Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----eval=FALSE, echo=TRUE----------------------------------------------------
# library(tidyverse)
# 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, "example5.log"))
#
# sep("Prepare Data")
#
# # Create libname for csv data
# libname(sdtm, pkg, "csv")
#
# # Load data into workspace
# lib_load(sdtm)
#
# put("Join and prepare data")
# prep <- sdtm.DM |>
# left_join(sdtm.VS, by = c("USUBJID" = "USUBJID")) |>
# select(USUBJID, VSTESTCD, VISIT, VISITNUM, VSSTRESN, ARM, VSBLFL) |>
# filter(VSTESTCD %in% c("PULSE", "RESP", "TEMP", "DIABP", "SYSBP"),
# !(VISIT == "SCREENING" & VSBLFL != "Y")) |>
# arrange(USUBJID, VSTESTCD, VISITNUM) |>
# group_by(USUBJID, VSTESTCD) |>
# datastep(retain = list(BSTRESN = 0), {
#
# # Combine treatment groups
# # And distingish 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
#
# }) |>
# ungroup()
#
# put("Get population counts")
# pop_A <- prep |> select(USUBJID, GRP) |> filter(GRP == "A_BASE") |>
# distinct() |> count() |> deframe() |> put()
# pop_O <- prep |> select(USUBJID, GRP) |> filter(GRP == "O_BASE") |>
# distinct() |> count() |> deframe() |> put()
#
# put("Prepare final data frame")
# final <- prep |>
# select(VSTESTCD, GRP, VSSTRESN, BSTRESN) |>
# group_by(VSTESTCD, GRP) |>
# summarize(Mean = fmt_mean_sd(VSSTRESN),
# Median = fmt_median(VSSTRESN),
# Quantiles = fmt_quantile_range(VSSTRESN),
# Range = fmt_range(VSSTRESN)) |>
# ungroup() |>
# pivot_longer(cols = c(Mean, Median, Quantiles, Range),
# names_to = "stats",
# values_to = "values") |>
# pivot_wider(names_from = GRP,
# values_from = values) |>
# put()
#
#
# sep("Create formats")
#
# # Vital sign lookup format
# vs_fmt <- c(PULSE = "Pulse",
# TEMP = "Temperature °C",
# RESP = "Respirations/min",
# SYSBP = "Systolic Blood Pressure",
# DIABP = "Diastolic Blood Pressure") |>
# put()
#
# # Statistics user-defined format
# stat_fmt <- value(condition(x == "Mean", "Mean (SD)"),
# condition(x == "Quantiles", "Q1 - Q3")) |>
# put()
#
# sep("Create Report")
#
#
# # Apply sort
# final <- final |>
# mutate(VSTESTCD = factor(VSTESTCD, levels = names(vs_fmt))) |>
# arrange(VSTESTCD)
#
# # Define table object
# tbl <- create_table(final, borders = "bottom") |>
# 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(VSTESTCD, stats), width = 2.5) |>
# define(VSTESTCD, "Vital Sign", format = vs_fmt,
# blank_after = TRUE, dedupe = TRUE, label_row = TRUE) |>
# define(stats, indent = .25, format = stat_fmt) |>
# define(A_BASE, "Baseline") |>
# define(A_TRT, "After Treatment") |>
# define(O_BASE, "Baseline") |>
# define(O_TRT, "After Treatment")
#
# # Construct output path
# pth <- file.path(tmp, "output/t_vs.pdf")
#
# # Define report object
# rpt <- create_report(pth, output_type = "PDF", font = "Times",
# font_size = 11) |>
# page_header("Sponsor: Company", "Study: ABC") |>
# titles("Table 4.0", "Selected Vital Signs", bold = TRUE, font_size = 12) |>
# add_content(tbl, align = "center") |>
# page_footer(Sys.time(), "CONFIDENTIAL", "Page [pg] of [tpg]")
#
# # Write report to file system
# write_report(rpt)
#
# # Unload data from workspace
# lib_unload(sdtm)
#
# # Close log
# log_close()
#
# # View files
# # file.show(pth)
# # file.show(lgpth)
#
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