[Pomp-commits] r1058 - in pkg/pomp: . R tests

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

Author: kingaa
Date: 2015-01-26 02:35:51 +0100 (Mon, 26 Jan 2015)
New Revision: 1058

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/pomp-methods.R
   pkg/pomp/tests/ou2-mif.Rout.save
Log:
- dimnames of arrays returned by 'states' and 'obs' will have names

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-01-26 01:27:50 UTC (rev 1057)
+++ pkg/pomp/DESCRIPTION	2015-01-26 01:35:51 UTC (rev 1058)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.58-6
-Date: 2015-01-22
+Version: 0.58-7
+Date: 2015-01-25
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

Modified: pkg/pomp/R/pomp-methods.R
===================================================================
--- pkg/pomp/R/pomp-methods.R	2015-01-26 01:27:50 UTC (rev 1057)
+++ pkg/pomp/R/pomp-methods.R	2015-01-26 01:35:51 UTC (rev 1058)
@@ -44,7 +44,9 @@
     vars <- varnames
   else if (!all(vars%in%varnames))
     stop("some elements of ",sQuote("vars")," correspond to no observed variable")
-  object at data[vars,,drop=FALSE]
+  y <- object at data[vars,,drop=FALSE]
+  dimnames(y) <- list(variable=rownames(y),time=time(object))
+  y
 }
 
 ## a simple method to extract the data array
@@ -52,20 +54,20 @@
 setMethod("data.array","pomp",obs.internal)
 
 ## a simple method to extract the array of states
-setMethod(
-          "states",
-          "pomp",
-          function (object, vars, ...) {
-            if (length(object at states)==0) {
-              NULL
-            } else {
-              if (missing(vars))
-                vars <- seq(length=nrow(object at states))
-              object at states[vars,,drop=FALSE]
-            }
-          }
-          )
+states.internal <- function (object, vars, ...) {
+  if (length(object at states)==0) {
+    NULL
+  } else {
+    if (missing(vars))
+      vars <- seq(length=nrow(object at states))
+    x <- object at states[vars,,drop=FALSE]
+    dimnames(x) <- list(variable=rownames(x),time=time(object))
+    x
+  }
+}
 
+setMethod("states","pomp",states.internal)
+
 ## a simple method to extract the vector of times
 setMethod(
           "time",

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2015-01-26 01:27:50 UTC (rev 1057)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2015-01-26 01:35:51 UTC (rev 1058)
@@ -26,12 +26,14 @@
 > set.seed(64857673L)
 > 
 > obs(window(ou2,end=20,start=15))
-        [,1]       [,2]       [,3]      [,4]      [,5]      [,6]
-y1  8.598190   2.199643  -1.134924 -2.564136 -4.915368 -4.338996
-y2 -4.903347 -10.251144 -10.362431 -8.168859 -7.220312 -2.310222
+        time
+variable        15         16         17        18        19        20
+      y1  8.598190   2.199643  -1.134924 -2.564136 -4.915368 -4.338996
+      y2 -4.903347 -10.251144 -10.362431 -8.168859 -7.220312 -2.310222
 > obs(window(ou2,end=5),"y1")
-        [,1]      [,2]     [,3]     [,4]     [,5]
-y1 -1.700816 0.2421701 3.767589 5.685888 3.774526
+        time
+variable         1         2        3        4        5
+      y1 -1.700816 0.2421701 3.767589 5.685888 3.774526
 > 
 > fit1.pfilter <- pfilter(ou2,Np=1000)
 > cat("coefficients at `truth'\n")
@@ -281,4 +283,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 11.452   0.064  11.704 
+ 14.827   0.050  14.879