R/aquamat_data.R

In erincr/sweetspot: Find and Assess Treatment Effect Sweet Spots in Clinical Trial Data

#' @title Example randomized controlled trial data
#'
#' Data from a randomized controlled trial comparing artesunate to quinine in the treatment of severe falciparum malaria in African children, with outcome in-hospital mortality.
#' Missing values have been imputed with the median.
#'
#' @docType data
#'
#' @usage data(aquamat)
#'
#' @format A dataframe with the AQUAMAT data.
#'
#' @keywords datasets
#'
#' @references 
#' Dondorp, Arjen M., et al. "Artesunate versus quinine in the treatment of severe falciparum malaria in African children (AQUAMAT): an open-label, randomised trial." The Lancet 376.9753 (2010): 1647-1657.
#' (\href{https://www.sciencedirect.com/science/article/pii/S0140673610619241}{The Lancet})
#' Watson, Leopold et al. Collider bias and the apparent protective effect of glucose-6-phosphate dehydrogenase deficiency on cerebral malaria eLife (2019).
#' (\href{https://elifesciences.org/articles/43154}{eLife})
#' Leopold, Watson et al. Investigating causal pathways in severe falciparum malaria: a pooled retrospective analysis of clinical studies In Press, PLoS Medicine (2019).
#' (\href{https://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.1002858}{PLoS Medicine})
#' Watson, J.A., Holmes, C.C. Graphing and reporting heterogeneous treatment effects through reference classes. Trials 21, 386 (2020).
#' (\href{ https://doi.org/10.1186/s13063-020-04306-1}{Trials})
#' Craig, E., Redelmeier, D.A., Tibshirani, R. J. Finding and assessing treatment effect sweet spots in clinical trial data. Arxiv (2020).
#' (\href{https://arxiv.org/abs/2011.10157}{arXiv})
#'
#' @source \href{https://github.com/Stije/SevereMalariaAnalysis}{Github}
#'
#' @examples
#' data(aquamat)
#' covariates <- as.matrix(aquamat[, 1:(ncol(aquamat)-3)])
#' treated    <- aquamat$treated
#' negative.outcome <- aquamat$negative.outcome
#' positive.outcome <- aquamat$positive.outcome
#' \donttest{result <- sweetspot(treated, covariates, negative.outcome, positive.outcome, "binomial")}
#' \donttest{plot_sweetspot(result, title="Sweet spot analysis: AQUAMAT trial")}
"aquamat"