Output
Here is an image of the first page of the RTF report produced by the above 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.
Note the following about this example:
datastep
function from the libr package.header = TRUE parameter.footer = TRUE parameter.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.library(tidyverse)
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")
vsot <- vso |>
group_by(USUBJID, VISITNUM, VISIT) |>
pivot_wider(names_from = VSTESTCD,
values_from = VSCOMB) |>
ungroup() |>
arrange(USUBJID, VISITNUM) |> put()
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()Here is an image of the first page of the RTF report produced by the above subject listing:
Here is the log produced by the above subject listing:
=========================================================================
Log Path: C:/Users/dbosa/AppData/Local/Temp/RtmpeYEHwE/log/example11.log
Program Path: C:/packages/Testing/example11.R
Working Directory: C:/packages/Testing
User Name: dbosa
R Version: 4.2.1 (2022-06-23 ucrt)
Machine: SOCRATES x86-64
Operating System: Windows 10 x64 build 19044
Base Packages: stats graphics grDevices utils datasets methods base Other
Packages: tidylog_1.0.2 reporter_1.3.7 libr_1.2.6 fmtr_1.5.9 logr_1.3.3
sassy_1.0.8 forcats_0.5.2 stringr_1.4.0 dplyr_1.0.10 purrr_0.3.4 readr_2.1.2
tidyr_1.2.0 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.1 cranlogs_2.1.1
common_1.0.5
Log Start Time: 2022-10-09 19:18:43
=========================================================================
=========================================================================
Prepare formats
=========================================================================
# A user-defined format: 4 conditions
Name Type Expression Label Order
1 obj U x == "WHITE" White NA
2 obj U x == "BLACK OR AFRICAN AMERICAN" Black or African American NA
3 obj U x == "ASIAN OR PACIFIC ISLANDER" Asian or Pacific Islander NA
4 obj U TRUE Other NA
# A user-defined format: 3 conditions
Name Type Expression Label Order
1 obj U x == "NOT HISPANIC OR LATINO" Not Hispanic or Latino NA
2 obj U x == "HISPANIC OR LATINO" Hispanic or Latino NA
3 obj U TRUE Unknown NA
# A user-defined format: 5 conditions
Name Type Expression Label Order
1 obj U x == "ARM A" Placebo NA
2 obj U x == "ARM B" Drug 50mg NA
3 obj U x == "ARM C" Drug 100mg NA
4 obj U x == "ARM D" Competitor NA
5 obj U TRUE Not Treated/Screen Failure NA
# A user-defined format: 4 conditions
Name Type Expression Label Order
1 obj U x == "BEATS/MIN" bpm NA
2 obj U x == "BREATHS/MIN" brths/min NA
3 obj U x == "C" °C NA
4 obj U x == "mmHg" NA
# A user-defined format: 8 conditions
Name Type Expression Label Order
1 obj U x == "DAY 1" Day 1 NA
2 obj U x == "WEEK 2" Week 2 NA
3 obj U x == "WEEK 4" Week 4 NA
4 obj U x == "WEEK 6" Week 6 NA
5 obj U x == "WEEK 8" Week 8 NA
6 obj U x == "WEEK 12" Week 12 NA
7 obj U x == "WEEK 16" Week 16 NA
8 obj U TRUE Early Termination NA
# A format catalog: 10 formats
- $SEX: type V, 2 elements
- $AGE: type S, "%d Years"
- $RACE: type U, 4 conditions
- $WEIGHT: type S, "%6.2f kg"
- $EAR: type V, 2 elements
- $DOSE: type S, "%4.2fug"
- $ETHNIC: type U, 3 conditions
- $ARMT: type U, 5 conditions
- $UNITS: type U, 4 conditions
- $VISIT: type U, 8 conditions
=========================================================================
Prepare Data
=========================================================================
# library 'sdtm': 8 items
- attributes: csv not loaded
- path: C:/Users/dbosa/AppData/Local/R/win-library/4.2/sassy/extdata
