[Pomp-commits] r879 - in pkg/pomp: . R inst inst/examples man tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Jan 10 20:51:11 CET 2014
Author: kingaa
Date: 2014-01-10 20:51:10 +0100 (Fri, 10 Jan 2014)
New Revision: 879
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/example.R
pkg/pomp/inst/CITATION
pkg/pomp/inst/NEWS
pkg/pomp/inst/examples/bbs.R
pkg/pomp/inst/examples/blowflies.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/inst/examples/rw2.R
pkg/pomp/inst/examples/verhulst.R
pkg/pomp/man/example.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/gillespie.Rout.save
pkg/pomp/tests/gompertz.Rout.save
pkg/pomp/tests/logistic.Rout.save
pkg/pomp/tests/ou2-bsmc.Rout.save
pkg/pomp/tests/ou2-forecast.Rout.save
pkg/pomp/tests/ou2-icfit.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-trajmatch.Rout.save
pkg/pomp/tests/partrans.Rout.save
pkg/pomp/tests/pfilter.Rout.save
pkg/pomp/tests/pomppomp.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
pkg/pomp/tests/verhulst.Rout.save
Log:
- add optional 'envir' argument to 'pompExample'
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/DESCRIPTION 2014-01-10 19:51:10 UTC (rev 879)
@@ -1,8 +1,8 @@
Package: pomp
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.45-8
-Date: 2014-01-09
+Version: 0.46-1
+Date: 2014-01-10
Authors at R: c(
person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
Modified: pkg/pomp/R/example.R
===================================================================
--- pkg/pomp/R/example.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/R/example.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -1,16 +1,22 @@
-pompExample <- function (example) {
- if (missing(example)) {
+pompExample <- function (example, envir = .GlobalEnv) {
+ example <- as.character(substitute(example))
+ if (example=="") {
avlbl <- list.files(
path=system.file("examples",package="pomp"),
pattern=".+?R$"
)
avlbl <- gsub("\\.R$","",avlbl)
- cat("available pomp examples:\n",sQuote(avlbl),"\n")
+ avlbl
} else {
- ex <- as.character(substitute(example))
- file <- system.file(file.path("examples",paste(ex,".R",sep="")),package="pomp")
+ file <- system.file(
+ file.path("examples",paste(example,".R",sep="")),
+ package="pomp"
+ )
objs <- source(file,local=TRUE)
- cat("newly created pomp objects:\n",objs$value,"\n")
+ for (i in seq_along(objs$value)) {
+ assign(objs$value[i],get(objs$value[i]),envir=envir)
+ }
+ cat("newly created pomp object(s):\n",objs$value,"\n")
+ invisible(NULL)
}
- invisible(NULL)
}
Modified: pkg/pomp/inst/CITATION
===================================================================
--- pkg/pomp/inst/CITATION 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/CITATION 2014-01-10 19:51:10 UTC (rev 879)
@@ -7,17 +7,19 @@
as.person("Aaron A. King"),
as.person("Edward L. Ionides"),
as.person("Carles Martinez Bret\\'o"),
- as.person("Steve Ellner"),
- as.person("Bruce Kendall"),
- as.person("Helen Wearing"),
+ as.person("Stephen P. Ellner"),
as.person("Matthew J. Ferrari"),
+ as.person("Bruce E. Kendall"),
as.person("Michael Lavine"),
- as.person("Daniel C. Reuman")
+ as.person("Dao Nguyen"),
+ as.person("Daniel C. Reuman"),
+ as.person("Helen Wearing"),
+ as.person("Simon N. Wood")
),
- year=2010,
+ year=2014,
url="http://pomp.r-forge.r-rproject.org",
textVersion=paste(
- "Aaron A. King, E. L. Ionides, C. M. Bret\\'o, S. P. Ellner, B. E. Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, and Daniel C. Reuman",
+ "A. A. King, E. L. Ionides, C. M. Bret\\'o, S. P. Ellner, M. J. Ferrari, B. E. Kendall, M. Lavine, D. Nguyen, D. C. Reuman, H. Wearing, and S. N. Wood",
"pomp: Statistical inference for partially observed Markov processes (R package)",
"http://pomp.r-forge.r-project.org"
)
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/NEWS 2014-01-10 19:51:10 UTC (rev 879)
@@ -1,4 +1,9 @@
NEWS
+0.46-1
+ o 'pompExample' now has an optional argument, 'envir', determining which environment the pomp object will be loaded into.
