[Pomp-commits] r1164 - in pkg/pomp: . R inst/examples tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jun 1 14:58:25 CEST 2015
Author: kingaa
Date: 2015-06-01 14:58:24 +0200 (Mon, 01 Jun 2015)
New Revision: 1164
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/pomp.R
pkg/pomp/inst/examples/bbs.R
pkg/pomp/inst/examples/dacca.R
pkg/pomp/inst/examples/euler.sir.R
pkg/pomp/inst/examples/gillespie.sir.R
pkg/pomp/inst/examples/gompertz.R
pkg/pomp/inst/examples/ou2.R
pkg/pomp/inst/examples/ricker.R
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.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.R
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
Log:
- in 'pomp': add an informative message when objects are added to 'userdata' slot
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/DESCRIPTION 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.65-1
-Date: 2015-05-30
+Version: 0.65-2
+Date: 2015-06-01
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/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/R/pomp.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -25,7 +25,13 @@
if (missing(userdata)) userdata <- list()
added.userdata <- list(...)
- userdata[names(added.userdata)] <- added.userdata
+ if (length(added.userdata)>0) {
+ message("in ",sQuote("pomp"),
+ ": the following unrecognized argument(s) ",
+ "will be stored for use by user-defined functions: ",
+ paste(sQuote(names(added.userdata)),collapse=","))
+ userdata[names(added.userdata)] <- added.userdata
+ }
## name of shared object library
if (missing(PACKAGE)) PACKAGE <- NULL
Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/bbs.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -39,7 +39,6 @@
skeleton="_sir_ODE",
measurement.model=reports~nbinom(mu=rho*cases,size=1/sigma^2),
PACKAGE="pomp",
- obsnames = c("reports"),
statenames=c("S","I","R","cases","W"),
paramnames=c(
"gamma","mu","iota",
Modified: pkg/pomp/inst/examples/dacca.R
===================================================================
--- pkg/pomp/inst/examples/dacca.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/dacca.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -118,7 +118,6 @@
covar=covartable,
tcovar='time',
zeronames = c("M","count"),
- obsnames = "cholera.deaths",
statenames = c("S","I","Rs","R1","M","W","count"),
paramnames = c("tau","gamma","eps","delta","deltaI",
"log.omega1","sd.beta","beta.trend","log.beta1",
Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/euler.sir.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -233,7 +233,6 @@
rmeasure="_sir_binom_rmeasure",
dmeasure="_sir_binom_dmeasure",
PACKAGE="pomp",
- obsnames = c("reports"),
statenames=c("S","I","R","cases","W"),
paramnames=c(
"gamma","mu","iota",
Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -560,7 +560,6 @@
skeleton="_sir_ODE",
measurement.model=reports~binom(size=cases,prob=rho),
PACKAGE="pomp",
- obsnames = c("reports"),
statenames=c("S","I","R","N","cases"),
paramnames=c(
"gamma","mu","iota",
Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/gompertz.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -118,7 +118,6 @@
skeleton="_gompertz_skeleton",
paramnames=c("r","K","sigma","tau"),
statenames=c("X"),
- obsnames=c("Y"),
fromEstimationScale=function(params,...){
exp(params)
},
Modified: pkg/pomp/inst/examples/ou2.R
===================================================================
--- pkg/pomp/inst/examples/ou2.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/ou2.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -120,7 +120,6 @@
"tau"
),
statenames = c("x1","x2"),
- obsnames = c("y1","y2"),
params=c(
alpha.1=0.8, alpha.2=-0.5, alpha.3=0.3, alpha.4=0.9,
sigma.1=3, sigma.2=-0.5, sigma.3=2,
Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/inst/examples/ricker.R 2015-06-01 12:58:24 UTC (rev 1164)
@@ -68,7 +68,6 @@
skeleton="_ricker_skeleton",
paramnames=c("r","sigma","phi"),
statenames=c("N","e"),
- obsnames=c("y"),
toEstimationScale=function(params,...) {
params[c("r","sigma","phi","N.0")] <- log(params[c("r","sigma","phi","N.0")])
params
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,5 +1,5 @@
-R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -18,6 +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'
newly created object(s):
bbs
>
@@ -80,4 +81,4 @@
>
> proc.time()
user system elapsed
- 2.709 0.041 2.740
+ 2.244 0.056 2.307
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/bbs.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,10 +16,9 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> 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'
newly created object(s):
bbs
>
@@ -73,4 +72,4 @@
>
> proc.time()
user system elapsed
- 7.153 0.049 7.193
+ 5.864 0.072 5.951
