[Pomp-commits] r983 - in pkg/pomp: R tests

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

Author: kingaa
Date: 2014-06-25 19:39:18 +0200 (Wed, 25 Jun 2014)
New Revision: 983

Modified:
   pkg/pomp/R/abc-methods.R
   pkg/pomp/R/pmcmc-methods.R
   pkg/pomp/tests/ou2-abc.R
   pkg/pomp/tests/ou2-abc.Rout.save
   pkg/pomp/tests/ou2-pmcmc.R
   pkg/pomp/tests/ou2-pmcmc.Rout.save
Log:
- fix problems with 'conv.rec' on 'abc' and 'pmcmc' objects

Modified: pkg/pomp/R/abc-methods.R
===================================================================
--- pkg/pomp/R/abc-methods.R	2014-06-25 17:39:11 UTC (rev 982)
+++ pkg/pomp/R/abc-methods.R	2014-06-25 17:39:18 UTC (rev 983)
@@ -79,7 +79,7 @@
           'abc',
           function (object, pars, ...) {
             if (missing(pars)) pars <- colnames(object at conv.rec)
-            coda::mcmc(object at conv.rec[,pars,drop=FALSE],...)
+            coda::mcmc(object at conv.rec[,pars,drop=FALSE])
           }
           )
 

Modified: pkg/pomp/R/pmcmc-methods.R
===================================================================
--- pkg/pomp/R/pmcmc-methods.R	2014-06-25 17:39:11 UTC (rev 982)
+++ pkg/pomp/R/pmcmc-methods.R	2014-06-25 17:39:18 UTC (rev 983)
@@ -82,7 +82,7 @@
           signature=signature(object='pmcmc'),
           function (object, pars, ...) {
             if (missing(pars)) pars <- colnames(object at conv.rec)
-            coda::mcmc(object at conv.rec[,pars,drop=FALSE],...)
+            coda::mcmc(object at conv.rec[,pars,drop=FALSE])
           }
           )
 

Modified: pkg/pomp/tests/ou2-abc.R
===================================================================
--- pkg/pomp/tests/ou2-abc.R	2014-06-25 17:39:11 UTC (rev 982)
+++ pkg/pomp/tests/ou2-abc.R	2014-06-25 17:39:18 UTC (rev 983)
@@ -3,7 +3,7 @@
 library(pomp) 
 pompExample(ou2)
 
-pdf(file='abc.pdf')
+pdf(file='ou2-abc.pdf')
 
 set.seed(2079015564L)
 
@@ -97,7 +97,8 @@
 plot(abc7 <- c(abc2,abc4))
 plot(abc7,scatter=TRUE)
 plot(conv.rec(c(abc2,abc4)))
-plot(conv.rec(c(abc7,abc6),thin=10,start=5000))
+plot(conv.rec(c(abc7,abc6)))
+plot(window(conv.rec(c(abc7,abc6),c("alpha.1","alpha.2")),thin=20,start=1000))
 
 dev.off()
 

Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save	2014-06-25 17:39:11 UTC (rev 982)
+++ pkg/pomp/tests/ou2-abc.Rout.save	2014-06-25 17:39:18 UTC (rev 983)
@@ -28,7 +28,7 @@
 newly created pomp object(s):
  ou2 
 > 
-> pdf(file='abc.pdf')
+> pdf(file='ou2-abc.pdf')
 > 
 > set.seed(2079015564L)
 > 
@@ -125,7 +125,8 @@
 > plot(abc7 <- c(abc2,abc4))
 > plot(abc7,scatter=TRUE)
 > plot(conv.rec(c(abc2,abc4)))
-> plot(conv.rec(c(abc7,abc6),thin=10,start=5000))
+> plot(conv.rec(c(abc7,abc6)))
+> plot(window(conv.rec(c(abc7,abc6),c("alpha.1","alpha.2")),thin=20,start=1000))
 > 
 > dev.off()
 null device 
@@ -134,4 +135,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  9.980   0.064  10.288 
+  9.604   0.052   9.963 

Modified: pkg/pomp/tests/ou2-pmcmc.R
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.R	2014-06-25 17:39:11 UTC (rev 982)
+++ pkg/pomp/tests/ou2-pmcmc.R	2014-06-25 17:39:18 UTC (rev 983)
@@ -76,7 +76,8 @@
 plot(ff <- c(ff,f5))
 plot(conv.rec(c(f2,ff),c("alpha.2","alpha.3")))
 plot(conv.rec(ff[2],c("alpha.2")))
-plot(conv.rec(ff[2:3],c("alpha.3"),thin=3,start=2))
+plot(conv.rec(ff[2:3],c("alpha.3")))
+plot(window(conv.rec(ff[2:3],c("alpha.3")),thin=3,start=2))
 plot(conv.rec(ff[[3]],c("alpha.3")))
 
 dev.off()

Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save	2014-06-25 17:39:11 UTC (rev 982)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save	2014-06-25 17:39:18 UTC (rev 983)
@@ -107,7 +107,8 @@
 > plot(ff <- c(ff,f5))
 > plot(conv.rec(c(f2,ff),c("alpha.2","alpha.3")))
 > plot(conv.rec(ff[2],c("alpha.2")))
-> plot(conv.rec(ff[2:3],c("alpha.3"),thin=3,start=2))
+> plot(conv.rec(ff[2:3],c("alpha.3")))
+> plot(window(conv.rec(ff[2:3],c("alpha.3")),thin=3,start=2))
 > plot(conv.rec(ff[[3]],c("alpha.3")))
 > 
 > dev.off()
@@ -117,4 +118,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 23.325   0.088  23.646 
+ 24.093   0.136  24.494