[Pomp-commits] r1106 - in pkg/pomp: . tests

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

Author: kingaa
Date: 2015-02-27 03:57:40 +0100 (Fri, 27 Feb 2015)
New Revision: 1106

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/tests/ou2-kalman.Rout.save
   pkg/pomp/tests/rw2.Rout.save
   pkg/pomp/tests/synlik.Rout.save
Log:
- update tests

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-02-27 02:57:36 UTC (rev 1105)
+++ pkg/pomp/DESCRIPTION	2015-02-27 02:57:40 UTC (rev 1106)
@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.61-2
+Version: 0.61-3
 Date: 2015-02-26
 Authors at R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa at umich.edu"),

Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save	2015-02-27 02:57:36 UTC (rev 1105)
+++ pkg/pomp/tests/ou2-kalman.Rout.save	2015-02-27 02:57:40 UTC (rev 1106)
@@ -55,7 +55,7 @@
 + }
 > 
 > kalman <- function (x, object, params) {
-+   y <- data.array(object)
++   y <- obs(object)
 +   p <- params
 +   p[names(x)] <- x
 +   x0 <- init.state(object,params=p)
@@ -82,9 +82,6 @@
 Kalman filter log likelihood at truth
 > print(loglik.truth <- -kalman(p.truth,ou2,p.truth),digits=4)
 [1] -479
-Warning message:
-In data.array(object) :
-  'data.array' is deprecated and will be removed in a future release.  Use 'obs' instead.
 > 
 > # make a wild guess
 > p.guess <- p.truth[c('alpha.1','alpha.4','x1.0','x2.0')]*exp(rnorm(n=4,mean=0,sd=0.5))
@@ -97,9 +94,6 @@
 Kalman filter log likelihood at guess
 > print(loglik.guess <- -kalman(p.guess,ou2,p.truth),digits=4)
 [1] -511.8
-Warning message:
-In data.array(object) :
-  'data.array' is deprecated and will be removed in a future release.  Use 'obs' instead.
 > 
 > # find MLE using Kalman filter starting at the guess
 > cat("running Kalman filter estimation\n")
@@ -168,10 +162,9 @@
 HI-REDUCTION     115 477.241051 477.241042
 Exiting from Nelder Mead minimizer
     117 function evaluations used
-There were 50 or more warnings (use warnings() to see the first 50)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 3.404061 secs
+Time difference of 3.41739 secs
 > tic <- Sys.time()
 > print(loglik.mle <- -kalm.fit1$value,digits=4)
 [1] -477.2
@@ -195,4 +188,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.924   0.040   3.956 
+  3.933   0.035   3.954 

Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save	2015-02-27 02:57:36 UTC (rev 1105)
+++ pkg/pomp/tests/rw2.Rout.save	2015-02-27 02:57:40 UTC (rev 1106)
@@ -164,7 +164,7 @@
     }
     y
 }
-<environment: 0x1535468>
+<environment: 0x2300468>
 measurement model density, dmeasure = 
 function (y, x, t, params, log, covars, ...) 
 {
@@ -177,7 +177,7 @@
         f
     else exp(f)
 }
-<environment: 0x1535468>
+<environment: 0x2300468>
 prior simulator, rprior = 
 function not specified
 prior density, dprior = 
@@ -246,10 +246,7 @@
 > x <- simulate(rw2,nsim=10,params=p,obs=T,states=T)
 > x <- simulate(rw2,nsim=10,params=p[,1])
 > 
-> x <- data.array(rw2)
-Warning message:
-In data.array(rw2) :
-  'data.array' is deprecated and will be removed in a future release.  Use 'obs' instead.
+> x <- obs(rw2)
 > t <- time(rw2)
 > 
 > x0 <- init.state(rw2,params=p)
@@ -345,4 +342,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.903   0.036   0.923 
+  0.870   0.033   0.889 

Modified: pkg/pomp/tests/synlik.Rout.save
===================================================================
--- pkg/pomp/tests/synlik.Rout.save	2015-02-27 02:57:36 UTC (rev 1105)
+++ pkg/pomp/tests/synlik.Rout.save	2015-02-27 02:57:40 UTC (rev 1106)
@@ -59,7 +59,7 @@
 + }
 > 
 > kalman <- function (x, object, params) {
-+   y <- data.array(object)
++   y <- obs(object)
 +   p <- params
 +   p[names(x)] <- x
 +   x0 <- init.state(object,params=p)
@@ -76,9 +76,6 @@
 > # exact likelihood
 > p.truth <- coef(po)
 > loglik.truth <- -kalman(p.truth,po,p.truth)
-Warning message:
-In data.array(object) :
-  'data.array' is deprecated and will be removed in a future release.  Use 'obs' instead.
 > 
 > ## likelihood from probes (works since ou2 is Gaussian)
 > loglik.probe <- replicate(n=500,logLik(probe(po,nsim=200,probes=function(x)x)))
@@ -119,4 +116,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  7.404   0.033   7.432 
+  7.286   0.042   7.322