R/newMediatorOutcome.R

In dcoffman/tvmediation: Time Varying Mediation Analysis

#' Function to compute new Mediator and Outcome using time t and t-1 mean centered on the 
#' individual.
#' 
#' Part of the set of internal functions called within the \code{tvma} function to assist 
#' in the estimation of time varying mediation effect.
#' 
#' @param trt     numeric binary treatment group indicator for each individual
#' @param M       (t.seq x N) matrix where N = number of observations. 
#'                Column 1 is mediator at time t-1. Column 2 is mediator at time t.
#' @param Y       (Nx1) matrix were N = number of observations. Column 1 is outcome at time t-1.
#' 
#' @return \item{newMO}{list containing new mediators, outcomes, and index of complete cases}
#' 
#' 

newMediatorOutcome <- function(trt, M, Y) {
  if (dim(M)[2] != 2) {
    stop("Argument Mediator must be Nx2 matrix: ",
         "\n\tMatrix is Nx", dim(M)[2], ".")
  }
  
  N <- length(trt)
  
  M.new <- cbind(c(trt, rep(0, N)),
                 c(rep(0, N), trt),
                 c(rep(0, N), M[,1]))
  Y.new <- c(M[,2], Y)
  
  M.new <- scale(M.new, center = TRUE, scale = FALSE)
  Y.new <- scale(Y.new, center = TRUE, scale = FALSE)
  
  nomissing.M <- complete.cases(M.new)
  nomissing.Y <- complete.cases(Y.new)
  nomissing.index <- nomissing.M * nomissing.Y
  M.new <- M.new[which(nomissing.index == 1), ]
  Y.new <- Y.new[which(nomissing.index == 1)]
  
  newMO <- list(M = M.new, Y = Y.new, nomissingIndex = nomissing.index)
  return(newMO)
}