In Biogen-Inc/tidyCDISC: Quick Table Generation & Exploratory Analyses on ADaM-Ish Datasets

knitr::opts_chunk$set(dev="CairoPNG")

# always_allow_html: true killed my table of contents, maybe it was in the wrong spot.
# should try - 
# title: "Batch Download"
# always_allow_html: true
# output:
#   md_document:
#     toc: blah blah blah
# Could also play around with
# output:
#   md_document:
#   allow_html_dependencies: true

knitr::opts_chunk$set(echo = FALSE,
                      warning=FALSE,
                      message=FALSE,
                      progress = TRUE)
progress$inc(1) # first increment
# don't need these here, because not creating a new environment
# load in applicable packages
# library(tidyverse)
# library(plotly)
# library(knitr)
# library(rmarkdown)
# library(htmltools)
# select data from list
dat <- params$bds_data_
# some summary info, and vector of unique paramcd's
paramcds <- unique(dat$PARAMCD)
np <- length(paramcds)
# pat <- dat$USUBJID[1]
# study <- sub("\\/.*", "", dat$USUBJID[1])
print_report_summary <- !is.na(params$report_summary)
print_user_notes <- (!is.na(params$user_notes) & !rlang::is_null(params$user_notes) & params$user_notes != "")
progress$inc(1) # second increment - after libraries & light data work

knitr::asis_output("### Report Summary\\n") # Header that is only shown if print_option == TRUE

knitr::asis_output(params$report_summary) 

knitr::asis_output("### Notes\\n") # Header that is only shown if print_option == TRUE

knitr::asis_output(params$user_notes) 

Exploratory Plots

# if using ggplot, use results='hide'
plotter <- function(pcd){
  # Create Plot
  fn_output <- fnIndvExplVisits(
      watermark = TRUE,
      graph_output = "plotly",
      bds_data = lb_data,
      usubjid = usubjid(),
      input_plot_hor = input$plot_hor,
      input_visit_var = input$visit_var,
      input_plot_param = pcd,
      input_plot_adam = input$plot_adam,
      input_overlay_events = input$overlay_events,
      vline_dat = vline_dat(),
      vv_dy_name = vv_dy_name()
    )


  progress$inc(1) # increment progress bar


  # format display
  tagList(
    h4(pcd),
    fn_output,
    div(style = "color: #0275d8; font-size: 12px;",
        HTML(ifelse(is.na(params$html_filters),"",params$html_filters))),
    br(), br(), br(), br(),
  )
}
# test just one plot
# tagList(br(), br(), visitPlot(pcd = input$plot_param))
# Use prrrr to create as many plots as their are paramcd's
tagList(br(), br(), purrr::map(.x = paramcds, ~ plotter(pcd = .x)))
progress$inc(1) # last increment

Biogen-Inc/tidyCDISC documentation built on April 22, 2023, 2:12 p.m.