From noreply at r-forge.r-project.org  Mon Jun  3 23:39:03 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  3 Jun 2013 23:39:03 +0200 (CEST)
Subject: [Pomp-commits] r856 - in pkg/pomp: . R inst man tests
Message-ID: <20130603213903.936AF185036@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-03 23:39:03 +0200 (Mon, 03 Jun 2013)
New Revision: 856

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/NAMESPACE
   pkg/pomp/R/pfilter-methods.R
   pkg/pomp/inst/NEWS
   pkg/pomp/man/pfilter-methods.Rd
   pkg/pomp/tests/pfilter.R
   pkg/pomp/tests/pfilter.Rout.save
Log:
- add a new 'coerce' method: 'pfilterd.pomp' objects to data-frames


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/DESCRIPTION	2013-06-03 21:39:03 UTC (rev 856)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-1
-Date: 2013-05-14
+Version: 0.45-2
+Date: 2013-06-03
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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")),

Modified: pkg/pomp/NAMESPACE
===================================================================
--- pkg/pomp/NAMESPACE	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/NAMESPACE	2013-06-03 21:39:03 UTC (rev 856)
@@ -62,6 +62,7 @@
 
 export(
        as.data.frame.pomp,
+       as.data.frame.pfilterd.pomp,
        reulermultinom,
        deulermultinom,
        rgammawn,

Modified: pkg/pomp/R/pfilter-methods.R
===================================================================
--- pkg/pomp/R/pfilter-methods.R	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/R/pfilter-methods.R	2013-06-03 21:39:03 UTC (rev 856)
@@ -3,6 +3,31 @@
 setMethod("eff.sample.size",signature(object="pfilterd.pomp"),function(object,...)object at eff.sample.size)
 setMethod("cond.logLik",signature(object="pfilterd.pomp"),function(object,...)object at cond.loglik)
 
+## 'coerce' method: allows for coercion of a "pomp" object to a data-frame
+setAs(
+      from="pfilterd.pomp",
+      to="data.frame",
+      def = function (from) {
+        pm <- pred.mean(from)
+        pv <- pred.var(from)
+        fm <- filter.mean(from)
+        out <- cbind(
+                     as(as(from,"pomp"),"data.frame"),
+                     ess=eff.sample.size(from),
+                     cond.loglik=cond.logLik(from)
+                     )
+        if (length(pm)>0)
+          out <- cbind(out,pred.mean=t(pm))
+        if (length(pv)>0)
+          out <- cbind(out,pred.var=t(pv))
+        if (length(fm)>0)
+          out <- cbind(out,filter.mean=t(fm))
+        out
+      }
+      )
+
+as.data.frame.pfilterd.pomp <- function (x, row.names, optional, ...) as(x,"data.frame")
+
 ## extract the prediction means
 setMethod(
           "pred.mean",

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/inst/NEWS	2013-06-03 21:39:03 UTC (rev 856)
@@ -1,4 +1,7 @@
 NEWS
+0.45-2
+     o	new method to coerce 'pfilterd.pomp' objects to data-frames.
+
 0.45-1
      o	'profileDesign' can now handle variables of mixed type.
 

Modified: pkg/pomp/man/pfilter-methods.Rd
===================================================================
--- pkg/pomp/man/pfilter-methods.Rd	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/man/pfilter-methods.Rd	2013-06-03 21:39:03 UTC (rev 856)
@@ -18,6 +18,8 @@
 \alias{cond.logLik}
 \alias{cond.logLik,pfilterd.pomp-method}
 \alias{cond.logLik-pfilterd.pomp}
+\alias{as,pfilterd.pomp-method}
+\alias{coerce,pfilterd.pomp,data.frame-method}
 \title{Methods of the "pfilterd.pomp" class}
 \description{Methods of the "pfilterd.pomp" class.}
 \usage{
@@ -27,12 +29,24 @@
 \S4method{filter.mean}{pfilterd.pomp}(object, pars, \dots)
 \S4method{eff.sample.size}{pfilterd.pomp}(object, \dots)
 \S4method{cond.logLik}{pfilterd.pomp}(object, \dots)
+\S4method{as}{pfilterd.pomp}(object, class)
+\S4method{coerce}{pfilterd.pomp,data.frame}(from, to = "data.frame", strict = TRUE)
 }
 \arguments{
   \item{object}{
     An object of class \code{pfilterd.pomp} or inheriting class \code{pfilterd.pomp}.
   }
   \item{pars}{Names of parameters.}
+  \item{class}{
+    character;
+    name of the class to which \code{object} should be coerced.
+  }
+  \item{from, to}{
+    the classes between which coercion should be performed.
+  }
+  \item{strict}{
+    ignored.
+  }
   \item{\dots}{
     Additional arguments unused at present.
   }

Modified: pkg/pomp/tests/pfilter.R
===================================================================
--- pkg/pomp/tests/pfilter.R	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/tests/pfilter.R	2013-06-03 21:39:03 UTC (rev 856)
@@ -4,6 +4,8 @@
 
 set.seed(9994847L)
 
+pdf(file="pfilter.pdf")
+
 pf <- pfilter(ou2,Np=1000,seed=343439L)
 print(coef(ou2,c('x1.0','x2.0','alpha.1','alpha.4')),digits=4)
 cat("particle filter log likelihood at truth\n")
@@ -23,6 +25,11 @@
 p <- coef(euler.sir)
 euler.sir at params <- numeric(0)
 p["iota"] <- 1
-pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L)
+pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L,filter.mean=TRUE)
 print(coef(pf))
 print(logLik(pf),digits=4)
+plot(cond.loglik~time,data=as(pf,"data.frame"),type='l')
+plot(ess~time,data=as(pf,"data.frame"),type='l')
+plot(filter.mean.I~time,data=as(pf,"data.frame"),type='l')
+
+dev.off()

Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save	2013-05-14 19:47:29 UTC (rev 855)
+++ pkg/pomp/tests/pfilter.Rout.save	2013-06-03 21:39:03 UTC (rev 856)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.1 (2013-05-16) -- "Good Sport"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -27,6 +26,8 @@
 > 
 > set.seed(9994847L)
 > 
+> pdf(file="pfilter.pdf")
+> 
 > pf <- pfilter(ou2,Np=1000,seed=343439L)
 > print(coef(ou2,c('x1.0','x2.0','alpha.1','alpha.4')),digits=4)
    x1.0    x2.0 alpha.1 alpha.4 
@@ -59,7 +60,7 @@
 > p <- coef(euler.sir)
 > euler.sir at params <- numeric(0)
 > p["iota"] <- 1
-> pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L)
+> pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L,filter.mean=TRUE)
 > print(coef(pf))
    gamma       mu     iota    beta1    beta2    beta3  beta.sd      pop 
 2.60e+01 2.00e-02 1.00e+00 4.00e+02 4.80e+02 3.20e+02 1.00e-03 2.10e+06 
@@ -67,7 +68,14 @@
 6.00e-01 6.50e-02 1.00e-03 9.35e-01 
 > print(logLik(pf),digits=4)
 [1] -945.4
+> plot(cond.loglik~time,data=as(pf,"data.frame"),type='l')
+> plot(ess~time,data=as(pf,"data.frame"),type='l')
+> plot(filter.mean.I~time,data=as(pf,"data.frame"),type='l')
 > 
+> dev.off()
+null device 
+          1 
+> 
 > proc.time()
    user  system elapsed 
-  5.964   0.056   6.062 
+  6.044   0.104   6.320 


From noreply at r-forge.r-project.org  Tue Jun  4 13:54:01 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue,  4 Jun 2013 13:54:01 +0200 (CEST)
Subject: [Pomp-commits] r857 - in branches/premif2: . R inst man tests
Message-ID: <20130604115401.9D98E185635@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-04 13:54:01 +0200 (Tue, 04 Jun 2013)
New Revision: 857

Modified:
   branches/premif2/DESCRIPTION
   branches/premif2/NAMESPACE
   branches/premif2/R/pfilter-methods.R
   branches/premif2/inst/NEWS
   branches/premif2/man/pfilter-methods.Rd
   branches/premif2/tests/pfilter.R
   branches/premif2/tests/pfilter.Rout.save
Log:
- add a new 'coerce' method: 'pfilterd.pomp' objects to data-frames



Modified: branches/premif2/DESCRIPTION
===================================================================
--- branches/premif2/DESCRIPTION	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/DESCRIPTION	2013-06-04 11:54:01 UTC (rev 857)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.43-8
-Date: 2013-04-16
+Version: 0.43-9
+Date: 2013-06-03
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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")),

Modified: branches/premif2/NAMESPACE
===================================================================
--- branches/premif2/NAMESPACE	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/NAMESPACE	2013-06-04 11:54:01 UTC (rev 857)
@@ -62,6 +62,7 @@
 
 export(
        as.data.frame.pomp,
+       as.data.frame.pfilterd.pomp,
        reulermultinom,
        deulermultinom,
        rgammawn,

Modified: branches/premif2/R/pfilter-methods.R
===================================================================
--- branches/premif2/R/pfilter-methods.R	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/R/pfilter-methods.R	2013-06-04 11:54:01 UTC (rev 857)
@@ -3,6 +3,31 @@
 setMethod("eff.sample.size",signature(object="pfilterd.pomp"),function(object,...)object at eff.sample.size)
 setMethod("cond.logLik",signature(object="pfilterd.pomp"),function(object,...)object at cond.loglik)
 
+## 'coerce' method: allows for coercion of a "pomp" object to a data-frame
+setAs(
+      from="pfilterd.pomp",
+      to="data.frame",
+      def = function (from) {
+        pm <- pred.mean(from)
+        pv <- pred.var(from)
+        fm <- filter.mean(from)
+        out <- cbind(
+                     as(as(from,"pomp"),"data.frame"),
+                     ess=eff.sample.size(from),
+                     cond.loglik=cond.logLik(from)
+                     )
+        if (length(pm)>0)
+          out <- cbind(out,pred.mean=t(pm))
+        if (length(pv)>0)
+          out <- cbind(out,pred.var=t(pv))
+        if (length(fm)>0)
+          out <- cbind(out,filter.mean=t(fm))
+        out
+      }
+      )
+
+as.data.frame.pfilterd.pomp <- function (x, row.names, optional, ...) as(x,"data.frame")
+
 ## extract the prediction means
 setMethod(
           "pred.mean",

Modified: branches/premif2/inst/NEWS
===================================================================
--- branches/premif2/inst/NEWS	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/inst/NEWS	2013-06-04 11:54:01 UTC (rev 857)
@@ -1,4 +1,7 @@
 NEWS
+0.43-9
+     o	new method to coerce 'pfilterd.pomp' objects to data-frames.
+
 0.43-4
      o	Clean up tests.
 

