R/smartest.R

In tonizhong/SMARTAR: Sequential Multiple Assignment Randomized Trial and Adaptive Randomization

#' Conduct statistical tests using a SMART data
#'
#' Return a message that contains the results of
#'  statistical tests to compare the values of adaptive treatment
#'   strategies defined in a SMART data. The statistical tests
#'   include (1) a global test (2) a series of pairwise tests.
#' @param data Input data frame of the SMART data
#' used for analysis, which include the variables of
#'  stage-1 treatments (A1), intermediate outcome (O2),
#'  stage-2 treatment (A2) and final primary outcome (Y).
#'   If stage-1 treatment takes into account baseline
#'   information, baseline information (O1) also needs
#'   to be included.
#' @param family A character string to specify
#' the type of final primary outcome. The default
#' is family=“gaussian”, which refers to the continuous
#'  primary outcome. If family=”binomial” then the primary
#'   outcome will be treated as binary variable.
#' @param method Method used to estimate the value of
#' adaptive treatment strategy. "Gest" for G-computation
#'  method and "IPW" for Inversed Probabiliy Weight
#'  method. Default is method="Gest".
#' @param digits An integer indicating the number of
#'  decimal places for sequence-specific mean and
#'   variance. Default is digits=NULL.
#' @param common If common=TRUE, the pooled variance
#'  across all the treatment sequences are used in
#'   estimation. Otherwise use the sequence-specific
#'    variance. The default is common=FALSE.
#' @param alpha Significant level of confidence
#' interval. The default is alpha=0.05.
#' @param adjust A characteristic string to
#' indicate whether the confidence intervals pairwise
#'  distance adjusted for multiple comparison. The default
#'  is adjust=NULL, which indicated no adjustment for
#'  multiple comparison. If adjust=”Bon”, the CIs are
#'   adjusted for the Bonferroni correction.
#' @param ntest Number of pairwise tests adjusted for
#'  Bonferroni correction
#' @return
#' An objects of “Strategy” is return, which
#' lists all the adaptive treatment strategy defined
#'  in the input data with an index number.
##' \itemize{
##'    \item ATS: Index of the treatment adaptive
##'     treatment strategy defined in the input dataset
##'    \item ds: the sequence of decision makings
##'     that define an adaptive treatment strategy
##'    \item N: number of subjects following an
##'    adaptive treatment strategy in the intut dataset
##'    }
#' An objects of "Global.test" is return,
#' which give the result of the global test.
##' \itemize{
##'    \item size: the total number of subjects
##'    in the input dataset
##'    \item nATS: the total number of adaptive
##'     treatment strategies defined in the input dataset
##'    \item df: the degrees of freedom of the
##'     global test, which is a chisquare test
##'    \item chisq: the chisquare test statistics for the global test
##'    \item Pvalue: the P-value of the global test
##'    }
#' An object of "Pairwise.test"
##' \itemize{
##'    \item label: The labels of pairwise tests.
##'     The details of strategies are shown in $Strategy
##'    \item diff: Estimated pairwise distance between
##'     treatment and control adaptive treatment strategy
##'    \item lower.CI: Lower bound of confidence interval
##'     for pairwise distance
##'    \item upper.CI: Upper bound of confidence interval
##'     for pairwise distance
##'    \item Z: Test statistics of pairwise test
##'    \item P-value: P-value of pairwise test
##'    }
#' @references Murphy, S. A. (2005),``An experimental
#' design for the development of adaptive treatment
#' strategies'' \emph{Statistics in Medicine}, 24, 1455-1481.
#' @references Ogbagaber S. B., Karp, J., and
#' Wahed A.S. (2015), ``Design of sequentially randomization
#'  trials for testing adaptive treatment
#'  strategies,'' \emph{Statistics in Medicine},
#'  DOI: 10.1002/sim.6747.
#'
#' @examples
#'
#'smartest(data=codiacs,family="gaussian",method="Gest",
#'common=FALSE,alpha=0.05,adjust="Bon")
#'
#' @export

smartest<-function(data,family=c("gaussian","binomial")[1],
                  method=c("Gest","IPW")[1],digits=NULL,
                  common=FALSE,alpha=0.05,
                  adjust=NULL,ntest=NULL){
  D<-data
  FA<-family
  Ma<-method
  Al<-alpha
  Aj<-adjust
  Ntest<-ntest
  Com<-common
  Dmat<-as.data.frame(atsscan(data=D))
  chi<-x2test(data=D,family=FA,method=Ma,common=Com)
  pw<-pwtest(data=D,family=FA,method=Ma,
            alpha=Al,adjust=Aj,ntest=Ntest,common=Com)
  message(paste("$Strategy provides the details
                of decision makings under strategy labels (ATS)",
                "$Global.test assesses the
                null hypothesis of no difference
                across all the strategy values",
                "$Pairwise.test compares
                all the pairs of strategies,
                of which the labels are shown in $Strategy",
                sep="\n"))
  if (is.null(Aj)) {message("\n")} else
  if (Aj=="Bon") {message("The P values
                          should compare to the critical
                          value adjusted for the
                          Bonferroni correction \n")}
  if (is.null(digits)){return(list(Strategy=Dmat,
                                   Global.test=chi,
                                   Pairwise.comparisons=pw))}
  else {list(Strategy=Dmat,
             Global.test=round(chi,digits),
             Pairwise.comparisons=cbind(pw$label,
                                        round(pw[,-1],digits)))}
}