[Depmix-commits] r137 - in trunk: . R

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

Author: ingmarvisser
Date: 2008-06-09 13:55:55 +0200 (Mon, 09 Jun 2008)
New Revision: 137

Added:
   trunk/R/responseGLMGAMMA.R
Removed:
   trunk/R/responseGLMGAMMA.r
Modified:
   trunk/depmixNew-test2.R
Log:
Changed responseGLMGAMMA.r to responseGLMGAMMA.R (note the capital)

Added: trunk/R/responseGLMGAMMA.R
===================================================================
--- trunk/R/responseGLMGAMMA.R	                        (rev 0)
+++ trunk/R/responseGLMGAMMA.R	2008-06-09 11:55:55 UTC (rev 137)
@@ -0,0 +1,35 @@
+setClass("GAMMAresponse",contains="GLMresponse")
+
+# method 'fit'
+# use: in EM (M step)
+# returns: (fitted) response with (new) estimates of parameters
+
+# methods 'logDens' & dens
+# use: instead of density slot in rModel
+# returns: matrix with log(p(y|x,parameters))
+setMethod("logDens","GAMMAresponse",
+	function(object) {
+		dpois(x=object at y,shape=predict(object),log=TRUE)
+	}
+)
+
+setMethod("dens","GAMMAresponse",
+	function(object,log=FALSE) {
+		dpois(x=object at y,shape=predict(object),log=log)
+	}
+)
+
+setMethod("simulate",signature(object="GAMMAresponse"),
+  function(object,nsim=1,seed=NULL,time) {
+    if(missing(time)) {
+      # draw in one go
+      shape <- predict(object)
+    } else {
+      shape <- predict(object)[time,]
+    }
+    nt <- nrow(shape)
+    response <- rgamma(nt*nsim,shape=shape)
+    if(nsim > 1) response <- matrix(response,ncol=nsim)
+    return(response)
+  }
+)

Deleted: trunk/R/responseGLMGAMMA.r
===================================================================
--- trunk/R/responseGLMGAMMA.r	2008-05-29 10:50:55 UTC (rev 136)
+++ trunk/R/responseGLMGAMMA.r	2008-06-09 11:55:55 UTC (rev 137)
@@ -1,35 +0,0 @@
-setClass("GAMMAresponse",contains="GLMresponse")
-
-# method 'fit'
-# use: in EM (M step)
-# returns: (fitted) response with (new) estimates of parameters
-
-# methods 'logDens' & dens
-# use: instead of density slot in rModel
-# returns: matrix with log(p(y|x,parameters))
-setMethod("logDens","GAMMAresponse",
-	function(object) {
-		dpois(x=object at y,shape=predict(object),log=TRUE)
-	}
-)
-
-setMethod("dens","GAMMAresponse",
-	function(object,log=FALSE) {
-		dpois(x=object at y,shape=predict(object),log=log)
-	}
-)
-
-setMethod("simulate",signature(object="GAMMAresponse"),
-  function(object,nsim=1,seed=NULL,time) {
-    if(missing(time)) {
-      # draw in one go
-      shape <- predict(object)
-    } else {
-      shape <- predict(object)[time,]
-    }
-    nt <- nrow(shape)
-    response <- rgamma(nt*nsim,shape=shape)
-    if(nsim > 1) response <- matrix(response,ncol=nsim)
-    return(response)
-  }
-)

Modified: trunk/depmixNew-test2.R
===================================================================
--- trunk/depmixNew-test2.R	2008-05-29 10:50:55 UTC (rev 136)
+++ trunk/depmixNew-test2.R	2008-06-09 11:55:55 UTC (rev 137)
@@ -22,6 +22,7 @@
 logLik(mod)
 
 mod1 <- fit(mod)
+
 ll <- logLik(mod1)
 
 # 
@@ -42,6 +43,8 @@
 
 cat("Test 1: ", ll, "(loglike of speed data with covariate, hopefully better than 300.5701) \n")
 
+mod2 <- fit(mod,meth="EM")
+
 post <- cbind(viterbi(mod1),speed$Pacc)