[Pomp-commits] r1196 - pkg/pomp pkg/pomp/R pkg/pomp/inst pkg/pomp/tests www/content www/vignettes

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Mon Jun 8 14:21:06 CEST 2015 

Author: kingaa
Date: 2015-06-08 14:21:06 +0200 (Mon, 08 Jun 2015)
New Revision: 1196

Modified:
   pkg/pomp/DESCRIPTION
   pkg/pomp/R/mif2.R
   pkg/pomp/R/pomp.R
   pkg/pomp/inst/NEWS
   pkg/pomp/inst/NEWS.Rd
   pkg/pomp/tests/bbs-trajmatch.Rout.save
   pkg/pomp/tests/bbs.Rout.save
   pkg/pomp/tests/blowflies.Rout.save
   pkg/pomp/tests/dacca.Rout.save
   pkg/pomp/tests/dimchecks.Rout.save
   pkg/pomp/tests/fhn.Rout.save
   pkg/pomp/tests/filtfail.Rout.save
   pkg/pomp/tests/getting_started.Rout.save
   pkg/pomp/tests/gillespie.Rout.save
   pkg/pomp/tests/gompertz.Rout.save
   pkg/pomp/tests/logistic.Rout.save
   pkg/pomp/tests/ou2-abc.Rout.save
   pkg/pomp/tests/ou2-bsmc.Rout.save
   pkg/pomp/tests/ou2-bsmc2.Rout.save
   pkg/pomp/tests/ou2-forecast.Rout.save
   pkg/pomp/tests/ou2-kalman.Rout.save
   pkg/pomp/tests/ou2-mif-fp.Rout.save
   pkg/pomp/tests/ou2-mif.Rout.save
   pkg/pomp/tests/ou2-mif2.R
   pkg/pomp/tests/ou2-mif2.Rout.save
   pkg/pomp/tests/ou2-nlf.Rout.save
   pkg/pomp/tests/ou2-pmcmc.Rout.save
   pkg/pomp/tests/ou2-probe.Rout.save
   pkg/pomp/tests/ou2-procmeas.Rout.save
   pkg/pomp/tests/ou2-simulate.Rout.save
   pkg/pomp/tests/ou2-spect.Rout.save
   pkg/pomp/tests/ou2-trajmatch.Rout.save
   pkg/pomp/tests/partrans.Rout.save
   pkg/pomp/tests/pfilter.Rout.save
   pkg/pomp/tests/pomppomp.Rout.save
   pkg/pomp/tests/prior.Rout.save
   pkg/pomp/tests/ricker-bsmc.Rout.save
   pkg/pomp/tests/ricker-probe.Rout.save
   pkg/pomp/tests/ricker-spect.Rout.save
   pkg/pomp/tests/ricker.Rout.save
   pkg/pomp/tests/rw2.Rout.save
   pkg/pomp/tests/sir.Rout.save
   pkg/pomp/tests/skeleton.Rout.save
   pkg/pomp/tests/steps.Rout.save
   pkg/pomp/tests/synlik.Rout.save
   www/content/NEWS.html
   www/vignettes/pomp.pdf
Log:
- update NEWS
- minor changes to mif2
- update tests

Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/DESCRIPTION	2015-06-08 12:21:06 UTC (rev 1196)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.66-9
-Date: 2015-06-07
+Version: 0.66-10
+Date: 2015-06-08
 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/mif2.R
===================================================================
--- pkg/pomp/R/mif2.R	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/R/mif2.R	2015-06-08 12:21:06 UTC (rev 1196)
@@ -54,7 +54,6 @@
   verbose <- as.logical(verbose)
   filter.mean <- as.logical(filter.mean)
   mifiter <- as.integer(mifiter)
-  Np <- c(Np,Np[1L])
   Np <- as.integer(Np)
 
   times <- time(object,t0=TRUE)
@@ -203,6 +202,7 @@
   transform <- as.logical(transform)
   verbose <- as.logical(verbose)
   gnsi <- as.logical(.getnativesymbolinfo)
+  Np <- c(Np,Np[1L])
 
   cooling.fn <- mif.cooling.function(
                                      type=cooling.type,

Modified: pkg/pomp/R/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/R/pomp.R	2015-06-08 12:21:06 UTC (rev 1196)
@@ -26,7 +26,7 @@
   if (missing(userdata)) userdata <- list()
   added.userdata <- list(...)
   if (length(added.userdata)>0) {
-    message("in ",sQuote("pomp"),
+    message("In ",sQuote("pomp"),
             ": the following unrecognized argument(s) ",
             "will be stored for use by user-defined functions: ",
             paste(sQuote(names(added.userdata)),collapse=","))

Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/inst/NEWS	2015-06-08 12:21:06 UTC (rev 1196)
@@ -8,6 +8,14 @@
           to parameters and is generally more efficient and stable than
           IF1.
 
