Get Started"

In admiralvaccine: Vaccine Extension Package for ADaM in 'R' Asset Library

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
link <- function(text, url) {
  return(
    paste0(
      "[", text, "]",
      "(", url, ")"
    )
  )
}
dyn_link <- function(text,
                     base_url,
                     relative_url = "",
                     # Change to TRUE when admiral adopts multiversion docs
                     is_multiversion = FALSE,
                     multiversion_default_ref = "main") {
  url <- paste(base_url, relative_url, sep = "/")
  if (is_multiversion) {
    url <- paste(
      base_url,
      Sys.getenv("BRANCH_NAME", multiversion_default_ref),
      relative_url,
      sep = "/"
    )
  }
  return(link(text, url))
}
# Other variables
admiral_homepage <- "https://pharmaverse.github.io/admiral"

Introduction

As this is a package extension, if you are new to {admiral} then the best place to first start reading would be this r dyn_link("Get Started", admiral_homepage, "articles/admiral.html") guide. This extension package follows the same main idea and conventions, and re-uses many functions from {admiral}, so it is important to thoroughly understand these to be able to use {admiralvaccine}.

Derivations

The most important functions in {admiralvaccine} are the derivations. Again these follow the same conventions as {admiral} but are focused to vaccine-specific needs.

Input and Output

It is expected that the input dataset is not grouped. Otherwise an error is issued.

The output dataset is ungrouped. The observations are not ordered in a dedicated way. In particular, the order of the observations of the input dataset may not be preserved.

Starting a Script

For the vaccine ADaM data structures, an overview of the flow and example function calls for the most common steps are provided by the following vignettes:

• Creating ADSL
• Creating ADCE
• Creating ADFACE
• Creating ADIS

{admiralvaccine} also provides template R scripts as a starting point. They can be created by calling use_ad_template() from {admiral}, e.g.,

library(admiral)

use_ad_template(
  adam_name = "adce",
  save_path = "./ad_adce.R",
  package = "admiralvaccine"
)

A list of all available templates can be obtained by list_all_templates() from {admiral}:

list_all_templates(package = "admiralvaccine")

Support

Support is provided via the admiral Slack channel.

admiralvaccine documentation built on Sept. 11, 2024, 6:35 p.m.