Modified: branches/premif2/man/pfilter-methods.Rd
===================================================================
--- branches/premif2/man/pfilter-methods.Rd	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/man/pfilter-methods.Rd	2013-06-04 11:54:01 UTC (rev 857)
@@ -18,6 +18,8 @@
 \alias{cond.logLik}
 \alias{cond.logLik,pfilterd.pomp-method}
 \alias{cond.logLik-pfilterd.pomp}
+\alias{as,pfilterd.pomp-method}
+\alias{coerce,pfilterd.pomp,data.frame-method}
 \title{Methods of the "pfilterd.pomp" class}
 \description{Methods of the "pfilterd.pomp" class.}
 \usage{
@@ -27,12 +29,24 @@
 \S4method{filter.mean}{pfilterd.pomp}(object, pars, \dots)
 \S4method{eff.sample.size}{pfilterd.pomp}(object, \dots)
 \S4method{cond.logLik}{pfilterd.pomp}(object, \dots)
+\S4method{as}{pfilterd.pomp}(object, class)
+\S4method{coerce}{pfilterd.pomp,data.frame}(from, to = "data.frame", strict = TRUE)
 }
 \arguments{
   \item{object}{
     An object of class \code{pfilterd.pomp} or inheriting class \code{pfilterd.pomp}.
   }
   \item{pars}{Names of parameters.}
+  \item{class}{
+    character;
+    name of the class to which \code{object} should be coerced.
+  }
+  \item{from, to}{
+    the classes between which coercion should be performed.
+  }
+  \item{strict}{
+    ignored.
+  }
   \item{\dots}{
     Additional arguments unused at present.
   }

Modified: branches/premif2/tests/pfilter.R
===================================================================
--- branches/premif2/tests/pfilter.R	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/tests/pfilter.R	2013-06-04 11:54:01 UTC (rev 857)
@@ -4,6 +4,8 @@
 
 set.seed(9994847L)
 
+pdf(file="pfilter.pdf")
+
 pf <- pfilter(ou2,Np=1000,seed=343439L)
 print(coef(ou2,c('x1.0','x2.0','alpha.1','alpha.4')),digits=4)
 cat("particle filter log likelihood at truth\n")
@@ -23,6 +25,11 @@
 p <- coef(euler.sir)
 euler.sir at params <- numeric(0)
 p["iota"] <- 1
-pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L)
+pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L,filter.mean=TRUE)
 print(coef(pf))
 print(logLik(pf),digits=4)
+plot(cond.loglik~time,data=as(pf,"data.frame"),type='l')
+plot(ess~time,data=as(pf,"data.frame"),type='l')
+plot(filter.mean.I~time,data=as(pf,"data.frame"),type='l')
+
+dev.off()

Modified: branches/premif2/tests/pfilter.Rout.save
===================================================================
--- branches/premif2/tests/pfilter.Rout.save	2013-06-03 21:39:03 UTC (rev 856)
+++ branches/premif2/tests/pfilter.Rout.save	2013-06-04 11:54:01 UTC (rev 857)
@@ -24,6 +24,8 @@
 > 
 > set.seed(9994847L)
 > 
+> pdf(file="pfilter.pdf")
+> 
 > pf <- pfilter(ou2,Np=1000,seed=343439L)
 > print(coef(ou2,c('x1.0','x2.0','alpha.1','alpha.4')),digits=4)
    x1.0    x2.0 alpha.1 alpha.4 
@@ -54,7 +56,7 @@
 > p <- coef(euler.sir)
 > euler.sir at params <- numeric(0)
 > p["iota"] <- 1
-> pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L)
+> pf <- pfilter(euler.sir,params=p,Np=100,seed=394343L,filter.mean=TRUE)
 > print(coef(pf))
    gamma       mu     iota    beta1    beta2    beta3  beta.sd      pop 
 2.60e+01 2.00e-02 1.00e+00 4.00e+02 4.80e+02 3.20e+02 1.00e-03 2.10e+06 


From noreply at r-forge.r-project.org  Thu Jun  6 01:07:40 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  6 Jun 2013 01:07:40 +0200 (CEST)
Subject: [Pomp-commits] r858 - pkg/pomp/man
Message-ID: <20130605230740.B93E7185250@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-06 01:07:40 +0200 (Thu, 06 Jun 2013)
New Revision: 858

Modified:
   pkg/pomp/man/pfilter-methods.Rd
Log:
- add documentation for 'as.data.frame.pfilterd.pomp'


Modified: pkg/pomp/man/pfilter-methods.Rd
===================================================================
--- pkg/pomp/man/pfilter-methods.Rd	2013-06-04 11:54:01 UTC (rev 857)
+++ pkg/pomp/man/pfilter-methods.Rd	2013-06-05 23:07:40 UTC (rev 858)
@@ -19,6 +19,7 @@
 \alias{cond.logLik,pfilterd.pomp-method}
 \alias{cond.logLik-pfilterd.pomp}
 \alias{as,pfilterd.pomp-method}
+\alias{as.data.frame.pfilterd.pomp}
 \alias{coerce,pfilterd.pomp,data.frame-method}
 \title{Methods of the "pfilterd.pomp" class}
 \description{Methods of the "pfilterd.pomp" class.}
@@ -31,9 +32,10 @@
 \S4method{cond.logLik}{pfilterd.pomp}(object, \dots)
 \S4method{as}{pfilterd.pomp}(object, class)
 \S4method{coerce}{pfilterd.pomp,data.frame}(from, to = "data.frame", strict = TRUE)
+\S3method{as.data.frame}{pfilterd.pomp}(x, row.names, optional, \dots)
 }
 \arguments{
-  \item{object}{
+  \item{object, x}{
     An object of class \code{pfilterd.pomp} or inheriting class \code{pfilterd.pomp}.
   }
   \item{pars}{Names of parameters.}
@@ -47,6 +49,9 @@
   \item{strict}{
     ignored.
   }
+  \item{row.names, optional}{
+    ignored.
+  }
   \item{\dots}{
     Additional arguments unused at present.
   }


From noreply at r-forge.r-project.org  Thu Jun  6 02:03:29 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  6 Jun 2013 02:03:29 +0200 (CEST)
Subject: [Pomp-commits] r859 - in pkg/pomp: . R inst
Message-ID: <20130606000329.61F21185898@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-06 02:03:28 +0200 (Thu, 06 Jun 2013)
New Revision: 859

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/mif.R
   pkg/pomp/inst/NEWS
Log:
- fix bug in 'continue' when 'mif2' method is used