+
+ o 'logmeanexp' now has an optional argument, 'se', allowing for computation of an approximate standard error.
+
0.45-8
o bug fix in 'gompertz' example.
Modified: pkg/pomp/inst/examples/bbs.R
===================================================================
--- pkg/pomp/inst/examples/bbs.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/bbs.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -18,67 +18,63 @@
14;5
")
-po <- pomp(
- data=flu,
- times="day",
- t0=0,
- rprocess=euler.sim(
- step.fun="_sir_euler_simulator",
- delta.t=1/12,
- PACKAGE="pomp"
- ),
- skeleton.type="vectorfield",
- skeleton="_sir_ODE",
- measurement.model=reports~norm(mean=rho*cases,sd=1+sigma*cases),
- PACKAGE="pomp",
- obsnames = c("reports"),
- statenames=c("S","I","R","cases","W"),
- paramnames=c(
- "gamma","mu","iota",
- "beta","beta.sd","pop","rho",
- "S.0","I.0","R.0"
- ),
- zeronames=c("cases"),
- comp.names=c("S","I","R"),
- ic.names=c("S.0","I.0","R.0"),
- nbasis=1L,
- degree=0L,
- period=1.0,
- logvar=c(
- "beta","gamma","mu","iota","sigma","beta.sd",
- "S.0","I.0","R.0"
- ),
- logitvar="rho",
- parameter.inv.transform=function (params, logvar, logitvar, ...) {
- params[logvar] <- log(params[logvar])
- params[logitvar] <- qlogis(params[logitvar])
- params
- },
- parameter.transform=function (params, logvar, logitvar, ...) {
- params[logvar] <- exp(params[logvar])
- params[logitvar] <- plogis(params[logitvar])
- params
- },
- initializer=function(params, t0, comp.names, ic.names, ...) {
- snames <- c("S","I","R","cases","W")
- fracs <- params[ic.names]
- x0 <- numeric(length(snames))
- names(x0) <- snames
- x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
- x0
- }
- )
+pomp(
+ data=flu,
+ times="day",
+ t0=0,
+ params=c(
+ gamma=1/3,mu=0.0,iota=0.0,
+ beta=1.4,
+ beta.sd=0,
+ pop=1400,
+ rho=0.9,sigma=3.6,
+ S.0=0.999,I.0=0.001,R.0=0
+ ),
+ rprocess=euler.sim(
+ step.fun="_sir_euler_simulator",
+ delta.t=1/12,
+ PACKAGE="pomp"
+ ),
+ skeleton.type="vectorfield",
+ skeleton="_sir_ODE",
+ measurement.model=reports~norm(mean=rho*cases,sd=1+sigma*cases),
+ PACKAGE="pomp",
+ obsnames = c("reports"),
+ statenames=c("S","I","R","cases","W"),
+ paramnames=c(
+ "gamma","mu","iota",
+ "beta","beta.sd","pop","rho",
+ "S.0","I.0","R.0"
+ ),
+ zeronames=c("cases"),
+ comp.names=c("S","I","R"),
+ ic.names=c("S.0","I.0","R.0"),
+ nbasis=1L,
+ degree=0L,
+ period=1.0,
+ logvar=c(
+ "beta","gamma","mu","iota","sigma","beta.sd",
+ "S.0","I.0","R.0"
+ ),
+ logitvar="rho",
+ parameter.inv.transform=function (params, logvar, logitvar, ...) {
+ params[logvar] <- log(params[logvar])
+ params[logitvar] <- qlogis(params[logitvar])
+ params
+ },
+ parameter.transform=function (params, logvar, logitvar, ...) {
+ params[logvar] <- exp(params[logvar])
+ params[logitvar] <- plogis(params[logitvar])
+ params
+ },
+ initializer=function(params, t0, comp.names, ic.names, ...) {
+ snames <- c("S","I","R","cases","W")
+ fracs <- params[ic.names]
+ x0 <- numeric(length(snames))
+ names(x0) <- snames
+ x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
+ x0
+ }
+ ) -> bbs
-coef(po) <- c(
- gamma=1/3,mu=0.0,iota=0.0,
- beta=1.4,
- beta.sd=0,
- pop=1400,
- rho=0.9,sigma=3.6,
- S.0=0.999,I.0=0.001,R.0=0
- )
-
-bbs <- po
-
-assign("bbs",bbs,envir=.GlobalEnv)
c("bbs")
Modified: pkg/pomp/inst/examples/blowflies.R
===================================================================
--- pkg/pomp/inst/examples/blowflies.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/blowflies.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -970,7 +970,4 @@