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/blowflies.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,10 +16,10 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> 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'
newly created object(s):
blowflies1 blowflies2
>
@@ -72,4 +72,4 @@
>
> proc.time()
user system elapsed
- 1.304 0.044 1.380
+ 1.172 0.044 1.218
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/dacca.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,12 +16,11 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> 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'
newly created object(s):
dacca
>
@@ -107,4 +106,4 @@
>
> proc.time()
user system elapsed
- 10.852 0.064 10.968
+ 10.412 0.040 10.482
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/dimchecks.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(1420306530L)
>
@@ -179,4 +177,4 @@
>
> proc.time()
user system elapsed
- 0.560 0.092 0.677
+ 0.488 0.048 0.531
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/fhn.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pdf.options(useDingbats=FALSE)
> pdf(file="fhn.pdf")
@@ -93,4 +91,4 @@
>
> proc.time()
user system elapsed
- 1.084 0.064 1.285
+ 0.948 0.028 1.143
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/filtfail.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(834454394L)
>
@@ -116,4 +114,4 @@
>
> proc.time()
user system elapsed
- 0.576 0.068 0.660
+ 0.464 0.068 0.528
Modified: pkg/pomp/tests/getting_started.Rout.save
===================================================================
--- pkg/pomp/tests/getting_started.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/getting_started.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -188,4 +188,4 @@
>
> proc.time()
user system elapsed
- 77.416 0.464 79.733
+ 77.484 0.432 79.814
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/gillespie.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> params <- c(
+ nu=1/70,
@@ -117,6 +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'
newly created object(s):
gillespie.sir
>
@@ -131,4 +130,4 @@
>
> proc.time()
user system elapsed
- 2.564 0.048 2.635
+ 2.372 0.056 2.454
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/gompertz.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
> options(digits=4)
>
> pompExample(gompertz)
@@ -136,4 +134,4 @@
>
> proc.time()
user system elapsed
- 1.838 0.040 1.853
+ 1.444 0.032 1.473
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/logistic.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> po <- pomp(
+ data=rbind(obs=rep(0,1000)),
@@ -124,4 +122,4 @@
>
> proc.time()
user system elapsed
- 0.976 0.052 1.175
+ 0.744 0.072 0.920
Modified: pkg/pomp/tests/ou2-abc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-abc.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-abc.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -18,8 +18,6 @@
> ### OU2 test of abc for pomp
>
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
> pompExample(ou2)
newly created object(s):
ou2
@@ -139,4 +137,4 @@
>
> proc.time()
user system elapsed
- 11.422 0.073 11.497
+ 8.712 0.072 8.959
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(398585L)
> pompExample(ou2)
@@ -59,7 +57,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.789886 secs
+Time difference of 2.096587 secs
>
> print(
+ cbind(
@@ -101,4 +99,4 @@
>
> proc.time()
user system elapsed
- 4.688 0.064 4.785
+ 3.596 0.048 3.652
Modified: pkg/pomp/tests/ou2-bsmc2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-bsmc2.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -16,8 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(398585L)
> pompExample(ou2)
@@ -56,7 +54,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.022153 secs
+Time difference of 1.743809 secs
>
> print(
+ cbind(
@@ -98,4 +96,4 @@
>
> proc.time()
user system elapsed
- 3.588 0.084 3.697
+ 3.060 0.120 3.183
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(921625222L)
>
@@ -61,4 +59,4 @@
>
> proc.time()
user system elapsed
- 1.420 0.036 1.559
+ 1.312 0.036 1.447
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(577639485L)
>
@@ -164,7 +162,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 3.41739 secs
+Time difference of 2.500251 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -188,4 +186,4 @@
>
> proc.time()
user system elapsed
- 3.933 0.035 3.954
+ 3.004 0.056 3.064
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -74,4 +72,4 @@
>
> proc.time()
user system elapsed
- 25.136 0.029 25.180
+ 18.277 0.060 18.531
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -277,4 +277,4 @@
>
> proc.time()
user system elapsed
- 11.468 0.028 11.712
+ 10.860 0.036 11.083
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -142,4 +140,4 @@
>
> proc.time()
user system elapsed
- 66.324 0.058 66.448
+ 46.974 0.116 47.441