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_5-_2:
+
+        • In the ‘pomp’ constructor, unrecognized arguments are stored
+          internally for use with user-supplied model functions.  As of
+          this version, an informative message is generated when this
+          happens.  Previously, this silent behavior was a source of
+          confusion for some users.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_5-_1:
 
         • The unfortunately named ‘pomp’ arguments

Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/inst/NEWS.Rd	2015-06-08 12:21:06 UTC (rev 1196)
@@ -6,6 +6,13 @@
     This allows a more general structure for the random perturbations applied to parameters and is generally more efficient and stable than IF1.
   }
 }
+\section{Changes in \pkg{pomp} version 0.65-2}{
+  \itemize{
+    \item In the \code{pomp} constructor, unrecognized arguments are stored internally for use with user-supplied model functions.
+    As of this version, an informative message is generated when this happens.
+    Previously, this silent behavior was a source of confusion for some users.
+  }
+}
 \section{Changes in \pkg{pomp} version 0.65-1}{
   \itemize{
     \item The unfortunately named \code{pomp} arguments \code{parameter.transform} and \code{parameter.inv.transform} have been deprecated in favor of the more mnemonic \code{toEstimationScale} and \code{fromEstimationScale}.

Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -18,7 +18,7 @@
 > library(pomp)
 > 
 > pompExample(bbs)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period','logvar','logitvar'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period','logvar','logitvar'
 newly created object(s):
  bbs 
 > 
@@ -81,4 +81,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.244   0.056   2.307 
+  2.216   0.056   2.277 

Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/bbs.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -18,7 +18,7 @@
 > library(pomp)
 > 
 > pompExample(bbs)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period','logvar','logitvar'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period','logvar','logitvar'
 newly created object(s):
  bbs 
 > 
@@ -72,4 +72,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.864   0.072   5.951 
+  5.836   0.080   5.930 

Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/blowflies.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -18,8 +18,8 @@
 > library(pomp)
 > 
 > pompExample(blowflies)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'y.init'
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'y.init'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'y.init'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'y.init'
 newly created object(s):
  blowflies1 blowflies2 
 > 
@@ -72,4 +72,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.172   0.044   1.218 
+  1.144   0.048   1.193 

Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/dacca.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -20,7 +20,7 @@
 > set.seed(1420306530L)
 > 
 > pompExample(dacca)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nrstage','all.state.names','comp.names','comp.ic.names'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nrstage','all.state.names','comp.names','comp.ic.names'
 newly created object(s):
  dacca 
 > 
@@ -106,4 +106,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 10.412   0.040  10.482 
+ 10.344   0.068  10.445 

Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/dimchecks.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -177,4 +177,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.488   0.048   0.531 
+  0.472   0.052   0.524 

Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/fhn.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -91,4 +91,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.948   0.028   1.143 
+  0.932   0.040   1.151 

Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/filtfail.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -114,4 +114,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.464   0.068   0.528 
+  0.484   0.052   0.532 

Modified: pkg/pomp/tests/getting_started.Rout.save
===================================================================
--- pkg/pomp/tests/getting_started.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/getting_started.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -188,4 +188,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 77.892   0.420  80.054 
+ 77.372   0.508  80.185 

Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/gillespie.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -115,7 +115,7 @@
 105 0.1666667
 > 
 > pompExample(gillespie.sir)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
 newly created object(s):
  gillespie.sir 
 > 
@@ -130,4 +130,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.372   0.056   2.454 
+  2.396   0.040   2.574 

Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/gompertz.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -134,4 +134,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.444   0.032   1.473 
+  1.400   0.072   1.479 

Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/logistic.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -122,4 +122,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.744   0.072   0.920 
+  0.776   0.028   0.933 

Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-abc.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -137,4 +137,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  8.712   0.072   8.959 
+  8.716   0.064   9.016 

Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -57,7 +57,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 2.096587 secs
+Time difference of 2.093374 secs
 > 
 > print(
 +       cbind(
@@ -99,4 +99,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.596   0.048   3.652 
+  3.604   0.044   3.657 

Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -54,7 +54,7 @@
 > post <- smc$post
 > 
 > print(etime <- toc-tic)
-Time difference of 1.743809 secs
+Time difference of 1.774082 secs
 > 
 > print(
 +       cbind(
@@ -96,4 +96,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.060   0.120   3.183 
+  3.196   0.060   3.260 

Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-forecast.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -59,4 +59,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.312   0.036   1.447 
+  1.312   0.040   1.461 

Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-kalman.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -162,7 +162,7 @@
     117 function evaluations used
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 2.500251 secs
+Time difference of 2.517805 secs
 > tic <- Sys.time()
 > print(loglik.mle <- -kalm.fit1$value,digits=4)
 [1] -477.2
@@ -186,4 +186,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.004   0.056   3.064 
+  3.032   0.044   3.077 

Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -72,4 +72,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 18.277   0.060  18.531 
+ 18.301   0.056  18.632 

Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-mif.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -277,4 +277,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 10.860   0.036  11.083 
+ 10.936   0.040  11.153 

Modified: pkg/pomp/tests/ou2-mif2.R
===================================================================
--- pkg/pomp/tests/ou2-mif2.R	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-mif2.R	2015-06-08 12:21:06 UTC (rev 1196)
@@ -134,4 +134,24 @@
              alpha.2=ifelse(time==1,0.2,0.1),
              alpha.3=0.2*(time<10)))
 
+m4 <- mif2(ou2,Nmif=3,start=guess1,
+           Np=function(k)if(k<20) 200 else 100,
+           cooling.fraction=0.2,
+           rw.sd=rw.sd(
+             x1.0=c(0.5,rep(0.2,99)),
+             x2.0=ivp(0.5),
+             alpha.2=ifelse(time==1,0.2,0.1),
+             alpha.3=0.2*(time<10)))
+
+m4 <- mif2(m4,Nmif=2,Np=c(rep(200,20),rep(100,80),200))
+m4 <- continue(m4,Nmif=2,cooling.fraction=0.1)
+pf <- pfilter(m4)
+m4 <- mif2(pf,Nmif=2,
+           cooling.fraction=0.2,
+           rw.sd=rw.sd(
+             x1.0=c(0.5,rep(0.2,99)),
+             x2.0=ivp(0.5),
+             alpha.2=ifelse(time==1,0.2,0.1),
+             alpha.3=0.2*(time<10)))
+
 dev.off()

Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-mif2.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -173,10 +173,30 @@
 +              alpha.2=ifelse(time==1,0.2,0.1),
 +              alpha.3=0.2*(time<10)))
 > 
+> m4 <- mif2(ou2,Nmif=3,start=guess1,
++            Np=function(k)if(k<20) 200 else 100,
++            cooling.fraction=0.2,
++            rw.sd=rw.sd(
++              x1.0=c(0.5,rep(0.2,99)),
++              x2.0=ivp(0.5),
++              alpha.2=ifelse(time==1,0.2,0.1),
++              alpha.3=0.2*(time<10)))
+> 
+> m4 <- mif2(m4,Nmif=2,Np=c(rep(200,20),rep(100,80),200))
+> m4 <- continue(m4,Nmif=2,cooling.fraction=0.1)
+> pf <- pfilter(m4)
+> m4 <- mif2(pf,Nmif=2,
++            cooling.fraction=0.2,
++            rw.sd=rw.sd(
++              x1.0=c(0.5,rep(0.2,99)),
++              x2.0=ivp(0.5),
++              alpha.2=ifelse(time==1,0.2,0.1),
++              alpha.3=0.2*(time<10)))
+> 
 > dev.off()
 null device 
           1 
 > 
 > proc.time()
    user  system elapsed 
- 65.656   0.092  66.121 
+ 65.800   0.072  66.297 

Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-nlf.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -83,4 +83,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  3.876   0.040   3.947 
+  3.900   0.048   3.997 

Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -138,4 +138,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 23.761   0.072  24.043 
+ 23.765   0.076  24.071 

Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-probe.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -341,4 +341,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  7.108   0.056   7.341 
+  7.112   0.064   7.359 

Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -52,4 +52,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.484   0.036   0.514 
+  0.476   0.052   0.525 

Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-simulate.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -33,7 +33,7 @@
 > ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.005967617 secs
+Time difference of 0.004858494 secs
 > 
 > coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
 > 
@@ -44,4 +44,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.488   0.040   0.526 
+  0.488   0.040   0.527 

Modified: pkg/pomp/tests/ou2-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-spect.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-spect.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -36,4 +36,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 17.505   0.040  17.600 
+ 18.209   0.032  18.302 

Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -173,4 +173,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.340   0.056   1.399 
+  1.400   0.032   1.434 

Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/partrans.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -67,4 +67,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.472   0.052   0.520 
+  0.444   0.076   0.521 

Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/pfilter.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -43,7 +43,7 @@
   -479.61      0.46 
 > 
 > pompExample(euler.sir)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
 newly created object(s):
  euler.sir 
 > pf <- pfilter(euler.sir,Np=100,seed=394343L)
@@ -76,4 +76,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  8.196   0.048   8.417 
+  8.224   0.052   8.455 

Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/pomppomp.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -53,4 +53,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.468   0.040   0.528 
+  0.500   0.032   0.562 

Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/prior.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -71,4 +71,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.608   0.036   0.642 
+  0.604   0.040   0.643 

Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -52,4 +52,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  2.164   0.052   2.343 
+  2.148   0.084   2.405 

Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ricker-probe.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -295,4 +295,4 @@
 > 
 > proc.time()
    user  system elapsed 
- 11.436   0.072  11.720 
+ 11.348   0.060  11.606 

Modified: pkg/pomp/tests/ricker-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-spect.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ricker-spect.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -68,4 +68,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  1.900   0.052   2.101 
+  1.920   0.032   2.118 

Modified: pkg/pomp/tests/ricker.Rout.save
===================================================================
--- pkg/pomp/tests/ricker.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/ricker.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -81,4 +81,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.580   0.056   0.735 
+  0.572   0.060   0.734 

Modified: pkg/pomp/tests/rw2.Rout.save
===================================================================
--- pkg/pomp/tests/rw2.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/rw2.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -107,7 +107,7 @@
 +             t0=0,
 +             useless=23
 +             )
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'useless'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'useless'
 > 
 > invisible(show(rw2))
 100 records of 2 observables, recorded from t = 1 to 100 
@@ -163,7 +163,7 @@
     }
     y
 }
-<environment: 0x385db18>
+<environment: 0x2feca80>
 measurement model density, dmeasure = 
 function (y, x, t, params, log, covars, ...) 
 {
@@ -176,7 +176,7 @@
         f
     else exp(f)
 }
-<environment: 0x385db18>
+<environment: 0x2feca80>
 prior simulator, rprior = 
 function not specified
 prior density, dprior = 
@@ -340,4 +340,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.828   0.032   0.861 
+  0.844   0.028   0.869 

Modified: pkg/pomp/tests/sir.Rout.save
===================================================================
--- pkg/pomp/tests/sir.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/sir.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -190,7 +190,7 @@
         method = 0L, zeronames = zeronames, tcovar = tcovar, 
         covar = covar, args = pairlist(...), gnsi = .getnativesymbolinfo)
 }
-<environment: 0x343cff8>
+<environment: 0x3dd6360>
 process model density, dprocess = 
 function (x, times, params, ..., tcovar, covar, log = FALSE, 
     .getnativesymbolinfo = TRUE) 
@@ -199,7 +199,7 @@
         params = params, tcovar = tcovar, covar = covar, log = log, 
         args = pairlist(...), gnsi = .getnativesymbolinfo)
 }
-<environment: 0x3479380>
+<environment: 0x3e1ce38>
 measurement model simulator, rmeasure = 
 function (x, t, params, covars, ...) 
 {
@@ -272,7 +272,7 @@
 > x <- simulate(po,nsim=3)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.7381604 secs
+Time difference of 0.75108 secs
 > 
 > pdf(file='sir.pdf')
 > 
@@ -289,7 +289,7 @@
 > X3 <- trajectory(po,times=t3,hmax=1/52)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.4446917 secs
+Time difference of 0.4465754 secs
 > plot(t3,X3['I',1,],type='l')
 > 
 > f1 <- dprocess(
@@ -333,7 +333,7 @@
 > 
 > ## now repeat using the compiled native codes built into the package
 > pompExample(euler.sir)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
 newly created object(s):
  euler.sir 
 > po <- euler.sir
@@ -344,7 +344,7 @@
 > x <- simulate(po,nsim=100)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 2.498907 secs
+Time difference of 2.476219 secs
 > plot(x[[1]],variables=c("S","I","R","cases","W"))
 > 
 > t3 <- seq(0,20,by=1/52)
@@ -352,7 +352,7 @@
 > X4 <- trajectory(po,times=t3,hmax=1/52)
 > toc <- Sys.time()
 > print(toc-tic)
-Time difference of 0.01583052 secs
+Time difference of 0.01562929 secs
 > plot(t3,X4['I',1,],type='l')
 > 
 > g2 <- dmeasure(
@@ -406,7 +406,7 @@
 > ## test of vectorfield integrator
 > 
 > pompExample(euler.sir)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
 newly created object(s):
  euler.sir 
 > 
@@ -450,4 +450,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  4.624   0.056   4.894 
+  4.596   0.056   4.826 