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-06-05 23:07:40 UTC (rev 858)
+++ pkg/pomp/DESCRIPTION	2013-06-06 00:03:28 UTC (rev 859)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-2
-Date: 2013-06-03
+Version: 0.45-3
+Date: 2013-06-05
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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")),

Modified: pkg/pomp/R/mif.R
===================================================================
--- pkg/pomp/R/mif.R	2013-06-05 23:07:40 UTC (rev 858)
+++ pkg/pomp/R/mif.R	2013-06-06 00:03:28 UTC (rev 859)
@@ -94,7 +94,8 @@
                           tol, max.fail,
                           verbose, transform, .ndone = 0L,
                           paramMatrix = NULL,
-                          .getnativesymbolinfo = TRUE) {
+                          .getnativesymbolinfo = TRUE,
+                          ...) {
   
   gnsi <- as.logical(.getnativesymbolinfo)
 
@@ -459,7 +460,8 @@
                          tol=tol,
                          max.fail=max.fail,
                          verbose=verbose,
-                         transform=transform
+                         transform=transform,
+                         ...
                          )
             
           }

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2013-06-05 23:07:40 UTC (rev 858)
+++ pkg/pomp/inst/NEWS	2013-06-06 00:03:28 UTC (rev 859)
@@ -1,4 +1,7 @@
 NEWS
+0.45-3
+     o	fix bug with 'continue' and method 'mif2'
+
 0.45-2
      o	new method to coerce 'pfilterd.pomp' objects to data-frames.
 


From noreply at r-forge.r-project.org  Fri Jun  7 14:13:08 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  7 Jun 2013 14:13:08 +0200 (CEST)
Subject: [Pomp-commits] r860 - in pkg/pomp: . R inst inst/include src
Message-ID: <20130607121308.8FA47185212@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-07 14:13:08 +0200 (Fri, 07 Jun 2013)
New Revision: 860

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/builder.R
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/include/pomp.h
   pkg/pomp/src/R_init_pomp.c
   pkg/pomp/src/eulermultinom.c
   pkg/pomp/src/lookup_table.c
   pkg/pomp/src/pomp.h
Log:
- reulermultinom, deulermultinom, and dot_product are no longer linkables exported in src/R_init_pomp.c but rather are defined as static inlines in the pomp.h header file.


Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/DESCRIPTION	2013-06-07 12:13:08 UTC (rev 860)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.45-3
-Date: 2013-06-05
+Version: 0.45-4
+Date: 2013-06-06
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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")),

Modified: pkg/pomp/R/builder.R
===================================================================
--- pkg/pomp/R/builder.R	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/R/builder.R	2013-06-07 12:13:08 UTC (rev 860)
@@ -107,7 +107,6 @@
 
 decl <- list(
              periodic_bspline_basis_eval="\tvoid (*periodic_bspline_basis_eval)(double,double,int,int,double*);\nperiodic_bspline_basis_eval = (void (*)(double,double,int,int,double*)) R_GetCCallable(\"pomp\",\"periodic_bspline_basis_eval\");\n",
-             reulermultinom="\tvoid (*reulermultinom)(int,double,double*,double,double*);\nreulermultinom = (void (*)(int,double,double*,double,double*)) R_GetCCallable(\"pomp\",\"reulermultinom\");\n",
              get_pomp_userdata="\tconst SEXP (*get_pomp_userdata)(const char *);\npomp_get_userdata = (const SEXP (*)(const char*)) R_GetCCallable(\"pomp\",\"get_pomp_userdata\");\n",
              get_pomp_userdata_int="\tconst int * (*get_pomp_userdata_int)(const char *);\npomp_get_userdata_int = (const int *(*)(const char*)) R_GetCCallable(\"pomp\",\"get_pomp_userdata_int\");\n",
              get_pomp_userdata_double="\tconst double * (*get_pomp_userdata_double)(const char *);\npomp_get_userdata_double = (const double *(*)(const char*)) R_GetCCallable(\"pomp\",\"get_pomp_userdata_double\");\n"

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/inst/NEWS	2013-06-07 12:13:08 UTC (rev 860)
@@ -1,4 +1,7 @@
 NEWS
+0.45-4
+     o	changes in the way 'reulermultinom', 'deulermultinom', 'dot_product' are exported to other packages.  Rather than being exported as linkables, these are now defined as static inline functions in the 'pomp.h' header.
+
 0.45-3
      o	fix bug with 'continue' and method 'mif2'
 

Modified: pkg/pomp/inst/include/pomp.h
===================================================================
--- pkg/pomp/inst/include/pomp.h	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/inst/include/pomp.h	2013-06-07 12:13:08 UTC (rev 860)
@@ -5,15 +5,15 @@
 
 #include <R.h>
 #include <Rmath.h>
-#include <Rdefines.h>
+#include <Rinternals.h>
 #include <R_ext/Rdynload.h>
 
-// facility for extracting R objects from the 'userdata' slot
+// facilities for extracting R objects from the 'userdata' slot
 const SEXP get_pomp_userdata (const char *name);
 const int *get_pomp_userdata_int (const char *name);
 const double *get_pomp_userdata_double (const char *name);
 
-// facility for computing evaluating a basis of periodic bsplines
+// facility for evaluating a set of periodic bspline basis functions
 void periodic_bspline_basis_eval (double x, double period, int degree, int nbasis, double *y);
 
 // Prototype for parameter transformation function.
@@ -191,7 +191,13 @@
 
 // facility for computing the inner product of 
 // a vector of parameters ('coef') against a vector of basis-function values ('basis')
-double dot_product (int dim, const double *basis, const double *coef);
+static R_INLINE double dot_product (int dim, const double *basis, const double *coef) {
+  int j;
+  double trans = 0.0;
+  for (j = 0; j < dim; j++)
+    trans += coef[j]*basis[j];
+  return(trans);
+}
 
 static R_INLINE double logit (double p) {
   return log(p/(1.0-p));
@@ -201,17 +207,88 @@
   return 1.0/(1.0+exp(-x));
 }
 