}
-assign("blowflies1",blowflies1,envir=.GlobalEnv)
-assign("blowflies2",blowflies2,envir=.GlobalEnv)
-
c("blowflies1","blowflies2")
Modified: pkg/pomp/inst/examples/dacca.R
===================================================================
--- pkg/pomp/inst/examples/dacca.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/dacca.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -105,6 +105,7 @@
data=cholera,
times='time',
t0=t0,
+ params=mle,
nrstage = nrstage,
rprocess = euler.sim(
step.fun = "_cholmodel_one",
@@ -153,7 +154,4 @@
}
) -> dacca
-coef(dacca) <- mle
-
-assign("dacca",dacca,envir=.GlobalEnv)
c("dacca")
Modified: pkg/pomp/inst/examples/euler.sir.R
===================================================================
--- pkg/pomp/inst/examples/euler.sir.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/euler.sir.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -211,56 +211,54 @@
4;168
'
+pomp(
+ data=read.csv2(text=dat),
+ times="time",
+ t0=0,
+ params=c(
+ gamma=26,mu=0.02,iota=0.01,
+ beta1=400,beta2=480,beta3=320,
+ beta.sd=1e-3,
+ pop=2.1e6,
+ rho=0.6,
+ S.0=26/400,I.0=0.001,R.0=1-26/400
+ ),
+ rprocess=euler.sim(
+ step.fun="_sir_euler_simulator",
+ delta.t=1/52/20,
+ PACKAGE="pomp"
+ ),
+ skeleton.type="vectorfield",
+ skeleton="_sir_ODE",
+ 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",
+ "beta1","beta.sd","pop","rho",
+ "S.0","I.0","R.0"
+ ),
+ zeronames=c("cases"),
+ comp.names=c("S","I","R"),
+ ic.names=c("S.0","I.0","R.0"),
+ parameter.transform="_sir_par_trans",
+ parameter.inv.transform="_sir_par_untrans",
+ nbasis=3L,
+ degree=3L,
+ period=1.0,
+ initializer=function(params, t0, comp.names, ic.names, ...) {
+ snames <- c("S","I","R","cases","W")
+ fracs <- params[ic.names]
+ x0 <- numeric(length(snames))
+ names(x0) <- snames
+ x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
+ x0
+ }
+ ) -> euler.sir
-po <- pomp(
- data=read.csv2(text=dat),
- times="time",
- t0=0,
- params=c(
- gamma=26,mu=0.02,iota=0.01,
- beta1=400,beta2=480,beta3=320,
- beta.sd=1e-3,
- pop=2.1e6,
- rho=0.6,
- S.0=26/400,I.0=0.001,R.0=1-26/400
- ),
- rprocess=euler.sim(
- step.fun="_sir_euler_simulator",
- delta.t=1/52/20,
- PACKAGE="pomp"
- ),
- skeleton.type="vectorfield",
- skeleton="_sir_ODE",
- 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",
- "beta1","beta.sd","pop","rho",
- "S.0","I.0","R.0"
- ),
- zeronames=c("cases"),
- comp.names=c("S","I","R"),
- ic.names=c("S.0","I.0","R.0"),
- parameter.transform="_sir_par_trans",
- parameter.inv.transform="_sir_par_untrans",
- nbasis=3L,
- degree=3L,
- period=1.0,
- initializer=function(params, t0, comp.names, ic.names, ...) {
- snames <- c("S","I","R","cases","W")
- fracs <- params[ic.names]
- x0 <- numeric(length(snames))
- names(x0) <- snames
- x0[comp.names] <- round(params['pop']*fracs/sum(fracs))
- x0
- }
- )
-
## the following was originally used to generate the data
## simulate(po,nsim=1,seed=329343545L) -> euler.sir
-assign("euler.sir",po,envir=.GlobalEnv)
c("euler.sir")
Modified: pkg/pomp/inst/examples/gillespie.sir.R
===================================================================
--- pkg/pomp/inst/examples/gillespie.sir.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/gillespie.sir.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -583,10 +583,9 @@
x0[comp.names] <- round(params["pop"]*fracs/sum(fracs))
x0
}
- ) -> po
+ ) -> gillespie.sir