- items:
Name Extension Rows Cols Size LastModified
1 AE csv 150 27 88.5 Kb 2022-09-05 10:57:47
2 DA csv 3587 18 528.2 Kb 2022-09-05 10:57:47
3 DM csv 87 24 45.5 Kb 2022-09-05 10:57:47
4 DS csv 174 9 34.1 Kb 2022-09-05 10:57:47
5 EX csv 84 11 26.4 Kb 2022-09-05 10:57:47
6 IE csv 2 14 13.4 Kb 2022-09-05 10:57:47
7 SV csv 685 10 70.3 Kb 2022-09-05 10:57:47
8 VS csv 3358 17 467.4 Kb 2022-09-05 10:57:47
lib_load: library 'sdtm' loaded
Format desired vital signs
datastep: columns decreased from 17 to 5
# A tibble: 2,764 × 5
USUBJID VSTESTCD VSCOMB VISITNUM VISIT
<chr> <chr> <chr> <dbl> <chr>
1 ABC-01-049 DIABP "76 " 1 DAY 1
2 ABC-01-049 DIABP "66 " 2 WEEK 2
3 ABC-01-049 DIABP "84 " 4 WEEK 4
4 ABC-01-049 DIABP "68 " 6 WEEK 6
5 ABC-01-049 DIABP "80 " 8 WEEK 8
6 ABC-01-049 DIABP "70 " 12 WEEK 12
7 ABC-01-049 DIABP "70 " 16 WEEK 16
8 ABC-01-049 PULSE "84 bpm" 1 DAY 1
9 ABC-01-049 PULSE "84 bpm" 2 WEEK 2
10 ABC-01-049 PULSE "76 bpm" 4 WEEK 4
# … with 2,754 more rows
# ℹ Use `print(n = ...)` to see more rows
Pivot vitals signs
group_by: 3 grouping variables (USUBJID, VISITNUM, VISIT)
pivot_wider: reorganized (VSTESTCD, VSCOMB) into (DIABP, PULSE, RESP, SYSBP, TEMP) [was 2764x5, now 554x8]
ungroup: no grouping variables
# A tibble: 554 × 8
USUBJID VISITNUM VISIT DIABP PULSE RESP SYSBP TEMP
<chr> <dbl> <chr> <chr> <chr> <chr> <chr> <chr>
1 ABC-01-049 1 DAY 1 "76 " 84 bpm 20 brths/min "120 " 36.4°C
2 ABC-01-049 2 WEEK 2 "66 " 84 bpm 16 brths/min "128 " 36.6°C
3 ABC-01-049 4 WEEK 4 "84 " 76 bpm 16 brths/min "134 " 35.7°C
4 ABC-01-049 6 WEEK 6 "68 " 64 bpm 20 brths/min "100 " 36.5°C
5 ABC-01-049 8 WEEK 8 "80 " 84 bpm 16 brths/min "128 " 36.4°C
6 ABC-01-049 12 WEEK 12 "70 " 60 bpm 20 brths/min "120 " 36.6°C
7 ABC-01-049 16 WEEK 16 "70 " 72 bpm 18 brths/min "130 " 36.2°C
8 ABC-01-050 1 DAY 1 "78 " 68 bpm 18 brths/min "100 " 36.7°C
9 ABC-01-050 2 WEEK 2 "64 " 68 bpm 18 brths/min "110 " 36.7°C
10 ABC-01-050 4 WEEK 4 "86 " 82 bpm 16 brths/min "128 " 36.6°C
# … with 544 more rows
# ℹ Use `print(n = ...)` to see more rows
Assign and apply formats
# A tibble: 87 × 24
STUDYID DOMAIN USUBJID SUBJID RFSTDTC RFENDTC RFXSTDTC RFXENDTC RFICDTC RFPENDTC DTHDTC DTHFL SITEID
<chr> <chr> <chr> <chr> <date> <date> <lgl> <lgl> <date> <date> <lgl> <lgl> <chr>
1 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
2 ABC DM ABC-01-050 050 2006-11-02 NA NA NA 2006-10-25 NA NA NA 01
3 ABC DM ABC-01-051 051 2006-11-02 NA NA NA 2006-10-25 NA NA NA 01
4 ABC DM ABC-01-052 052 2006-11-06 NA NA NA 2006-10-31 NA NA NA 01
5 ABC DM ABC-01-053 053 2006-11-08 NA NA NA 2006-11-01 NA NA NA 01
6 ABC DM ABC-01-054 054 2006-11-16 NA NA NA 2006-11-07 NA NA NA 01
7 ABC DM ABC-01-055 055 2006-12-06 NA NA NA 2006-10-31 NA NA NA 01
8 ABC DM ABC-01-056 056 2006-11-28 NA NA NA 2006-11-21 NA NA NA 01
9 ABC DM ABC-01-113 113 2006-12-05 NA NA NA 2006-11-28 NA NA NA 01
10 ABC DM ABC-01-114 114 2006-12-14 NA NA NA 2006-12-01 NA NA NA 01
# … with 77 more rows, and 11 more variables: BRTHDTC <date>, AGE <chr>, AGEU <chr>, SEX <chr>, RACE <chr>,
# ETHNIC <chr>, ARMCD <chr>, ARM <chr>, ACTARMCD <lgl>, ACTARM <lgl>, COUNTRY <lgl>
# ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names
Prepare final data for reporting
datastep: columns increased from 24 to 36
# A tibble: 554 × 36
STUDYID DOMAIN USUBJID SUBJID RFSTDTC RFENDTC RFXSTDTC RFXENDTC RFICDTC RFPENDTC DTHDTC DTHFL SITEID
<chr> <chr> <chr> <chr> <date> <date> <lgl> <lgl> <date> <date> <lgl> <lgl> <chr>
1 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