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(583615606L)
>
@@ -85,4 +83,4 @@
>
> proc.time()
user system elapsed
- 4.380 0.092 6.425
+ 3.876 0.040 3.947
Modified: pkg/pomp/tests/ou2-pmcmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-pmcmc.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -138,4 +136,4 @@
>
> proc.time()
user system elapsed
- 28.662 0.057 28.743
+ 23.849 0.080 24.151
Modified: pkg/pomp/tests/ou2-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-probe.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-probe.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,5 +1,5 @@
-R version 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -341,4 +341,4 @@
>
> proc.time()
user system elapsed
- 9.307 0.094 9.395
+ 7.108 0.056 7.341
Modified: pkg/pomp/tests/ou2-procmeas.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-procmeas.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-procmeas.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -54,4 +52,4 @@
>
> proc.time()
user system elapsed
- 0.408 0.048 0.479
+ 0.484 0.036 0.514
Modified: pkg/pomp/tests/ou2-simulate.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-simulate.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-simulate.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -35,7 +33,7 @@
> ou2.sim <- simulate(ou2,params=p,nsim=100,seed=32043858)
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 0.006910086 secs
+Time difference of 0.005967617 secs
>
> coef(ou2,c('x1.0','x2.0')) <- c(-50,50)
>
@@ -46,4 +44,4 @@
>
> proc.time()
user system elapsed
- 0.508 0.040 0.572
+ 0.488 0.040 0.526
Modified: pkg/pomp/tests/ou2-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-spect.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-spect.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
> pompExample(ou2)
newly created object(s):
ou2
@@ -38,4 +36,4 @@
>
> proc.time()
user system elapsed
- 21.537 0.040 21.670
+ 17.505 0.040 17.600
Modified: pkg/pomp/tests/ou2-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ou2-trajmatch.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(93885485L)
>
@@ -175,4 +173,4 @@
>
> proc.time()
user system elapsed
- 1.712 0.060 1.801
+ 1.340 0.056 1.399
Modified: pkg/pomp/tests/partrans.Rout.save
===================================================================
--- pkg/pomp/tests/partrans.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/partrans.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -67,4 +67,4 @@
>
> proc.time()
user system elapsed
- 0.504 0.024 0.526
+ 0.472 0.052 0.520
Modified: pkg/pomp/tests/pfilter.Rout.save
===================================================================
--- pkg/pomp/tests/pfilter.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/pfilter.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -45,6 +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'
newly created object(s):
euler.sir
> pf <- pfilter(euler.sir,Np=100,seed=394343L)
@@ -77,4 +76,4 @@
>
> proc.time()
user system elapsed
- 8.448 0.080 8.699
+ 8.196 0.048 8.417
Modified: pkg/pomp/tests/pomppomp.Rout.save
===================================================================
--- pkg/pomp/tests/pomppomp.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/pomppomp.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ricker)
newly created object(s):
@@ -55,4 +53,4 @@
>
> proc.time()
user system elapsed
- 0.580 0.064 0.663
+ 0.468 0.040 0.528
Modified: pkg/pomp/tests/prior.Rout.save
===================================================================
--- pkg/pomp/tests/prior.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/prior.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ou2)
newly created object(s):
@@ -73,4 +71,4 @@
>
> proc.time()
user system elapsed
- 0.736 0.056 0.809
+ 0.608 0.036 0.642
Modified: pkg/pomp/tests/ricker-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-bsmc.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ricker-bsmc.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 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 +16,6 @@
Type 'q()' to quit R.
> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
>
> pompExample(ricker)
newly created object(s):
@@ -54,4 +52,4 @@
>
> proc.time()
user system elapsed
- 2.604 0.072 2.860
+ 2.164 0.052 2.343
Modified: pkg/pomp/tests/ricker-probe.Rout.save
===================================================================
--- pkg/pomp/tests/ricker-probe.Rout.save 2015-06-01 12:58:00 UTC (rev 1163)
+++ pkg/pomp/tests/ricker-probe.Rout.save 2015-06-01 12:58:24 UTC (rev 1164)
@@ -1,6 +1,6 @@
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
+R version 3.2.0 (2015-04-16) -- "Full of Ingredients"
+Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1164
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