[Pomp-commits] r816 - in pkg/pomp: . R tests

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

Author: kingaa
Date: 2013-01-15 11:28:51 +0100 (Tue, 15 Jan 2013)
New Revision: 816

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/mif.R
   pkg/pomp/tests/ou2-mif2.R
   pkg/pomp/tests/ou2-mif2.Rout.save
Log:
- fig bug in mif: non-constant Np was ignored


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-01-14 16:57:25 UTC (rev 815)
+++ pkg/pomp/DESCRIPTION	2013-01-15 10:28:51 UTC (rev 816)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Statistical inference for partially observed Markov processes
 Version: 0.44-1
-Date: 2013-01-10
+Date: 2013-01-15
 Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
 Maintainer: Aaron A. King <kingaa at umich.edu>
 URL: http://pomp.r-forge.r-project.org

Modified: pkg/pomp/R/mif.R
===================================================================
--- pkg/pomp/R/mif.R	2013-01-14 16:57:25 UTC (rev 815)
+++ pkg/pomp/R/mif.R	2013-01-15 10:28:51 UTC (rev 816)
@@ -170,6 +170,8 @@
     if (!missing(cooling.factor) && !(is.na(cooling.factor)))
       warning(sQuote("cooling.factor")," ignored for method = ",sQuote("mif2"),call.=FALSE)
     cooling.factor <- as.numeric(NA)
+    if (Np[1]!=Np[ntimes+1])
+      stop("the first and last values of ",sQuote("Np")," must agree when method = ",sQuote("mif2"))
   } else {
     if (missing(cooling.factor) || is.na(cooling.factor))
       stop("mif error: ",sQuote("cooling.factor")," must be specified",call.=FALSE)
@@ -228,7 +230,7 @@
   obj <- as(object,"pomp")
   
   if (Nmif>0) {
-    tmp.mif <- new("mif",object,particles=particles,Np=Np)
+    tmp.mif <- new("mif",object,particles=particles,Np=Np[1])
   } else {
     pfp <- obj
   }
@@ -272,6 +274,7 @@
                pfilter.internal(
                                 object=obj,
                                 params=P, 
+                                Np=Np,
                                 tol=tol,
                                 max.fail=max.fail,
                                 pred.mean=(n==Nmif),

Modified: pkg/pomp/tests/ou2-mif2.R
===================================================================
--- pkg/pomp/tests/ou2-mif2.R	2013-01-14 16:57:25 UTC (rev 815)
+++ pkg/pomp/tests/ou2-mif2.R	2013-01-15 10:28:51 UTC (rev 816)
@@ -2,11 +2,6 @@
 
 pompExample(ou2)
 
-
-set.seed(1285370209L)
-
-set.seed(409003325L)
-
 pdf(file="ou2-mif2.pdf")
 
 p.truth <- coef(ou2)

Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save	2013-01-14 16:57:25 UTC (rev 815)
+++ pkg/pomp/tests/ou2-mif2.Rout.save	2013-01-15 10:28:51 UTC (rev 816)
@@ -25,11 +25,6 @@
 newly created pomp objects:
  ou2 
 > 
-> 
-> set.seed(1285370209L)
-> 
-> set.seed(409003325L)
-> 
 > pdf(file="ou2-mif2.pdf")
 > 
 > p.truth <- coef(ou2)
@@ -53,7 +48,7 @@
 +              tol=1e-8
 +              )
 Warning message:
-'cooling.factor' ignored for method = 'mif2' 
+'cooling.factor' ignored for method='mif2' 
 > 
 > mif2a <- mif(ou2,Nmif=100,start=guess1,
 +              pars=c('alpha.2','alpha.3'),ivps=c('x1.0','x2.0'),
@@ -71,7 +66,7 @@
 +              tol=1e-8
 +              )  
 Warning message:
-'cooling.fraction' ignored for method != 'mif2' 
+'cooling.fraction' ignored for method!='mif2' 
 > 
 > compare.mif(list(mif1a,mif2a))
 > 
@@ -90,7 +85,7 @@
 +              method="mif2"
 +              )
 Warning message:
-'cooling.factor' ignored for method = 'mif2' 
+'cooling.factor' ignored for method='mif2' 
 > mif1b <- continue(mif1b,Nmif=50)
 > 
 > mif2b <- mif(ou2,Nmif=50,start=guess1,
@@ -120,4 +115,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 42.378   0.072  42.737 
+ 42.274   0.064  42.654