# End-to-End Example

This vignette walks through a program in a fuller context. Here we’re going to create a simple demographics table.

First we’ll start by preparing the data. We’ll use our other package {Tplyr} to take care of the summaries.

    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

Great - our data are presentation ready now. Using {clinify} we’ll get everything ready. Looking at some of these sections:

- We use `clin_auto_page()` to let Word figure out page breaks for us.
- Column headers are set using `clin_column_headers()`. We grabbed our header N’s from {Tplyr} and inserted them here.
- We want our headers and parts of the body center aligned. Remember, we can use {flextable} functions directly on the `clintable` to do this.
- Column widths are set using `clin_col_widths()` by using a proportion of the total desired table width.
- Lastly we’ll add our titles and footnotes. We’re putting current and total pages in the top right of our titles. Given the default styling functions in {clinify}, which you can override yourself, page numbers are auto detected by using the strings `{PAGE}` and `{NUMPAGES}`.

    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)

Protocol: CDISCPILOT01 | Page of
Table 14-2.01
Summary of Demographic and Baseline Characteristics

|  |  | Xanomeline | Xanomeline
--- | --- | --- | --- | ---
|  | Placebo (N=86) | Low Dose (N=84) | High Dose (N=84)
Sex n (%) | Female | 53 ( 61.6%) | 50 ( 59.5%) | 40 ( 47.6%)
| Male | 33 ( 38.4%) | 34 ( 40.5%) | 44 ( 52.4%)
| Missing | 0 | 0 | 0
Age (Years) | n | 86 | 84 | 84
| Mean (SD) | 75.2 ( 8.59) | 75.7 ( 8.29) | 74.4 ( 7.89)
| Median | 76.0 | 77.5 | 76.0
| Q1, Q3 | 69.2, 81.8 | 71.0, 82.0 | 70.8, 80.0
| Min, Max | 52, 89 | 51, 88 | 56, 88
| Missing | 0 | 0 | 0
Age Categories n (%) | 65-80 | 42 ( 48.8%) | 47 ( 56.0%) | 55 ( 65.5%)
| <65 | 14 ( 16.3%) | 8 ( 9.5%) | 11 ( 13.1%)
| >80 | 30 ( 34.9%) | 29 ( 34.5%) | 18 ( 21.4%)
| Missing | 0 | 0 | 0
Race n (%) | AMERICAN INDIAN OR ALASKA NATIVE | 0 | 0 | 1 ( 1.2%)
| ASIAN | 0 | 0 | 0

Source: /my/file/path.R | 13:38 Monday, July 07, 2025

With everything ready to go, we can write our table out to its destination using `write_clindoc()`.

    write_clindoc(ct, "demo_table.docx")