# Example 11: Subject Listing

Here is an example of a subject listing using the sassy system of functions. The example shows demographics for each patient and vital signs by visit.

## Program

Note the following about this example:

- The example makes extensive use of the `datastep` function from the libr package.
- A label row has been created that spans the width of the page, and contains a selection of demographic attributes of each subject.
- Titles have been placed in the document header using the `header = TRUE` parameter.
- Footnotes have been placed in the document footer using the `footer = TRUE` parameter.
- The `supsc` and `symbol` functions from the common package have been used to create superscripts and symbols in the titles, footnotes, and body of the report.
- A variable “PG” has been created to force a page break every three subjects.
- The program produces both RTF and PDF outputs from the same report object.

    library(sassy)

    # Prepare Log -------------------------------------------------------------

    options("logr.autolog" = TRUE,
            "logr.on" = TRUE,
            "logr.notes" = FALSE)

    # Get path to temp directory
    tmp <- tempdir()

    # Get sample data directory
    dir <- system.file("extdata", package = "sassy")

    # Open log
    lf <- log_open(file.path(tmp, "example11.log"))

    # Prepare formats ---------------------------------------------------------

    sep("Prepare formats")

    fc <- fcat(SEX = c("M" = "Male", "F" = "Female"),
               AGE = "%d Years",
               RACE = value(condition(x == "WHITE", "White"),
                            condition(x == "BLACK OR AFRICAN AMERICAN", "Black or African American"),
                            condition(x == "ASIAN OR PACIFIC ISLANDER", "Asian or Pacific Islander"),
                            condition(TRUE, "Other")),
               WEIGHT = "%6.2f kg",
               EAR = c("L" = "Left", "R" = "Right"),
               DOSE = "%4.2fug",
               ETHNIC = value(condition(x == "NOT HISPANIC OR LATINO", "Not Hispanic or Latino"),
                              condition(x == "HISPANIC OR LATINO", "Hispanic or Latino"),
                              condition(TRUE, "Unknown")),
               ARMT = value(condition(x == "ARM A", "Placebo"),
                            condition(x == "ARM B", "Drug 50mg"),
                            condition(x == "ARM C", "Drug 100mg"),
                            condition(x == "ARM D", "Competitor"),
                            condition(TRUE, "Not Treated/Screen Failure")),
               UNITS = value(condition(x ==  "BEATS/MIN", "bpm"),
                             condition(x == "BREATHS/MIN", "brths/min"),
                             condition(x == "C", symbol("degC")),
                             condition(x == "mmHg", "")),
               VISIT = value(condition(x == "DAY 1", "Day 1"),
                             condition(x == "WEEK 2", "Week 2"),
                             condition(x == "WEEK 4", "Week 4"),
                             condition(x == "WEEK 6", "Week 6"),
                             condition(x == "WEEK 8", "Week 8"),
                             condition(x == "WEEK 12", "Week 12"),
                             condition(x == "WEEK 16", "Week 16"),
                             condition(TRUE, "Early Termination"))
    )

    # Prepare Data ------------------------------------------------------------

    sep("Prepare Data")

    libname(sdtm, dir, "csv")

    lib_load(sdtm)

    put("Format desired vital signs")
    datastep(sdtm.VS,
             keep = v(USUBJID, VSTESTCD, VSCOMB, VISITNUM, VISIT),
             where = expression(VSTESTCD != 'HEIGHT' & VISITNUM > 0),
             {

               if (VSORRESU == "C")
                 VSCOMB <- paste0(VSORRES, fapply(VSORRESU, fc$UNITS))
               else
                 VSCOMB <- paste(VSORRES, fapply(VSORRESU, fc$UNITS))
             }) -> vso

    put("Pivot vitals signs")
    proc_transpose(vso, id = VSTESTCD, var = VSCOMB,
                   by = v(USUBJID, VISITNUM, VISIT)) |>
      proc_sort(by = v(USUBJID, VISITNUM)) -> vsot

    put("Assign and apply formats")
    formats(sdtm.DM) <- fc
    dmf <- fdata(sdtm.DM) |> put()

    put("Prepare final data for reporting")
    datastep(dmf, format = fc,
             by = USUBJID,
             retain = list(PTCNT = 0, PG = 1),
             merge = vsot, merge_by = USUBJID,
             {

