## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

options(rmarkdown.html_vignette.check_title = FALSE)


## ----eval=FALSE, echo=TRUE----------------------------------------------------
# library(sassy)
# 
# options("logr.autolog" = TRUE,
#         "logr.notes" = FALSE)
# 
# # Get temp location for log and report output
# tmp <- tempdir()
# 
# # Open log
# lf <- log_open(file.path(tmp, "example1.log"))
# 
# 
# # Prepare Data ------------------------------------------------------------
# 
# sep("Prepare Data")
# 
# # Get path to sample data
# pkg <- system.file("extdata", package = "libr")
# 
# # Create libname for csv data
# libname(sdtm, pkg, "csv", quiet = TRUE)
# 
# 
# put("Join and prepare data")
# 
# put("Join DM to VS and keep desired columns")
# datastep(sdtm$DM, merge = sdtm$VS, merge_by = USUBJID,
#          keep = v(USUBJID, VSTESTCD, VISIT, VISITNUM, VSSTRESN, ARM, VSBLFL),
#          where = expression(VSTESTCD %in% c("PULSE", "RESP", "TEMP", "DIABP", "SYSBP") &
#                             !(VISIT == "SCREENING" & VSBLFL != "Y")), {}) -> dm_joined
# 
# put("Sort by variables")
# proc_sort(dm_joined, by = v(USUBJID, VSTESTCD, VISITNUM)) -> dm_sorted
# 
# put("Differentiate baseline from treated vital signs")
# datastep(dm_sorted, by = v(USUBJID, VSTESTCD),
#          retain = list(BSTRESN = 0), {
# 
#   # Combine treatment groups
#   # And distinguish baseline time points
#   if (ARM == "ARM A") {
#     if (VSBLFL %eq% "Y") {
#       GRP <- "A_BASE"
#     } else {
#       GRP <- "A_TRT"
#     }
#   } else {
#     if (VSBLFL %eq% "Y") {
#       GRP <- "O_BASE"
#     } else {
#       GRP <- "O_TRT"
#     }
#   }
# 
#   # Populate baseline value
#   if (first.)
#     BSTRESN = VSSTRESN
# 
# }) -> prep
# 
# 
# put("Get population counts")
# pop_A <- subset(prep, GRP == "A_BASE", v(USUBJID, GRP)) |>
#   proc_sort(options = nodupkey) |>
#   proc_freq(tables = GRP,
#             options = v(nocum, nonobs, nopercent),
#             output = long) |>
#   subset(select = "A_BASE", drop = TRUE)
# 
# pop_O <- subset(prep, GRP == "O_BASE", v(USUBJID, GRP)) |>
#   proc_sort(options = nodupkey) |>
#   proc_freq(tables = GRP,
#             options = v(nocum, nonobs, nopercent),
#             output = long) |>
#   subset(select = "O_BASE", drop = TRUE)
# 
# 
# # Prepare formats ---------------------------------------------------------
# 
# sep("Prepare formats")
# 
# 
# 
# put("Vital sign lookup format")
# vs_fmt <- c(PULSE = "Pulse",
#             TEMP = "Temperature °C",
#             RESP = "Respirations/min",
#             SYSBP = "Systolic Blood Pressure",
#             DIABP = "Diastolic Blood Pressure") |> put()
# 
# put("Statistics lookup format")
# stat_fmt <- c(MEANSTD = "Mean (SD)",
#               MEDIAN = "Median",
#               Q1Q3 = "Q1 - Q3",
#               MINMAX = "Min - Max") |> put()
# 
# 
# put("Create format catalog")
# fc <- fcat(MEAN = "%.1f",
#            STD = "(%.2f)",
#            MEDIAN = "%.1f",
#            Q1 = "%.1f",
#            Q3 = "%.1f",
#            MIN = "%.1f",
#            MAX = "%.1f")
# 
# # Prepare final data frame ------------------------------------------------
# 
# sep("Prepare final data")
# 
# put("Calculate statistics and prepare final data frame")
# proc_means(prep, var = VSSTRESN, class = VSTESTCD, by = GRP,
#            stats = v(mean, std, median, q1, q3, min, max),
#            options = v(notype, nofreq, nway)) |>
#   datastep(format = fc,
#            drop = v(MEAN, STD, Q1, Q3, MIN, MAX, VAR),
#            rename = c("CLASS" = "VAR"),
#            {
#              MEANSTD <- fapply2(MEAN, STD)
#              Q1Q3 <- fapply2(Q1, Q3, sep = " - ")
#              MINMAX <- fapply2(MIN, MAX, sep = " - ")
#            }) |>
#   proc_transpose(id = BY, var = v(MEANSTD, MEDIAN, Q1Q3, MINMAX),
#                  by = VAR, name = "LABEL") -> final
# 
# put("Prepare factor for sorting")
# final$VAR <- factor(final$VAR, names(vs_fmt))
# 
# 
# put("Final sort")
# proc_sort(final, by = VAR) -> final
# 
# 
# # Create Report -----------------------------------------------------------
# sep("Create Report")
# 
# 
# # Define table object
# tbl <- create_table(final) |>
#   spanning_header(A_BASE, A_TRT, "Placebo", n = pop_A) |>
#   spanning_header(O_BASE, O_TRT, "Treated", n = pop_O) |>
#   column_defaults(width = 1.25, align = "center") |>
#   stub(c(VAR, LABEL), width = 2.5) |>
#   define(VAR, "Vital Sign", format = vs_fmt,
#          blank_after = TRUE, dedupe = TRUE, label_row = TRUE) |>
#   define(LABEL, indent = .25, format = stat_fmt) |>
#   define(A_BASE, "Baseline") |>
#   define(A_TRT, "After Treatment") |>
#   define(O_BASE, "Baseline") |>
#   define(O_TRT, "After Treatment")
# 
# 
# # Define report object
# rpt <- create_report(file.path(tmp, "./output/example2.rtf"), output_type = "RTF",
#                      font = "Times", font_size = 12) |>
#   page_header("Sponsor: Company", "Study: ABC") |>
#   titles("Table 4.0", "Selected Vital Signs", bold = TRUE) |>
#   add_content(tbl, align = "center") |>
#   page_footer(Sys.time(), "CONFIDENTIAL", "Page [pg] of [tpg]")
# 
# # Write report to file system
# res <- write_report(rpt)
# 
# 
# # Clean Up ----------------------------------------------------------------
# sep("Clean Up")
# 
# # Close log
# log_close()
# 
# # View report
# # file.show(res$file_path)
# 
# # View log
# # file.show(lf)
# 
#