[Pomp-commits] r999 - in pkg/mif2: . tests

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

Author: kingaa
Date: 2014-07-15 12:23:19 +0200 (Tue, 15 Jul 2014)
New Revision: 999

Modified:
   pkg/mif2/DESCRIPTION
   pkg/mif2/tests/ou2-mif2.R
   pkg/mif2/tests/ou2-mif2.Rout.save
Log:
- improve description of mif2 package
- use Imports where appropriate
- bring up to date with pomp v. 0.53

Modified: pkg/mif2/DESCRIPTION
===================================================================
--- pkg/mif2/DESCRIPTION	2014-07-15 10:23:16 UTC (rev 998)
+++ pkg/mif2/DESCRIPTION	2014-07-15 10:23:19 UTC (rev 999)
@@ -1,16 +1,17 @@
 Package: mif2
 Type: Package
-Title: Statistical inference for partially observed Markov processes
-Version: 1.0-3
-Date: 2014-05-01
+Title: MIF2 algorithm development package
+Version: 1.0-4
+Date: 2014-07-15
 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")),
 	  person(given="Dao",family="Nguyen",role=c("ctb"))
 	  )
 URL: http://pomp.r-forge.r-project.org
-Description: Inference methods for partially-observed Markov processes
-Depends: R(>= 3.0.0), pomp(>= 0.49-1), methods
+Description: MIF2 algorithm: for eventual integration into pomp
+Depends: R(>= 3.0.0), pomp(>= 0.53-1)
+Imports: methods
 License: GPL(>= 2)
 LazyData: true
 BuildVignettes: true

Modified: pkg/mif2/tests/ou2-mif2.R
===================================================================
--- pkg/mif2/tests/ou2-mif2.R	2014-07-15 10:23:16 UTC (rev 998)
+++ pkg/mif2/tests/ou2-mif2.R	2014-07-15 10:23:19 UTC (rev 999)
@@ -44,7 +44,7 @@
              tol=1e-8
              )  
 
-compare.mif(list(mif1a,mif2a))
+plot(c(mif1a,mif2a))
 
 set.seed(64857673L)
 mif1b <- mif(
@@ -106,10 +106,10 @@
              )  
 mif2c <- continue(mif2c,Nmif=50)
 
-compare.mif(list(mif1b,mif2b))
-compare.mif(list(mif1a,mif1b))
-compare.mif(list(mif2a,mif2b))
-compare.mif(list(mif1b,mif2c))
+plot(c(mif1b,mif2b))
+plot(c(mif1a,mif1b))
+plot(c(mif2a,mif2b))
+plot(c(mif1b,mif2c))
 
 mif3a <- mif2(
               ou2,

Modified: pkg/mif2/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/mif2/tests/ou2-mif2.Rout.save	2014-07-15 10:23:16 UTC (rev 998)
+++ pkg/mif2/tests/ou2-mif2.Rout.save	2014-07-15 10:23:19 UTC (rev 999)
@@ -1,5 +1,5 @@
 
-R version 3.1.0 (2014-04-10) -- "Spring Dance"
+R version 3.1.1 (2014-07-10) -- "Sock it to Me"
 Copyright (C) 2014 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
@@ -21,6 +21,8 @@
 Loading required package: subplex
 Loading required package: nloptr
 Loading required package: deSolve
+Loading required package: coda
+Loading required package: lattice
 > 
 > pompExample(ou2)
 newly created pomp object(s):
@@ -68,7 +70,7 @@
 +              tol=1e-8
 +              )  
 > 
-> compare.mif(list(mif1a,mif2a))
+> plot(c(mif1a,mif2a))
 > 
 > set.seed(64857673L)
 > mif1b <- mif(
@@ -133,10 +135,10 @@
 +              )  
 > mif2c <- continue(mif2c,Nmif=50)
 > 
-> compare.mif(list(mif1b,mif2b))
-> compare.mif(list(mif1a,mif1b))
-> compare.mif(list(mif2a,mif2b))
-> compare.mif(list(mif1b,mif2c))
+> plot(c(mif1b,mif2b))
+> plot(c(mif1a,mif1b))
+> plot(c(mif2a,mif2b))
+> plot(c(mif1b,mif2c))
 > 
 > mif3a <- mif2(
 +               ou2,
@@ -174,4 +176,4 @@
 > 
 > proc.time()
    user  system elapsed 
-273.761   0.368 275.385 
+304.090   0.029 304.494