[Pomp-commits] r208 - in pkg: . inst tests

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

Author: kingaa
Date: 2010-03-15 13:54:01 +0100 (Mon, 15 Mar 2010)
New Revision: 208

Added:
   pkg/inst/data-R/
Removed:
   pkg/inst/data-src/
Modified:
   pkg/DESCRIPTION
   pkg/tests/ou2-forecast.Rout.save
   pkg/tests/sir.Rout.save
Log:
- rename data-src data-R
- update the test .Rout.save files


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-03-15 12:45:06 UTC (rev 207)
+++ pkg/DESCRIPTION	2010-03-15 12:54:01 UTC (rev 208)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.28-1
-Date: 2010-03-13
+Version: 0.28-2
+Date: 2010-03-15
 Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall
 Maintainer: Aaron A. King <kingaa at umich.edu>
 Description: Inference methods for partially-observed Markov processes

Copied: pkg/inst/data-R (from rev 207, pkg/inst/data-src)

Modified: pkg/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/tests/ou2-forecast.Rout.save	2010-03-15 12:45:06 UTC (rev 207)
+++ pkg/tests/ou2-forecast.Rout.save	2010-03-15 12:54:01 UTC (rev 208)
@@ -1,6 +1,6 @@
 
-R version 2.9.1 (2009-06-26)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.11.0 Under development (unstable) (2010-02-25 r51179)
+Copyright (C) 2010 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,6 +22,7 @@
 > 
 > set.seed(921625222L)
 > 
+> data(ou2)
 > pf <- pfilter(ou2,Np=1000,save.states=TRUE)
 > ll <- cumsum(pf$cond.loglik)
 > pp <- matrix(data=coef(ou2),nrow=length(coef(ou2)),ncol=1000,dimnames=list(names(coef(ou2)),NULL))

Modified: pkg/tests/sir.Rout.save
===================================================================
--- pkg/tests/sir.Rout.save	2010-03-15 12:45:06 UTC (rev 207)
+++ pkg/tests/sir.Rout.save	2010-03-15 12:54:01 UTC (rev 208)
@@ -1,6 +1,6 @@
 
-R version 2.10.1 (2009-12-14)
-Copyright (C) 2009 The R Foundation for Statistical Computing
+R version 2.11.0 Under development (unstable) (2010-02-25 r51179)
+Copyright (C) 2010 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -423,7 +423,7 @@
     }
     y
 }
-<environment: 0x28d8c68>
+<environment: 0x2c7b448>
 measurement model density, dmeasure = 
 function (y, x, t, params, log, covars, ...) 
 {
@@ -436,7 +436,7 @@
         f
     else exp(f)
 }
-<environment: 0x28d8c68>
+<environment: 0x2c7b448>
 initializer = 
 function (params, t0, ...) 
 {
@@ -507,7 +507,7 @@
 > x <- simulate(po,params=log(params),nsim=3)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 2.041221 secs
+Time difference of 2.009282 secs
 > 
 > pdf(file='sir.pdf')
 > 
@@ -524,7 +524,7 @@
 > X3 <- trajectory(po,params=log(params),times=t3,hmax=1/52)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 4.547439 secs
+Time difference of 4.513309 secs
 > plot(t3,X3['I',1,],type='l')
 > 
 > f1 <- dprocess(
@@ -575,7 +575,7 @@
 R -30746 -26601 -22900 -16156.5  -6714   5662  22453
 > 
 > ## now repeat using the compiled native codes built into the package
-> 
+> data(euler.sir)
 > po <- euler.sir
 > 
 > set.seed(3049953)
@@ -584,7 +584,7 @@
 > x <- simulate(po,nsim=100)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 2.148207 secs
+Time difference of 2.146718 secs
 > plot(x[[1]],variables=c("S","I","R","cases","W"))
 > 
 > t3 <- seq(0,20,by=1/52)
@@ -592,7 +592,7 @@
 > X4 <- trajectory(po,times=t3,hmax=1/52)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.70203 secs
+Time difference of 0.7040031 secs
 > plot(t3,X4['I',1,],type='l')
 > 
 > g2 <- dmeasure(