-// prototypes for C-level access to Euler-multinomial distribution functions
+// C-level definitions of Euler-multinomial distribution functions
 
 // simulate Euler-multinomial transitions
 // NB: 'reulermultinom' does not call GetRNGstate() and PutRNGstate() internally
 // this must be done by the calling program
 // But note that when reulermultinom is called inside a pomp 'rprocess', there is no need to call
 // {Get,Put}RNGState() as this is handled by pomp
-void reulermultinom (int m, double size, double *rate, double dt, double *trans);
+static void reulermultinom (int m, double size, double *rate, double dt, double *trans) {
+  double p = 0.0;
+  int j, k;
+  if ((size < 0.0) || (dt < 0.0) || (floor(size+0.5) != size)) {
+    for (k = 0; k < m; k++) trans[k] = R_NaN;
+    return;
+  }  
+  for (k = 0; k < m; k++) {
+    if (rate[k] < 0.0) {
+      for (j = 0; j < m; j++) trans[j] = R_NaN;
+      return;
+    }
+    p += rate[k]; // total event rate
+  }
+  if (p > 0.0) {
+    size = rbinom(size,1-exp(-p*dt)); // total number of events
+    if (!(R_FINITE(size)))
+      warning("reulermultinom: result of binomial draw is not finite");
+    m -= 1;
+    for (k = 0; k < m; k++) {
+      if (rate[k] > p) p = rate[k];
+      trans[k] = ((size > 0) && (p > 0)) ? rbinom(size,rate[k]/p) : 0;
+      if (!(R_FINITE(size)&&R_FINITE(p)&&R_FINITE(rate[k])&&R_FINITE(trans[k])))
+	warning("reulermultinom: result of binomial draw is not finite");
+      size -= trans[k];
+      p -= rate[k];
+    }
+    trans[m] = size;
+  } else {
+    for (k = 0; k < m; k++) trans[k] = 0.0;
+  }
+}
 
-// compute probabilities of eulermultinomial transitions
-double deulermultinom (int m, double size, double *rate, double dt, double *trans, int give_log);
+// compute probabilities of Euler-multinomial transitions
+static double deulermultinom (int m, double size, double *rate, double dt, double *trans, int give_log) {
+  double p = 0.0;
+  double n = 0.0;
+  double ff = 0.0;
+  int k;
+  if ((dt < 0.0) || (size < 0.0) || (floor(size+0.5) != size)) {
+    warning("NaNs produced");
+    return R_NaN;
+  }
+  for (k = 0; k < m; k++) {
+    if (rate[k] < 0.0) {
+      warning("NaNs produced");
+      return R_NaN;
+    }
+    if (trans[k] < 0.0) {
+      ff = (give_log) ? R_NegInf: 0.0;
+      return ff;
+    }
+    p += rate[k]; // total event rate
+    n += trans[k]; // total number of events
+  }
+  if (n > size) {
+    ff = (give_log) ? R_NegInf: 0.0;
+    return ff;
+  }
+  ff = dbinom(n,size,1-exp(-p*dt),1); // total number of events
+  m -= 1;
+  for (k = 0; k < m; k++) {
+    if ((n > 0) && (p > 0)) {
+      if (rate[k] > p) p = rate[k];
+      ff += dbinom(trans[k],n,rate[k]/p,1);
+    } else if (trans[k] > 0.0) {
+      ff = R_NegInf;
+      return ff;
+    }
+    n -= trans[k];
+    p -= rate[k];
+  }
+  ff = (give_log) ? ff : exp(ff);
+  return ff;
+}
 
 static R_INLINE double rbetabinom (double size, double prob, double theta) {
   return rbinom(size,rbeta(prob*theta,(1.0-prob)*theta));

Modified: pkg/pomp/src/R_init_pomp.c
===================================================================
--- pkg/pomp/src/R_init_pomp.c	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/src/R_init_pomp.c	2013-06-07 12:13:08 UTC (rev 860)
@@ -4,9 +4,6 @@
 
 void R_init_pomp (DllInfo *info) {
   R_RegisterCCallable("pomp","periodic_bspline_basis_eval",(DL_FUNC) &periodic_bspline_basis_eval);
-  R_RegisterCCallable("pomp","dot_product",(DL_FUNC) &dot_product);
-  R_RegisterCCallable("pomp","reulermultinom",(DL_FUNC) &reulermultinom);
-  R_RegisterCCallable("pomp","deulermultinom",(DL_FUNC) &deulermultinom);
   R_RegisterCCallable("pomp","get_pomp_userdata",(DL_FUNC) &get_pomp_userdata);
   R_RegisterCCallable("pomp","get_pomp_userdata_int",(DL_FUNC) &get_pomp_userdata_int);
   R_RegisterCCallable("pomp","get_pomp_userdata_double",(DL_FUNC) &get_pomp_userdata_double);

Modified: pkg/pomp/src/eulermultinom.c
===================================================================
--- pkg/pomp/src/eulermultinom.c	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/src/eulermultinom.c	2013-06-07 12:13:08 UTC (rev 860)
@@ -4,82 +4,6 @@
 
 #include "pomp_internal.h"
 
