Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# library(ggplot2)
# library(sassy)
#
# options("logr.autolog" = TRUE,
# "logr.notes" = FALSE)
#
# # Get path to temp directory
# tmp <- tempdir()
#
# # Get path to sample data
# pkg <- system.file("extdata", package = "sassy")
#
# # Open log
# lgpth <- log_open(file.path(tmp, "example6.log"))
#
#
# # Prepare Data ------------------------------------------------------------
#
#
#
# sep("Prepare Data")
#
# put("Create libname for csv data")
# libname(sdtm, pkg, "csv")
#
# put("Load data into workspace")
# lib_load(sdtm)
#
# put("Perform joins and basic filters")
# datastep(sdtm.DM, merge = sdtm.VS, merge_by = c("USUBJID" = "USUBJID"),
# keep = v(USUBJID, ARMCD, ARM, VSTESTCD, VSTEST, VSORRES, VISITNUM, VISIT),
# where = expression(VSTESTCD %in% c("SYSBP", "DIABP", "PULSE", "TEMP", "RESP") &
# ARMCD != "SCRNFAIL"), {}) -> prep
#
# put("Change VISIT to factor so it sorts properly")
# prep$VISIT <- factor(prep$VISIT, levels = c("DAY 1", "WEEK 2", "WEEK 4",
# "WEEK 6","WEEK 8", "WEEK 12",
# "WEEK 16"))
# put("Group and summarize")
# proc_means(prep,
# var = VSORRES,
# class = v(ARM, VSTEST, VISITNUM, VISIT),
# options = v(nway, nofreq, notype),
# stats = mean) |>
# datastep(where = expression(VISITNUM > 0 & VISITNUM < 20),{}) -> final
#
# put("Rename variables for clarity")
# names(final) <- toupper(labels(final))
#
#
# # Create Plots ------------------------------------------------------------
#
#
#
# sep("Create plots and print report")
#
# put("Create plot")
# p <- final |>
# ggplot(mapping = aes(y = MEAN, x = VISIT , group = ARM)) +
# geom_point(aes(shape = ARM, color = ARM)) +
# geom_line(aes(linetype = ARM, color = ARM)) +
# scale_x_discrete(name = "Visit") +
# scale_y_continuous(name = "Value")
#
#
# # Create Report -----------------------------------------------------------
#
# put("Construct output path")
# pth <- file.path(tmp, "output/example6.rtf")
#
# put("Define report object")
# rpt <- create_report(pth, output_type = "RTF", font = "Arial") |>
# set_margins(top = 1, bottom = 1) |>
# page_header("Sponsor: Company", "Study: ABC") |>
# page_by(VSTEST, "Vital Sign: ", blank_row = "none") |>
# titles("Figure 1.0", "Vital Signs Change from Baseline",
# "Safety Population", bold = TRUE) |>
# add_content(create_plot(p, 4.5, 9)) |>
# footnotes("R Program: VS_Figure.R") |>
# page_footer(paste0("Date Produced: ", fapply(Sys.time(), "%d%b%y %H:%M")),
# right = "Page [pg] of [tpg]")
#
# put("Write report to file system")
# write_report(rpt)
#
# put("Close libname")
# lib_unload(sdtm)
#
# put("Close log")
# log_close()
#
# # View report
# # file.show(pth)
#
# # View log
# # file.show(lgpth)
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