## originally, the data were created via:
## simulate(po,nsim=1,seed=1165270654L) -> gillespie.sir
-assign("gillespie.sir",po,envir=.GlobalEnv)
c("gillespie.sir")
Modified: pkg/pomp/inst/examples/gompertz.R
===================================================================
--- pkg/pomp/inst/examples/gompertz.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/gompertz.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -104,31 +104,30 @@
100;1,28071364632546;1,23495259845453
'
-po <- pomp(
- data=subset(read.csv2(text=dat),select=-X),
- times="time",
- t0=0,
- params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),
- rprocess=discrete.time.sim(
- step.fun="_gompertz_simulator"
- ),
- rmeasure="_gompertz_normal_rmeasure",
- dmeasure="_gompertz_normal_dmeasure",
- skeleton.type="map",
- skeleton="_gompertz_skeleton",
- paramnames=c("r","K","sigma","tau"),
- statenames=c("X"),
- obsnames=c("Y"),
- parameter.transform=function(params,...){
- exp(params)
- },
- parameter.inv.transform=function(params,...){
- log(params)
- }
- )
+pomp(
+ data=subset(read.csv2(text=dat),select=-X),
+ times="time",
+ t0=0,
+ params=c(K=1,r=0.1,sigma=0.1,tau=0.1,X.0=1),
+ rprocess=discrete.time.sim(
+ step.fun="_gompertz_simulator"
+ ),
+ rmeasure="_gompertz_normal_rmeasure",
+ dmeasure="_gompertz_normal_dmeasure",
+ skeleton.type="map",
+ skeleton="_gompertz_skeleton",
+ paramnames=c("r","K","sigma","tau"),
+ statenames=c("X"),
+ obsnames=c("Y"),
+ parameter.transform=function(params,...){
+ exp(params)
+ },
+ parameter.inv.transform=function(params,...){
+ log(params)
+ }
+ ) -> gompertz
## the following was used to create the data included
## simulate(po,nsim=1,seed=299438676L) -> gompertz
-assign("gompertz",po,envir=.GlobalEnv)
c("gompertz")
Modified: pkg/pomp/inst/examples/ou2.R
===================================================================
--- pkg/pomp/inst/examples/ou2.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/ou2.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -127,7 +127,6 @@
tau=1,
x1.0=-3, x2.0=4
)
- ) -> po
+ ) -> ou2
-assign("ou2",po,envir=.GlobalEnv)
c("ou2")
Modified: pkg/pomp/inst/examples/ricker.R
===================================================================
--- pkg/pomp/inst/examples/ricker.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/ricker.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -78,7 +78,6 @@
params
},
PACKAGE="pomp"
- ) -> po
+ ) -> ricker
-assign("ricker",po,envir=.GlobalEnv)
c("ricker")
Modified: pkg/pomp/inst/examples/rw2.R
===================================================================
--- pkg/pomp/inst/examples/rw2.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/rw2.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -133,7 +133,6 @@
y1 ~ norm(mean=x1,sd=tau),
y2 ~ norm(mean=x2,sd=tau)
)
- ) -> po
+ ) -> rw2
-assign("rw2",po,envir=.GlobalEnv)
c("rw2")
Modified: pkg/pomp/inst/examples/verhulst.R
===================================================================
--- pkg/pomp/inst/examples/verhulst.R 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/inst/examples/verhulst.R 2014-01-10 19:51:10 UTC (rev 879)
@@ -1047,7 +1047,6 @@
names(f) <- "n"
f
}
- ) -> po
+ ) -> verhulst
-assign("verhulst",po,envir=.GlobalEnv)
c("verhulst")
Modified: pkg/pomp/man/example.Rd
===================================================================
--- pkg/pomp/man/example.Rd 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/man/example.Rd 2014-01-10 19:51:10 UTC (rev 879)
@@ -5,13 +5,16 @@
\code{pompExample} loads pre-built example \code{pomp} objects.