-void reulermultinom (int m, double size, double *rate, double dt, double *trans) {
-  double p = 0.0;
-  int j, k;
-  if ((size < 0.0) || (dt < 0.0) || (floor(size+0.5) != size)) {
-    for (k = 0; k < m; k++) trans[k] = R_NaN;
-    return;
-  }  
-  for (k = 0; k < m; k++) {
-    if (rate[k] < 0.0) {
-      for (j = 0; j < m; j++) trans[j] = R_NaN;
-      return;
-    }
-    p += rate[k]; // total event rate
-  }
-  if (p > 0.0) {
-    size = rbinom(size,1-exp(-p*dt)); // total number of events
-    if (!(R_FINITE(size)))
-      warning("reulermultinom: result of binomial draw is not finite");
-    m -= 1;
-    for (k = 0; k < m; k++) {
-      if (rate[k] > p) p = rate[k];
-      trans[k] = ((size > 0) && (p > 0)) ? rbinom(size,rate[k]/p) : 0;
-      if (!(R_FINITE(size)&&R_FINITE(p)&&R_FINITE(rate[k])&&R_FINITE(trans[k])))
-	warning("reulermultinom: result of binomial draw is not finite");
-      size -= trans[k];
-      p -= rate[k];
-    }
-    trans[m] = size;
-  } else {
-    for (k = 0; k < m; k++) trans[k] = 0.0;
-  }
-}
-
-// probability density of Euler-multinomial transitions
-double deulermultinom (int m, double size, double *rate, double dt, double *trans, int give_log) {
-  double p = 0.0;
-  double n = 0.0;
-  double ff = 0.0;
-  int k;
-  if ((dt < 0.0) || (size < 0.0) || (floor(size+0.5) != size)) {
-    warning("NaNs produced");
-    return R_NaN;
-  }
-  for (k = 0; k < m; k++) {
-    if (rate[k] < 0.0) {
-      warning("NaNs produced");
-      return R_NaN;
-    }
-    if (trans[k] < 0.0) {
-      ff = (give_log) ? R_NegInf: 0.0;
-      return ff;
-    }
-    p += rate[k]; // total event rate
-    n += trans[k]; // total number of events
-  }
-  if (n > size) {
-    ff = (give_log) ? R_NegInf: 0.0;
-    return ff;
-  }
-  ff = dbinom(n,size,1-exp(-p*dt),1); // total number of events
-  m -= 1;
-  for (k = 0; k < m; k++) {
-    if ((n > 0) && (p > 0)) {
-      if (rate[k] > p) p = rate[k];
-      ff += dbinom(trans[k],n,rate[k]/p,1);
-    } else if (trans[k] > 0.0) {
-      ff = R_NegInf;
-      return ff;
-    }
-    n -= trans[k];
-    p -= rate[k];
-  }
-  ff = (give_log) ? ff : exp(ff);
-  return ff;
-}
-
 void reulermultinom_multi (int *n, int *ntrans, double *size, double *rate, double *dt, double *trans) {
   int k;
   int m = *ntrans;

Modified: pkg/pomp/src/lookup_table.c
===================================================================
--- pkg/pomp/src/lookup_table.c	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/src/lookup_table.c	2013-06-07 12:13:08 UTC (rev 860)
@@ -70,13 +70,3 @@
   }
 }
 
-// facility for computing the inner product of 
-// a vector of parameters ('coef') against a vector of basis-function values ('basis')
-double dot_product (int dim, const double *basis, const double *coef) {
-  int j;
-  double trans = 0.0;
-  for (j = 0; j < dim; j++)
-    trans += coef[j]*basis[j];
-  return(trans);
-}
-

Modified: pkg/pomp/src/pomp.h
===================================================================
--- pkg/pomp/src/pomp.h	2013-06-06 00:03:28 UTC (rev 859)
+++ pkg/pomp/src/pomp.h	2013-06-07 12:13:08 UTC (rev 860)
@@ -5,15 +5,15 @@
 
 #include <R.h>
 #include <Rmath.h>
-#include <Rdefines.h>
+#include <Rinternals.h>
 #include <R_ext/Rdynload.h>
 
-// facility for extracting R objects from the 'userdata' slot
+// facilities for extracting R objects from the 'userdata' slot
 const SEXP get_pomp_userdata (const char *name);
 const int *get_pomp_userdata_int (const char *name);
 const double *get_pomp_userdata_double (const char *name);
 
-// facility for computing evaluating a basis of periodic bsplines
+// facility for evaluating a set of periodic bspline basis functions
 void periodic_bspline_basis_eval (double x, double period, int degree, int nbasis, double *y);
 
 // Prototype for parameter transformation function.
@@ -191,7 +191,13 @@
 
 // facility for computing the inner product of 
 // a vector of parameters ('coef') against a vector of basis-function values ('basis')
-double dot_product (int dim, const double *basis, const double *coef);
+static R_INLINE double dot_product (int dim, const double *basis, const double *coef) {
+  int j;
+  double trans = 0.0;
+  for (j = 0; j < dim; j++)
+    trans += coef[j]*basis[j];
+  return(trans);
+}
 
 static R_INLINE double logit (double p) {
   return log(p/(1.0-p));
@@ -201,17 +207,88 @@
   return 1.0/(1.0+exp(-x));
 }
 
-// prototypes for C-level access to Euler-multinomial distribution functions
+// C-level definitions of Euler-multinomial distribution functions
 
