[Depmix-commits] r58 - trunk

[noreply at r-forge.r-project.org]

Author: ingmarvisser
Date: 2008-03-07 10:21:34 +0100 (Fri, 07 Mar 2008)
New Revision: 58

Added:
   trunk/viterbi2.R
Removed:
   trunk/viterbi.r
Modified:
   trunk/depmix-test1.R
Log:
Renamed viterbi to .R instead of .r

Modified: trunk/depmix-test1.R
===================================================================
--- trunk/depmix-test1.R	2008-03-06 23:39:46 UTC (rev 57)
+++ trunk/depmix-test1.R	2008-03-07 09:21:34 UTC (rev 58)
@@ -40,7 +40,7 @@
 # [1] -296.115107102
 
 
-setwd("/Users/ivisser/Documents/projects/depmixProject/depmixNew/code/depmix/trunk/")
+setwd("/Users/ivisser/Documents/projects/depmixProject/depmixNew/rforge/depmix/trunk/")
 
 source("depmixS4.R")
 source("classes.R")
@@ -48,7 +48,7 @@
 source("lystig.R")
 source("fb.R")
 
-load("speed.Rda")
+load("data/speed.Rda")
 
 # 
 # TEST 1: speed data model with optimal parameters, compute the likelihood

Deleted: trunk/viterbi.r
===================================================================
--- trunk/viterbi.r	2008-03-06 23:39:46 UTC (rev 57)
+++ trunk/viterbi.r	2008-03-07 09:21:34 UTC (rev 58)
@@ -1,64 +0,0 @@
-viterbi <- function(hmm) {
-    # returns the most likely state sequence
-    nt <- sum(hmm at ntimes)
-    lt <- length(hmm at ntimes)
-		et <- cumsum(hmm at ntimes)
-		bt <- c(1,et[-lt]+1)
-		
-    ns <- hmm at nstates
-    
-    delta <- psi <- matrix(nrow=nt,ncol=ns)
-    state <- vector(length=nt)
-    
-    prior <- exp(logDens(hmm at initModel))
-    
-    A <- hmm at trans
-    B <- apply(hmm at logdens,c(1,3),sum)
-    
-    for(case in 1:lt) {
-    # initialization
-      delta[bt[case],] <- - (log(prior[case,]) + B[bt[case],])
-      psi[bt[case],] <- 0
-      # recursion
-      for(i in ((bt[case]+1):et[case])) {
-          for(j in 1:ns) {
-              delta[i,j] <- min(delta[i-1,] - log(A[i,,j])) - B[i,j]
-              k <- which.min(delta[i-1,] - log(A[i,,j]))
-              if(length(k) == 0) k <- 0
-              psi[i,j] <- k
-          }
-      }
-      #trace maximum likely state
-      state[et[case]] <- which.min(delta[et[case],])
-      for(i in (et[case]-1):bt[case]) {
-          state[i] <- psi[i+1,state[i+1]]
-      }
-    }
-    return(state)
-}
-
-viterbi.fb <- function(A,B,prior) {
-    # returns the most likely state sequence
-    nt <- nrow(B)
-    ns <- ncol(A)
-    delta <- psi <- matrix(nrow=nt,ncol=ns)
-    state <- vector(length=nt)
-    # initialization
-    delta[1,] <- - (log(prior) + log(B[1,]))
-    psi[1,] <- 0
-    # recursion
-    for(i in 2:nt) {
-        for(j in 1:ns) {
-            delta[i,j] <- min(delta[i-1,] - log(A[,j])) - log(B[i,j])
-            k <- which.min(delta[i-1,] - log(A[,j]))
-            if(length(k) == 0) k <- 0
-            psi[i,j] <- k
-        }
-    }
-    #trace maximum likely state
-    state[nt] <- which.min(delta[nt,])
-    for(i in (nt-1):1) {
-        state[i] <- psi[i+1,state[i+1]]
-    }
-    return(state)
-}
\ No newline at end of file

Copied: trunk/viterbi2.R (from rev 57, trunk/viterbi.r)
===================================================================
--- trunk/viterbi2.R	                        (rev 0)
+++ trunk/viterbi2.R	2008-03-07 09:21:34 UTC (rev 58)
@@ -0,0 +1,64 @@
+viterbi <- function(hmm) {
+    # returns the most likely state sequence
+    nt <- sum(hmm at ntimes)
+    lt <- length(hmm at ntimes)
+		et <- cumsum(hmm at ntimes)
+		bt <- c(1,et[-lt]+1)
+		
+    ns <- hmm at nstates
+    
+    delta <- psi <- matrix(nrow=nt,ncol=ns)
+    state <- vector(length=nt)
+    
+    prior <- exp(logDens(hmm at initModel))
+    
+    A <- hmm at trans
+    B <- apply(hmm at logdens,c(1,3),sum)
+    
+    for(case in 1:lt) {
+    # initialization
+      delta[bt[case],] <- - (log(prior[case,]) + B[bt[case],])
+      psi[bt[case],] <- 0
+      # recursion
+      for(i in ((bt[case]+1):et[case])) {
+          for(j in 1:ns) {
+              delta[i,j] <- min(delta[i-1,] - log(A[i,,j])) - B[i,j]
+              k <- which.min(delta[i-1,] - log(A[i,,j]))
+              if(length(k) == 0) k <- 0
+              psi[i,j] <- k
+          }
+      }
+      #trace maximum likely state
+      state[et[case]] <- which.min(delta[et[case],])
+      for(i in (et[case]-1):bt[case]) {
+          state[i] <- psi[i+1,state[i+1]]
+      }
+    }
+    return(state)
+}
+
+viterbi.fb <- function(A,B,prior) {
+    # returns the most likely state sequence
+    nt <- nrow(B)
+    ns <- ncol(A)
+    delta <- psi <- matrix(nrow=nt,ncol=ns)
+    state <- vector(length=nt)
+    # initialization
+    delta[1,] <- - (log(prior) + log(B[1,]))
+    psi[1,] <- 0
+    # recursion
+    for(i in 2:nt) {
+        for(j in 1:ns) {
+            delta[i,j] <- min(delta[i-1,] - log(A[,j])) - log(B[i,j])
+            k <- which.min(delta[i-1,] - log(A[,j]))
+            if(length(k) == 0) k <- 0
+            psi[i,j] <- k
+        }
+    }
+    #trace maximum likely state
+    state[nt] <- which.min(delta[nt,])
+    for(i in (nt-1):1) {
+        state[i] <- psi[i+1,state[i+1]]
+    }
+    return(state)
+}
\ No newline at end of file