R/data-malaria.R

In openintro: Data Sets and Supplemental Functions from 'OpenIntro' Textbooks and Labs

#' Malaria Vaccine Trial
#'
#' Volunteer patients were randomized into one of two experiment groups where
#' they would receive an experimental vaccine or a placebo.  They were
#' subsequently exposed to a drug-sensitive strain of malaria and observed to
#' see whether they came down with an infection.
#'
#' In this study, volunteer patients were randomized into one of two experiment
#' groups: 14 patients received an experimental vaccine or 6 patients received
#' a placebo vaccine.  Nineteen weeks later, all 20 patients were exposed to a
#' drug-sensitive malaria virus strain; the motivation of using a
#' drug-sensitive strain of virus here is for ethical considerations, allowing
#' any infections to be treated effectively.
#'
#' @name malaria
#' @docType data
#' @format A data frame with 20 observations on the following 2 variables.
#' \describe{
#'   \item{treatment}{Whether a person was given the experimental `vaccine` or a `placebo`.}
#'   \item{outcome}{Whether the person got an `infection` or `no infection`.}
#' }
#' @source Lyke et al. 2017. PfSPZ vaccine induces strain-transcending T cells
#' and durable protection against heterologous controlled human malaria
#' infection. PNAS 114(10):2711-2716.
#' \doi{10.1073/pnas.1615324114}.
#' @keywords datasets
#' @examples
#'
#' library(dplyr)
#'
#' # Calculate conditional probabilities of infection after vaccine/placebo
#' malaria %>%
#'   count(treatment, outcome) %>%
#'   group_by(treatment) %>%
#'   mutate(prop = n / sum(n))
#'
#' # Fisher's exact text
#' fisher.test(table(malaria))
"malaria"