R/Inf.D3.calc2.R

In binGroup2: Identification and Estimation using Group Testing

# Start  Inf.D3.calc2() function
###################################################################
# Brianna Hitt

Inf.D3.calc2 <- function(alpha = NULL, probabilities = NULL, 
                         Se, Sp, ordering, group.mem, a, 
                         trace = TRUE, print.time = TRUE, ...) {
  start.time <- proc.time()
  
  I <- ncol(group.mem)
  
  # generate a joint probability vector for each individual
  if (!is.null(probabilities)) {
    joint.p <- probabilities
  } else {
    joint.p <- joint.p.create(alpha = alpha, I = I)
    row.names(joint.p) <- joint.p.row.labels(ordering)
    colnames(joint.p) <- as.character(1:I)
  }
  
  save.info <- TwoDisease.Hierarchical(joint.p = joint.p, group.mem = group.mem, 
                                       Se = Se, Sp = Sp, ordering = ordering, 
                                       a = 1:I, accuracy = TRUE)
  ind.acc1.all <- save.info$Disease1$Individual
  rownames(ind.acc1.all) <- ind.acc1.all[, "Individual"]
  ind.acc1 <- get.unique.index(ind.acc1.all[a,], 
                               which(colnames(ind.acc1.all) == "PSp"), 
                               rowlabel = a)[,-1]
  ind.acc2.all <- save.info$Disease2$Individual
  rownames(ind.acc2.all) <- ind.acc2.all[, "Individual"]
  ind.acc2 <- get.unique.index(ind.acc2.all[a,], 
                               which(colnames(ind.acc2.all) == "PSp"), 
                               rowlabel = a)[,-1]
  acc.dis1 <- save.info$Disease1$Overall
  acc.dis2 <- save.info$Disease2$Overall
  
  save.it <- c(I, save.info$Expt, save.info$Expt / I, acc.dis1, acc.dis2)
  
  accuracy.mat <- matrix(data = save.it[4:11], nrow = 2, ncol = 4, byrow = TRUE, 
                         dimnames = list("Disease" = 1:2, 
                                         c("PSe", "PSp", "PPPV", "PNPV")))
  
  Se.display <- matrix(data = Se, nrow = 2, ncol = 3, 
                       dimnames = list("Disease" = 1:2, "Stage" = 1:3))
  Sp.display <- matrix(data = Sp, nrow = 2, ncol = 3, 
                       dimnames = list("Disease" = 1:2, "Stage" = 1:3))
  
  # print time elapsed, if print.time == TRUE
  if (print.time) {
    time.it(start.time)
  }
  
  list("algorithm" = "Informative three-stage hierarchical testing",
       "joint.p" = probabilities, "alpha.vec" = alpha, 
       "Se" = Se.display, "Sp" = Sp.display, 
       "Config" = list("Stage1" = save.it[1], 
                       "Stage2" = get.pools(group.mem[2,])), 
       "p.mat" = joint.p, "ET" = save.it[2], "value" = save.it[3], 
       "Accuracy" = list("Disease 1 Individual" = ind.acc1,
                         "Disease 2 Individual" = ind.acc2, 
                         "Overall" = accuracy.mat))
}