 // simulate Euler-multinomial transitions
 // NB: 'reulermultinom' does not call GetRNGstate() and PutRNGstate() internally
 // this must be done by the calling program
 // But note that when reulermultinom is called inside a pomp 'rprocess', there is no need to call
 // {Get,Put}RNGState() as this is handled by pomp
-void reulermultinom (int m, double size, double *rate, double dt, double *trans);
+static void reulermultinom (int m, double size, double *rate, double dt, double *trans) {
+  double p = 0.0;
+  int j, k;
+  if ((size < 0.0) || (dt < 0.0) || (floor(size+0.5) != size)) {
+    for (k = 0; k < m; k++) trans[k] = R_NaN;
+    return;
+  }  
+  for (k = 0; k < m; k++) {
+    if (rate[k] < 0.0) {
+      for (j = 0; j < m; j++) trans[j] = R_NaN;
+      return;
+    }
+    p += rate[k]; // total event rate
+  }
+  if (p > 0.0) {
+    size = rbinom(size,1-exp(-p*dt)); // total number of events
+    if (!(R_FINITE(size)))
+      warning("reulermultinom: result of binomial draw is not finite");
+    m -= 1;
+    for (k = 0; k < m; k++) {
+      if (rate[k] > p) p = rate[k];
+      trans[k] = ((size > 0) && (p > 0)) ? rbinom(size,rate[k]/p) : 0;
+      if (!(R_FINITE(size)&&R_FINITE(p)&&R_FINITE(rate[k])&&R_FINITE(trans[k])))
+	warning("reulermultinom: result of binomial draw is not finite");
+      size -= trans[k];
+      p -= rate[k];
+    }
+    trans[m] = size;
+  } else {
+    for (k = 0; k < m; k++) trans[k] = 0.0;
+  }
+}
 
-// compute probabilities of eulermultinomial transitions
-double deulermultinom (int m, double size, double *rate, double dt, double *trans, int give_log);
+// compute probabilities of Euler-multinomial transitions
+static double deulermultinom (int m, double size, double *rate, double dt, double *trans, int give_log) {
+  double p = 0.0;
+  double n = 0.0;
+  double ff = 0.0;
+  int k;
+  if ((dt < 0.0) || (size < 0.0) || (floor(size+0.5) != size)) {
+    warning("NaNs produced");
+    return R_NaN;
+  }
+  for (k = 0; k < m; k++) {
+    if (rate[k] < 0.0) {
+      warning("NaNs produced");
+      return R_NaN;
+    }
+    if (trans[k] < 0.0) {
+      ff = (give_log) ? R_NegInf: 0.0;
+      return ff;
+    }
+    p += rate[k]; // total event rate
+    n += trans[k]; // total number of events
+  }
+  if (n > size) {
+    ff = (give_log) ? R_NegInf: 0.0;
+    return ff;
+  }
+  ff = dbinom(n,size,1-exp(-p*dt),1); // total number of events
+  m -= 1;
+  for (k = 0; k < m; k++) {
+    if ((n > 0) && (p > 0)) {
+      if (rate[k] > p) p = rate[k];
+      ff += dbinom(trans[k],n,rate[k]/p,1);
+    } else if (trans[k] > 0.0) {
+      ff = R_NegInf;
+      return ff;
+    }
+    n -= trans[k];
+    p -= rate[k];
+  }
+  ff = (give_log) ? ff : exp(ff);
+  return ff;
+}
 
 static R_INLINE double rbetabinom (double size, double prob, double theta) {
   return rbinom(size,rbeta(prob*theta,(1.0-prob)*theta));


From noreply at r-forge.r-project.org  Fri Jun  7 14:27:52 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  7 Jun 2013 14:27:52 +0200 (CEST)
Subject: [Pomp-commits] r861 - in pkg/pomp: inst src
Message-ID: <20130607122752.716221812D4@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-07 14:27:52 +0200 (Fri, 07 Jun 2013)
New Revision: 861

Modified:
   pkg/pomp/inst/NEWS
   pkg/pomp/src/R_init_pomp.c
Log:
- to preserve backward-compatibility, continue to export 'reulermultinom', 'deulermultinom', and 'dot_product'


Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2013-06-07 12:13:08 UTC (rev 860)
+++ pkg/pomp/inst/NEWS	2013-06-07 12:27:52 UTC (rev 861)
@@ -1,6 +1,6 @@
 NEWS
 0.45-4
-     o	changes in the way 'reulermultinom', 'deulermultinom', 'dot_product' are exported to other packages.  Rather than being exported as linkables, these are now defined as static inline functions in the 'pomp.h' header.
+     o	changes in the way 'reulermultinom', 'deulermultinom', 'dot_product' are exported to other packages.  Rather than just being exported as linkables, these are now also defined as static inline functions in the 'pomp.h' header.
 
 0.45-3
      o	fix bug with 'continue' and method 'mif2'

Modified: pkg/pomp/src/R_init_pomp.c
===================================================================
--- pkg/pomp/src/R_init_pomp.c	2013-06-07 12:13:08 UTC (rev 860)
+++ pkg/pomp/src/R_init_pomp.c	2013-06-07 12:27:52 UTC (rev 861)
@@ -4,6 +4,9 @@
 
 void R_init_pomp (DllInfo *info) {
   R_RegisterCCallable("pomp","periodic_bspline_basis_eval",(DL_FUNC) &periodic_bspline_basis_eval);
+  R_RegisterCCallable("pomp","dot_product",(DL_FUNC) &dot_product);
+  R_RegisterCCallable("pomp","reulermultinom",(DL_FUNC) &reulermultinom);
+  R_RegisterCCallable("pomp","deulermultinom",(DL_FUNC) &deulermultinom);
   R_RegisterCCallable("pomp","get_pomp_userdata",(DL_FUNC) &get_pomp_userdata);
   R_RegisterCCallable("pomp","get_pomp_userdata_int",(DL_FUNC) &get_pomp_userdata_int);
   R_RegisterCCallable("pomp","get_pomp_userdata_double",(DL_FUNC) &get_pomp_userdata_double);


From noreply at r-forge.r-project.org  Fri Jun  7 21:41:32 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  7 Jun 2013 21:41:32 +0200 (CEST)
Subject: [Pomp-commits] r862 - in pkg/pompExamples: . src tests
Message-ID: <20130607194132.D685D185559@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-07 21:41:32 +0200 (Fri, 07 Jun 2013)
New Revision: 862

Added:
   pkg/pompExamples/src/Makevars
Modified:
   pkg/pompExamples/DESCRIPTION
   pkg/pompExamples/src/pertussis.c
   pkg/pompExamples/tests/budmoth.Rout.save
   pkg/pompExamples/tests/pertussis.Rout.save
Log:
- update to use new facilities from pomp v 0.45-4