}
\usage{
-pompExample(example)
+pompExample(example, envir = .GlobalEnv)
}
\arguments{
\item{example}{
example to load given as a name or literal character string.
Evoked without an argument, \code{pompExample} lists all available examples.
}
+ \item{envir}{
+ the environment into which the objects should be loaded.
+ }
}
\value{
\code{pompExample} has the side effect of creating one or more \code{pomp} objects in the global workspace.
@@ -23,5 +26,8 @@
pompExample("gompertz")
}
\seealso{
- \code{\link{blowflies}}, \code{\link{dacca}}, \code{\link{gompertz}}, \code{\link{ou2}}, \code{\link{ricker}}, \code{\link{rw2}}, \code{\link{euler.sir}}, \code{\link{gillespie.sir}}, \code{\link{bbs}}, \code{\link{verhulst}}
+ \code{\link{blowflies}}, \code{\link{dacca}}, \code{\link{gompertz}},
+ \code{\link{ou2}}, \code{\link{ricker}}, \code{\link{rw2}},
+ \code{\link{euler.sir}}, \code{\link{gillespie.sir}},
+ \code{\link{bbs}}, \code{\link{verhulst}}
}
Modified: pkg/pomp/tests/bbs-trajmatch.Rout.save
===================================================================
--- pkg/pomp/tests/bbs-trajmatch.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/bbs-trajmatch.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -22,7 +21,7 @@
Loading required package: deSolve
>
> pompExample(bbs)
-newly created pomp objects:
+newly created pomp object(s):
bbs
>
> guess <- c(
@@ -70,4 +69,4 @@
>
> proc.time()
user system elapsed
- 2.176 0.032 2.241
+ 2.152 0.044 2.211
Modified: pkg/pomp/tests/bbs.Rout.save
===================================================================
--- pkg/pomp/tests/bbs.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/bbs.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -22,7 +21,7 @@
Loading required package: deSolve
>
> pompExample(bbs)
-newly created pomp objects:
+newly created pomp object(s):
bbs
>
> set.seed(48857734L)
@@ -60,4 +59,4 @@
>
> proc.time()
user system elapsed
- 2.648 0.048 2.732
+ 2.884 0.060 3.003
Modified: pkg/pomp/tests/blowflies.Rout.save
===================================================================
--- pkg/pomp/tests/blowflies.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/blowflies.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -22,7 +21,7 @@
Loading required package: deSolve
>
> pompExample(blowflies)
-newly created pomp objects:
+newly created pomp object(s):
blowflies1 blowflies2
>
> init.state(blowflies1)
@@ -72,4 +71,4 @@
>
> proc.time()
user system elapsed
- 1.124 0.056 1.204
+ 1.232 0.056 1.300
Modified: pkg/pomp/tests/dacca.Rout.save
===================================================================
--- pkg/pomp/tests/dacca.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/dacca.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -24,7 +23,7 @@
> set.seed(1420306530L)
>
> pompExample(dacca)
-newly created pomp objects:
+newly created pomp object(s):
dacca
>
> x <- as.data.frame(dacca)
@@ -52,4 +51,4 @@
>
> proc.time()
user system elapsed
- 3.304 0.044 3.379
+ 3.492 0.048 3.555
Modified: pkg/pomp/tests/dimchecks.Rout.save
===================================================================
--- pkg/pomp/tests/dimchecks.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/dimchecks.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -24,7 +23,7 @@
> set.seed(1420306530L)
>
> pompExample(ricker)
-newly created pomp objects:
+newly created pomp object(s):
ricker
> po <- ricker
>
@@ -154,7 +153,7 @@
> stopifnot(identical(g1,g3[,4:6,]))
>
> pompExample(gompertz)
-newly created pomp objects:
+newly created pomp object(s):
gompertz
> p <- parmat(coef(gompertz),5)
> f1 <- partrans(gompertz,p,"inv")
@@ -164,4 +163,4 @@
>
> proc.time()
user system elapsed
- 0.452 0.044 0.518
+ 0.480 0.052 0.542
Modified: pkg/pomp/tests/fhn.Rout.save
===================================================================
--- pkg/pomp/tests/fhn.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/fhn.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -93,4 +92,4 @@
>
> proc.time()
user system elapsed
- 0.908 0.060 1.204
+ 1.016 0.040 1.178
Modified: pkg/pomp/tests/filtfail.Rout.save
===================================================================
--- pkg/pomp/tests/filtfail.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/filtfail.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