               # Combine subject info into label row
               BASELINE <- paste0(USUBJID, ", Site=", SITEID,
                                  ", Age=", AGE, ", Sex=", SEX, ", Race=", RACE,
                                  ", Ethnic=", ETHNIC)

               # Deal with non-recorded blood pressure
               if (is.na(DIABP))
                 DIABP <- "-"

               if (is.na(SYSBP))
                 SYSBP <- "-"

               # Combine distolic and systolic in one column
               BP <- paste0(trimws(DIABP), "/", trimws(SYSBP), " mmHg")

               # Format treatment group
               if (first.)
                 TREATMENT <- fapply(ARM, fc$ARMT)
               else
                 TREATMENT <- ""

               # Count up patients
               if (first.) {
                 PTCNT <- PTCNT + 1
               }

               # Create paging variable with 3 patients per page
               if (PTCNT == 4) {

                 PTCNT <- 1
                 PG <- PG + 1
               }

             }) -> final

    # Create report -----------------------------------------------------------

    sep("Create and Print Report")

    tbl <- create_table(final, show_cols = "none",
                        width = 9, first_row_blank = FALSE,
                        header_bold = TRUE) |>
      column_defaults(from = "VISIT", to = "BP", width = 1.25) |>
      stub(v(BASELINE, TREATMENT), label = "Subject/Treatment") |>
      define(BASELINE, label_row = TRUE) |>
      define(TREATMENT) |>
      define(VISIT, label = "Visit") |>
      define(TEMP, label = "Temperature") |>
      define(PULSE, label = "Pulse") |>
      define(RESP, label = "Respirations") |>
      define(BP, label = "Blood Pressure") |>
      define(USUBJID, blank_after = TRUE, visible = FALSE) |>
      define(PG, page_break = TRUE, visible = FALSE)

    rpt <- create_report(file.path(tmp, "example11"), font = "Courier", font_size = 9) |>
      add_content(tbl) |>
      set_margins(top = 1, bottom = 1) |>
      page_header("Program:" %p% Sys.path(), right = "Draft", width = 7) |>
      titles( "Study: ABC", "Appendix 10.2.6.1.2.1", "Source: DM, VS",
              columns = 3, header = TRUE, blank_row = "none") |>
      titles("Subject Listing with Vital Signs by Visit{supsc('1')}",
             "All Randomized Patients", align = "center", header = TRUE, blank_row = "below") |>
      footnotes("{supsc('1')} Baseline through completion of study or early termination.",
                "Values flagged with {symbol('dagger')} were excluded from the by-visit " %p%
                  "analysis in tables showing the qualitative test results.",
                blank_row = "none", footer = TRUE) |>
      page_footer("Date: " %p% toupper(fapply(Sys.time(), "%d%b%Y %H:%M:%S")),
                  "Archytas", "Page [pg] of [tpg]")

    # Generate both RTF and PDF with same report object
    res1 <- write_report(rpt, output_type = "RTF")
    res2 <- write_report(rpt, output_type = "PDF")

    # Uncomment to show reports
    # file.show(res1$modified_path)
    # file.show(res2$modified_path)

    # Uncomment to show log
    # file.show(lf)

    # Clean Up ----------------------------------------------------------------

    lib_unload(sdtm)

    log_close()

## Output

Here is an image of the first page of the RTF report produced by the above subject listing:

## Log

Here is the log produced by the above subject listing:

    =========================================================================
    Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpkNnsUE/log/example12.log
    Program Path: C:/packages/Testing/procs/ProcsCombinedFigure.R
    Working Directory: C:/packages/Testing/procs
    User Name: dbosa
    R Version: 4.3.1 (2023-06-16 ucrt)
    Machine: SOCRATES x86-64
    Operating System: Windows 10 x64 build 22621
    Base Packages: stats graphics grDevices utils datasets methods base Other
    Packages: tidylog_1.0.2 ggplot2_3.4.2 patchwork_1.1.3 procs_1.0.3
    reporter_1.4.1 libr_1.2.8 fmtr_1.5.9 logr_1.3.4 common_1.0.8 sassy_1.1.0
    Log Start Time: 2023-09-06 21:06:40.53712
    =========================================================================

    =========================================================================
    Prepare Data
    =========================================================================

    Define data library

    # library 'sdtm': 7 items
    - attributes: csv not loaded
    - path: C:/Users/dbosa/AppData/Local/R/win-library/4.3/sassy/extdata
    - items:
      Name Extension Rows Cols     Size        LastModified
    1   AE       csv  150   27  88.5 Kb 2023-08-07 17:51:40
    2   DM       csv   87   24  45.5 Kb 2023-08-07 17:51:40
    3   DS       csv  174    9  34.1 Kb 2023-08-07 17:51:40
    4   EX       csv   84   11  26.4 Kb 2023-08-07 17:51:40
    5   IE       csv    2   14  13.4 Kb 2023-08-07 17:51:40
    6   SV       csv  685   10  70.3 Kb 2023-08-07 17:51:40
    7   VS       csv 3358   17 467.4 Kb 2023-08-07 17:51:40

    Load data into workspace

    lib_load: library 'sdtm' loaded

    Prepare format

    # A user-defined format: 4 conditions
      Name Type        Expression    Label Order
    1  obj    U x >= 18 & x <= 24 18 to 24    NA
    2  obj    U x >= 25 & x <= 44 25 to 44    NA
    3  obj    U x >= 45 & x <= 64 45 to 64    NA
    4  obj    U           x >= 65    >= 65    NA

    Prepare data

    datastep: columns decreased from 24 to 5

    # A tibble: 85 × 5
       USUBJID    SEX     AGE ARM   AGECAT
       <chr>      <chr> <dbl> <chr> <chr>
     1 ABC-01-049 M        39 ARM D 25 to 44
     2 ABC-01-050 M        47 ARM B 45 to 64
     3 ABC-01-051 M        34 ARM A 25 to 44
     4 ABC-01-052 F        45 ARM C 45 to 64
     5 ABC-01-053 F        26 ARM B 25 to 44
     6 ABC-01-054 M        44 ARM D 25 to 44
     7 ABC-01-055 F        47 ARM C 45 to 64
     8 ABC-01-056 M        31 ARM A 25 to 44
     9 ABC-01-113 M        74 ARM D >= 65
    10 ABC-01-114 F        72 ARM B >= 65
    # ℹ 75 more rows
    # ℹ Use `print(n = ...)` to see more rows

    Convert agecat to factor it will sort correctly

    Split by ARM

    =========================================================================
    Create Plots
    =========================================================================

    Create plot for ARM A

    Create plot for ARM B

    Create plot for ARM C

    Create plot for ARM D

    Combine 4 plots into 1 using patchwork

    =========================================================================
    Create and print report
    =========================================================================

    # A report specification: 1 pages
    - file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpkNnsUE/output/example12.rtf'
    - output_type: RTF
    - units: inches
    - orientation: landscape
    - margins: top 1 bottom 1 left 1 right 1
    - line size/count: 9/36
    - page_header: left=Sponsor: Company right=Study: ABC
    - footnote 1: 'Program: DM_Figure.R'
    - page_footer: left=Date Produced: 06Sep23 21:06 center= right=Page [pg] of [tpg]
    - content:
    # A plot specification:
    - height: 4.5
    - width: 7
    - title 1: 'Figure 3.2'
    - title 2: 'Distribution of Subjects by Treatment Group'

    lib_sync: synchronized data in library 'sdtm'

    lib_unload: library 'sdtm' unloaded

    =========================================================================
    Log End Time: 2023-09-06 21:06:43.938549
    Log Elapsed Time: 0 00:00:03
    =========================================================================

Next: Example 12: Combined Figure