          string = .,
          format_group = 2,
          condition = x == 0,
          replacement = ""
        ),
        .
      )
    )
  )

# Sort all the row values out, add row masks and breaks
dat <- dat |>
  arrange(ord_layer_index, ord_layer_1, ord_layer_2) |>
  apply_row_masks() |>
  select(
    starts_with("row_label"),
    var1_Placebo,
    `var1_Xanomeline Low Dose`,
    `var1_Xanomeline High Dose`,
    ord_layer_index
  )

# Grab the header Ns for column header help
header_n <- t$header_n$n
names(header_n) <- t$header_n$TRT01P

ct <- clintable(dat) |>
  # Use group changes to let Word naturally split pages
  clin_auto_page("ord_layer_index", drop = TRUE) |>
  # Add padding to changes within the group
  # By using `notempty`, paging groups are determined by populated
  # values of `row_label1`
  clin_group_pad('row_label1', when = "notempty") |>
  # Assign column headers with spanning rows
  clin_column_headers(
    row_label1 = "",
    row_label2 = "",
    var1_Placebo = sprintf("Placebo\n(N=%s)", header_n["Placebo"]),
    `var1_Xanomeline Low Dose` = c(
      "Xanomeline",
      sprintf("Low Dose\n(N=%s)", header_n["Xanomeline Low Dose"])
    ),
    `var1_Xanomeline High Dose` = c(
      "Xanomeline",
      sprintf("High Dose\n(N=%s)", header_n["Xanomeline High Dose"])
    )
  ) |>
  # Use flextable functions directly to set all of the alignment
  flextable::align(align = "center", part = "header") |>
  flextable::align(
    j = c(
      "var1_Placebo",
      "var1_Xanomeline Low Dose",
      "var1_Xanomeline High Dose"
    ),
    align = "center"
  ) |>
  # Set column widths as proportion of the total document width
  clin_col_widths(
    row_label1 = .17,
    row_label2 = .3,
    var1_Placebo = .176,
    `var1_Xanomeline Low Dose` = .176,
    `var1_Xanomeline High Dose` = .176
  ) |>
  # Add titles here is using new_header_footer to allow flextable functions
  # to customize the titles block
  clin_add_titles(
    list(
      # We'll add tools to automate paging
      c("Protocol: CDISCPILOT01", "Page {PAGE} of {NUMPAGES}"),
      c("Table 14-2.01"),
      c("Summary of Demographic and Baseline Characteristics")
    )
  ) |>
  clin_add_footnotes(
    list(
      c(
        "Source: /my/file/path.R",
        format(Sys.time(), "%H:%M %A, %B %d, %Y")
      )
    )
  )

print(ct)

write_clindoc(ct, "demo_table.docx")