Modified: pkg/pomp/tests/skeleton.Rout.save
===================================================================
--- pkg/pomp/tests/skeleton.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/skeleton.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -41,7 +41,7 @@
 > ## non-autonomous case
 > 
 > pompExample(euler.sir)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
 newly created object(s):
  euler.sir 
 > euler.sir <- simulate(euler.sir,seed=266045243L)
@@ -93,4 +93,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.660   0.044   0.811 
+  0.644   0.068   0.813 

Modified: pkg/pomp/tests/steps.Rout.save
===================================================================
--- pkg/pomp/tests/steps.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/steps.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -29,7 +29,7 @@
 > stopifnot(identical(x,y))
 > 
 > pompExample(euler.sir)
-in 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'comp.names','ic.names','nbasis','degree','period'
 newly created object(s):
  euler.sir 
 > tm <- sort(runif(n=100,max=1))
@@ -58,4 +58,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  0.500   0.036   0.535 
+  0.476   0.052   0.526 

Modified: pkg/pomp/tests/synlik.Rout.save
===================================================================
--- pkg/pomp/tests/synlik.Rout.save	2015-06-07 23:51:14 UTC (rev 1195)
+++ pkg/pomp/tests/synlik.Rout.save	2015-06-08 12:21:06 UTC (rev 1196)
@@ -114,4 +114,4 @@
 > 
 > proc.time()
    user  system elapsed 
-  5.536   0.052   5.647 
+  5.572   0.044   5.667 

Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html	2015-06-07 23:51:14 UTC (rev 1195)
+++ www/content/NEWS.html	2015-06-08 12:21:06 UTC (rev 1196)
@@ -18,6 +18,18 @@
 
 
 
+<h3>Changes in <span class="pkg">pomp</span> version 0.65-2</h3>
+
+
+<ul>
+<li><p> In the <code>pomp</code> constructor, unrecognized arguments are stored internally for use with user-supplied model functions.
+As of this version, an informative message is generated when this happens.
+Previously, this silent behavior was a source of confusion for some users.
+</p>
+</li></ul>
+
+
+
 <h3>Changes in <span class="pkg">pomp</span> version 0.65-1</h3>
 
 

Modified: www/vignettes/pomp.pdf
===================================================================
--- www/vignettes/pomp.pdf	2015-06-07 23:51:14 UTC (rev 1195)
+++ www/vignettes/pomp.pdf	2015-06-08 12:21:06 UTC (rev 1196)
@@ -11,36 +11,33 @@
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+u.¾ûÐ=|Ù*|¦ô ÄéRe\\¶Ó—MºüÅýÐhó¡Ùo¿í+w„ 8þ`¶\u,ÍŠ?™¬ˆd6£Üö~³"ªIüç_~E‹º¢%
+‹GØâ|>'þŸÑ€ÁvÒl2hg<<kOÏnŸM¦ïÀÊ­;Ë a’d³KصT×ðU”bŠRLQŠ)J1E)ëîv
+orH;j,íXµ¡«¯¥Æô8Œåé'¶²®ÆÔZMy†¶è£`ymídÍh’u›’õ7”¬I²¦/Y{#ɺ!º‘øô}>Ã
+…çÇaÊÕ=¦œ¸!Sa$S+„’¥åðãÚl•þ7–U÷ÝuPmhU²onÚ›#±kûìºÊp¤ÕÓõÀ]Ç	Ö2ÌjÝÞHëˆïõ¿\g–¶øiY¡|}•ÝMe¤å¢L0	ÐÜH€CËšiõðýEÍßpIó#-¾¯Óp®…†ba?Òêúˆ®…ˆ‘âKÆ<xTžß™ÒæAºõÕIם}Í9®ÕòöQ»<nPž-Û4Ó®Âå­Hùn»<l–yuœn¼ø÷†&0%†„4•²´›e+G{pA¢4Èë\E{?hùòüm¹x2[¼[sDÒÜmά¶D;ÖX‹ÍpK\Ç6ï>EZÐ.O'sÆŸ¿x
+aðWY·<oJë‹K—ɪ‰CòïüüËýïÿòlvúö|uО>kÓÛ4/ôZLÛÃÙ★|Qsïd²d2qŒ¤%nÈ´K–³Ë˜ÜÄ&Yê… ‰QØI#¿žv'1#‰)Æõÿ©˜¬ö¯Ê]K“îɘ9ÒÆÞ§þ
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/pomp -r 1196

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