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2013-06-07 12:27:52 UTC (rev 861)
+++ pkg/pompExamples/DESCRIPTION	2013-06-07 19:41:32 UTC (rev 862)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.21-1
-Date: 2013-04-22
+Version: 0.21-2
+Date: 2013-06-07
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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")),
@@ -15,7 +15,7 @@
 	  person(given=c("Helen"),family="Wearing",role=c("ctb")))
 URL: http://pomp.r-forge.r-project.org
 Description: More 'pomp' examples.
-Depends: R(>= 3.0.0), stats, methods, graphics, pomp(>= 0.43-8)
+Depends: R(>= 3.0.0), stats, methods, graphics, pomp(>= 0.45-4)
 License: GPL (>= 2)
 LazyLoad: true
 LazyData: false

Added: pkg/pompExamples/src/Makevars
===================================================================
--- pkg/pompExamples/src/Makevars	                        (rev 0)
+++ pkg/pompExamples/src/Makevars	2013-06-07 19:41:32 UTC (rev 862)
@@ -0,0 +1,2 @@
+POMP_INC = $(shell "$(R_HOME)/bin$(R_ARCH_BIN)/Rscript" -e 'library(pomp); cat(system.file("include",package="pomp"))')
+PKG_CFLAGS = -I $(POMP_INC)

Modified: pkg/pompExamples/src/pertussis.c
===================================================================
--- pkg/pompExamples/src/pertussis.c	2013-06-07 12:27:52 UTC (rev 861)
+++ pkg/pompExamples/src/pertussis.c	2013-06-07 19:41:32 UTC (rev 862)
@@ -2,19 +2,10 @@
 
 #include <R.h>
 #include <Rmath.h>
-#include <Rdefines.h>
+#include <Rinternals.h>
 #include <R_ext/Rdynload.h>
+#include <pomp.h>
 
-inline double expit (double x) {return 1.0/(1.0+exp(-x));}
-
-inline double logit (double p) {return log(p/(1.0-p));}
-
-static inline double rgammawn (double sigma, double dt) {
-  double sigmasq;
-  sigmasq = sigma*sigma;
-  return (sigmasq > 0) ? rgamma(dt/sigmasq,sigmasq) : dt;
-}
-
 static double term_time (double t) {
   double day = 365.0 * (t - floor(t));
   int tt = (day >= 7.0 && day < 100.0) 
@@ -142,9 +133,6 @@
   double beta, alpha3;
   double dW;		// white noise process
   double foi;		// force of infection
-  void (*reulermultinom)(int, double, double *, double, double *);
-
-  reulermultinom = (void (*)(int,double,double*,double,double*)) R_GetCCallable("pomp","reulermultinom");
   
   alpha3 = ALPHA*ALPHA_RATIO;
   beta = MEANBETA*(1+AMPLBETA*term_time(t));

Modified: pkg/pompExamples/tests/budmoth.Rout.save
===================================================================
--- pkg/pompExamples/tests/budmoth.Rout.save	2013-06-07 12:27:52 UTC (rev 861)
+++ pkg/pompExamples/tests/budmoth.Rout.save	2013-06-07 19:41:32 UTC (rev 862)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.1 (2013-05-16) -- "Good Sport"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,8 +15,7 @@
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.
 
-> require(pompExamples)
-Loading required package: pompExamples
+> library(pompExamples)
 Loading required package: pomp
 Loading required package: mvtnorm
 Loading required package: subplex
@@ -130,4 +128,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.284   0.056   1.323 
+  0.604   0.064   0.689 

Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save	2013-06-07 12:27:52 UTC (rev 861)
+++ pkg/pompExamples/tests/pertussis.Rout.save	2013-06-07 19:41:32 UTC (rev 862)
@@ -1,7 +1,6 @@
 
-R version 2.15.2 (2012-10-26) -- "Trick or Treat"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.0.1 (2013-05-16) -- "Good Sport"
+Copyright (C) 2013 The R Foundation for Statistical Computing
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,8 +15,7 @@
 'help.start()' for an HTML browser interface to help.
 Type 'q()' to quit R.
 
-> require(pompExamples)
-Loading required package: pompExamples
+> library(pompExamples)
 Loading required package: pomp
 Loading required package: mvtnorm
 Loading required package: subplex
@@ -149,7 +147,7 @@
 > 
 > system.time(pf <- pfilter(pertussis.sim(full.small),seed=3445886L,Np=1000))
    user  system elapsed 
- 65.132   0.216  65.495 
+ 19.717   0.000  19.778 
 > logLik(pf)
 [1] -3829.33
 > 
@@ -173,4 +171,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 66.960   0.264  67.348 
+ 20.497   0.064  20.642 


From noreply at r-forge.r-project.org  Tue Jun 11 18:28:47 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 11 Jun 2013 18:28:47 +0200 (CEST)
Subject: [Pomp-commits] r863 - pkg/pompExamples
Message-ID: <20130611162847.E50BA1858B0@r-forge.r-project.org>

Author: kingaa
Date: 2013-06-11 18:28:47 +0200 (Tue, 11 Jun 2013)
New Revision: 863

Modified:
   pkg/pompExamples/DESCRIPTION
Log:
- bump to trigger r-forge rebuild


Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION	2013-06-07 19:41:32 UTC (rev 862)
+++ pkg/pompExamples/DESCRIPTION	2013-06-11 16:28:47 UTC (rev 863)
@@ -1,8 +1,8 @@
 Package: pompExamples
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.21-2
-Date: 2013-06-07
+Version: 0.21-3
+Date: 2013-06-11
 Maintainer: Aaron A. King <kingaa at umich.edu>
 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")),