In Novartis/subpat: Subpopulation and subgroups shiny modules

knitr::opts_chunk$set(echo = FALSE)
library(knitr)
library(pander)
library(kableExtra)
library(subpat)
library(dplyr)

panderOptions('knitr.auto.asis', FALSE)
panderOptions('keep.line.breaks', TRUE)

# Needs variables in environment:
# subjects
# population
# datasets

if(! is.null(population)) {
  toPandoc(population)
} else {
  pander::pandoc.header("Subpopulation: No sub-population used", level = 1)
}

dataset_names <- names(datasets)
if ("ADSL" %in% dataset_names) {
  # Add ADSL to top
  dataset_names <- union("ADSL", dataset_names)
}

for(s in subjects) {
  cat("\\pagebreak\n")
  pander::pandoc.header(paste0("Subject: ", s), level = 1)

  for(i in seq_along(dataset_names)) {
    pander::pandoc.header(names(datasets)[[i]], level = 2)

    if(length(colnames(datasets[[i]])) > 1) {
      # Remove the subject id since it is already in the header
      filtered_ds <- datasets[[i]] %>%
        filter(get(idvar) == s)

      filtered_ds <- filtered_ds[, !(idvar == colnames(filtered_ds))]

      pander::pander(filtered_ds, split.table=120)
    } else {
      pander::pandoc.p("No columns selected.")
    }


  }
}