2 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
3 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
4 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
5 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
6 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
7 ABC DM ABC-01-049 049 2006-11-07 NA NA NA 2006-10-25 NA NA NA 01
8 ABC DM ABC-01-050 050 2006-11-02 NA NA NA 2006-10-25 NA NA NA 01
9 ABC DM ABC-01-050 050 2006-11-02 NA NA NA 2006-10-25 NA NA NA 01
10 ABC DM ABC-01-050 050 2006-11-02 NA NA NA 2006-10-25 NA NA NA 01
# … with 544 more rows, and 23 more variables: BRTHDTC <date>, AGE <chr>, AGEU <chr>, SEX <chr>, RACE <chr>,
# ETHNIC <chr>, ARMCD <chr>, ARM <chr>, ACTARMCD <lgl>, ACTARM <lgl>, COUNTRY <lgl>, VISITNUM <dbl>, VISIT <chr>,
# DIABP <chr>, PULSE <chr>, RESP <chr>, SYSBP <chr>, TEMP <chr>, BASELINE <chr>, BP <chr>, TREATMENT <chr>, PG <dbl>,
# PTCNT <dbl>
# ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names
=========================================================================
Create and Print Report
=========================================================================
# A report specification: 29 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpeYEHwE/example11.rtf'
- output_type: RTF
- units: inches
- orientation: landscape
- margins: top 1 bottom 1 left 1 right 1
- line size/count: 9/37
- page_header: left=Program:C:/packages/Testing/example11.R right=Draft
- page_footer: left=Date: 09OCT2022 19:18:50 center=Archytas right=Page [pg] of [tpg]
- content:
# A table specification:
- data: tibble 'final' 554 rows 36 cols
- show_cols: none
- use_attributes: all
- width: 9
- stub: BASELINE TREATMENT 'Subject/Treatment' align='left'
- define: BASELINE dedupe='TRUE'
- define: TREATMENT
- define: VISIT 'Visit'
- define: TEMP 'Temperature'
- define: PULSE 'Pulse'
- define: RESP 'Respirations'
- define: BP 'Blood Pressure'
- define: USUBJID visible='FALSE'
- define: PG visible='FALSE' page_break='TRUE'
# A report specification: 29 pages
- file_path: 'C:\Users\dbosa\AppData\Local\Temp\RtmpeYEHwE/example11.pdf'
- output_type: PDF
- units: inches
- orientation: landscape
- margins: top 1 bottom 1 left 1 right 1
- line size/count: 9/42
- page_header: left=Program:C:/packages/Testing/example11.R right=Draft
- title 1: 'Study: ABC'
- title 2: 'Appendix 10.2.6.1.2.1'
- title 3: 'Source: DM, VS'
- title 4: 'Subject Listing with Vital Signs by Visit¹'
- title 5: 'All Randomized Patients'
- footnote 1: '¹ Baseline through completion of study or early termination.'
- footnote 2: 'Values flagged with † were excluded from the by-visit analysis in tables showing the qualitative test results.'
- page_footer: left=Date: 09OCT2022 19:18:50 center=Archytas right=Page [pg] of [tpg]
- content:
# A table specification:
- data: tibble 'final' 554 rows 36 cols
- show_cols: none
- use_attributes: all
- width: 9
- stub: BASELINE TREATMENT 'Subject/Treatment' align='left'
- define: BASELINE dedupe='TRUE'
- define: TREATMENT
- define: VISIT 'Visit'
- define: TEMP 'Temperature'
- define: PULSE 'Pulse'
- define: RESP 'Respirations'
- define: BP 'Blood Pressure'
- define: USUBJID visible='FALSE'
- define: PG visible='FALSE' page_break='TRUE'
lib_sync: synchronized data in library 'sdtm'
lib_unload: library 'sdtm' unloaded
=========================================================================
Log End Time: 2022-10-09 19:18:56
Log Elapsed Time: 0 00:00:12
=========================================================================