after fixing conflicts

R/PseudovaluesSP_A.R

@@ -0,0 +1,95 @@
+# simplified for debugging
+PseudovaluesSP_A <- function(dataset, FOM) {
+
+  NL <- dataset$ratings$NL
+  LL <- dataset$ratings$LL
+  maxNL <- dim(NL)[4]
+  maxLL <- dim(LL)[4]
+  I <- dim(NL)[1]
+  J <- dim(NL)[2]
+  K <- dim(NL)[3]
+  K2 <- dim(LL)[3]
+  K1 <- K - K2
+
+  t <- dataset$descriptions$truthTableStr
+
+  jkFomValues <- array(dim = c(I, J/I, K))
+  jkPseudoValues <- array(dim = c(I, J/I, K))
+
+  fomArray <- FOM_SP(dataset, FOM) 
+
+  lastCase <- 0
+  caseTransitions <- array(dim = J)
+  for (i in 1:I) {
+    for (j in (J/I*(i-1)+1):(J/I*i)) {
+      j1 <- j-J/I*(i-1) 
+      perCase_ij <- dataset$lesions$perCase 
+      lID_ij <- dataset$lesions$IDs
+      lW_ij <- dataset$lesions$weights
+      nl_ij <- NL[i, j, 1:K, 1:maxNL]; dim(nl_ij) <- c(K, maxNL)
+      ll_ij <- LL[i, j, 1:K2, 1:maxLL]; dim(ll_ij) <- c(K2, maxLL)
+
+      for (k in 1:K) {
+        if (k <= K1) {
+          nl_ij_jk <- nl_ij[-k, ];dim(nl_ij_jk) <- c(K - 1, maxNL)
+          ll_ij_jk <- ll_ij;dim(ll_ij_jk) <- c(K2, maxLL)
+          lID_ij_jk <- lID_ij;dim(lID_ij_jk) <- c(K2, maxLL)
+          lW_ij_jk <- lW_ij;dim(lW_ij_jk) <- c(K2, maxLL)
+          jkFomValues[i, j1, k] <- 
+            MyFom_ij_SP(nl_ij_jk, ll_ij_jk, perCase_ij, 
+                        lID_ij_jk, lW_ij_jk, maxNL, maxLL, 
+                        K1 - 1, K2, FOM)
+
+          jkPseudoValues[i, j1, k] <- 
+            fomArray[i, j1] * K - jkFomValues[i, j1, k] * (K - 1)
+        } else { # (k > K1)
+          nl_ij_jk <- nl_ij[-k, ];dim(nl_ij_jk) <- c(K - 1, maxNL)
+          ll_ij_jk <- ll_ij[-(k - K1), ];dim(ll_ij_jk) <- c(K2 - 1, maxLL)
+          lV_ij_jk <- perCase_ij[-(k - K1)]
+          lW_ij_jk <- lW_ij[-(k - K1), ];dim(lW_ij_jk) <- c(K2 - 1, maxLL)
+          lID_ij_jk <- lID_ij[-(k - K1), ];dim(lID_ij_jk) <- c(K2 - 1, maxLL)
+          jkFomValues[i, j1, k] <- 
+            MyFom_ij_SP(nl_ij_jk, ll_ij_jk, lV_ij_jk, 
+                        lID_ij_jk, lW_ij_jk, maxNL, maxLL, 
+                        K1, K2 - 1, FOM)
+          jkPseudoValues[i, j1, k] <- 
+            fomArray[i, j1] * K - jkFomValues[i, j1, k] * (K - 1)
+        }
+      }
+      # center the pseudovalues 
+      if (FOM %in% c("MaxNLF", "ExpTrnsfmSp", "HrSp")) {
+        # FOMs defined over NORMAL cases
+        jkPseudoValues[i, j1, ] <- jkPseudoValues[i, j1, ] + 
+          (fomArray[i, j1] - mean(jkPseudoValues[i, j1, ]))
+      }  else if (FOM %in% c("MaxLLF", "HrSe")) {
+        # FOMs defined over ABNORMAL cases
+        jkPseudoValues[i, j1, ] <- 
+          jkPseudoValues[i, j1, ] + 
+          (fomArray[i, j1] - mean(jkPseudoValues[i, j1, ]))
+      } else {
+        # FOMs defined over ALL cases
+        jkPseudoValues[i, j1, ] <- 
+          jkPseudoValues[i, j1, ] + (fomArray[i, j1] - mean(jkPseudoValues[i, j1, ]))
+      }
+      caseTransitions[j] <- lastCase
+      lastCase <- (lastCase + K) %% K
+    }
+  }
+
+  # there should not be any NAs in each of the following arrays
+  # any(is.na(jkPseudoValues))
+  # [1] FALSE
+  # any(is.na(jkFomValues))
+  # [1] FALSE
+  # any(is.na(fomArray))
+  # [1] FALSE
+
+  caseTransitions <- c(caseTransitions, K)
+  return(list(
+    jkPseudoValues = jkPseudoValues, 
+    jkFomValues = jkFomValues,
+    caseTransitions = caseTransitions
+  ))
+}
+
+

R/StSP.R

@@ -578,7 +578,7 @@ convert2dataset <- function(NL, LL, LL_IL,
 
 
 
-FOM_SP <- function(dataset, FOM = "wAFROC") { # dpc
+FOM_SP <- function(dataset, FOM) {
 
   # dataType <- dataset$descriptions$type
   # if (dataType == "ROC" && FOM != "Wilcoxon") {
@@ -665,9 +665,9 @@ FOM_SP <- function(dataset, FOM = "wAFROC") { # dpc
 
   modalityID <- dataset$descriptions$modalityID
   # readers in other treatments can have same names as there is not need to 
-  # distinguish between them - by definition readers with same names in 
+  # distinguish between them as, readers with same names in 
   # different treatments are different readers
-  readerID <- dataset$descriptions$readerID[1:(J/2)]
+  readerID <- dataset$descriptions$readerID[1:(J/I)]
   rownames(fomArray) <- paste("trt", sep = "", modalityID)
   colnames(fomArray) <- paste("rdr", sep = "", readerID)
   return(as.data.frame(fomArray))
@@ -677,7 +677,7 @@ FOM_SP <- function(dataset, FOM = "wAFROC") { # dpc
 
 
 
-PseudovaluesSP_A <- function(dataset, FOM) {
+PseudovaluesSP_A1 <- function(dataset, FOM) {
 
   dataType <- dataset$descriptions$type
   NL <- dataset$ratings$NL
@@ -808,7 +808,7 @@ PseudovaluesSP_A <- function(dataset, FOM) {
               jkPseudoValues[i, j1, kIndxAll] <- 
                 fomArray[i, j1] * K_ij - jkFomValues[i, j1, kIndxAll] * (K_ij - 1)
             } else stop("overwriting Pseudovalues")
-          } else {
+          } else { # (k > K1_ij)
             nlij_jk <- nl_ij[-k, ];dim(nlij_jk) <- c(K_ij - 1, maxNL)
             llij_jk <- ll_ij[-(k - K1_ij), ];dim(llij_jk) <- c(K2_ij - 1, maxLL)
             lV_j_jk <- perCase_ij[-(k - K1_ij)]