-R version 2.15.3 (2013-03-01) -- "Security Blanket"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -118,4 +117,4 @@
>
> proc.time()
user system elapsed
- 0.464 0.044 0.524
+ 0.516 0.048 0.574
Modified: pkg/pomp/tests/gillespie.Rout.save
===================================================================
--- pkg/pomp/tests/gillespie.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/gillespie.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -119,7 +118,7 @@
105 0.1666667
>
> pompExample(gillespie.sir)
-newly created pomp objects:
+newly created pomp object(s):
gillespie.sir
>
> tail(as.data.frame(simulate(gillespie.sir,times=time(gsir),t0=timezero(gsir),seed=1165270654L)))
@@ -133,4 +132,4 @@
>
> proc.time()
user system elapsed
- 2.392 0.040 2.459
+ 2.496 0.028 2.543
Modified: pkg/pomp/tests/gompertz.Rout.save
===================================================================
--- pkg/pomp/tests/gompertz.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/gompertz.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -23,7 +22,7 @@
> options(digits=4)
>
> pompExample(gompertz)
-newly created pomp objects:
+newly created pomp object(s):
gompertz
>
> po <- gompertz
@@ -135,4 +134,4 @@
>
> proc.time()
user system elapsed
- 1.488 0.048 1.562
+ 1.544 0.020 1.584
Modified: pkg/pomp/tests/logistic.Rout.save
===================================================================
--- pkg/pomp/tests/logistic.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/logistic.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -124,4 +123,4 @@
>
> proc.time()
user system elapsed
- 0.788 0.056 0.968
+ 0.868 0.056 1.028
Modified: pkg/pomp/tests/ou2-bsmc.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-bsmc.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-bsmc.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -23,7 +22,7 @@
>
> set.seed(398585L)
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
>
> time(ou2) <- 1:10
@@ -64,7 +63,7 @@
> post <- smc$post
>
> print(etime <- toc-tic)
-Time difference of 2.994066 secs
+Time difference of 3.214472 secs
>
> print(
+ cbind(
@@ -100,4 +99,4 @@
>
> proc.time()
user system elapsed
- 4.876 0.048 4.960
+ 5.148 0.104 5.279
Modified: pkg/pomp/tests/ou2-forecast.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-forecast.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-forecast.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -24,7 +23,7 @@
> set.seed(921625222L)
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
> tm <- time(ou2)
> y <- obs(ou2)
@@ -63,4 +62,4 @@
>
> proc.time()
user system elapsed
- 1.528 0.044 1.689
+ 1.472 0.028 1.603
Modified: pkg/pomp/tests/ou2-icfit.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-icfit.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-icfit.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -24,7 +23,7 @@
> set.seed(921625222L)
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
>
> ics <- c("x1.0","x2.0") # names of the initial condition parameters
@@ -109,4 +108,4 @@
>
> proc.time()
user system elapsed
- 16.897 0.048 17.022
+ 17.689 0.044 17.801
Modified: pkg/pomp/tests/ou2-kalman.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-kalman.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-kalman.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -70,7 +69,7 @@
+ }
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
>
> # true coefficients
@@ -166,7 +165,7 @@
117 function evaluations used
> toc <- Sys.time()
> print(toc-tic)
-Time difference of 5.084913 secs
+Time difference of 3.600606 secs
> tic <- Sys.time()
> print(loglik.mle <- -kalm.fit1$value,digits=4)
[1] -477.2
@@ -190,4 +189,4 @@
>
> proc.time()
user system elapsed
- 5.596 0.044 5.680
+ 4.112 0.064 4.207
Modified: pkg/pomp/tests/ou2-mif-fp.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-mif-fp.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -22,7 +21,7 @@
Loading required package: deSolve
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
>
> set.seed(64857673L)
@@ -72,4 +71,4 @@
>
> proc.time()
user system elapsed
- 19.653 0.024 19.956
+ 19.853 0.076 20.178
Modified: pkg/pomp/tests/ou2-mif.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-mif.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -1,5 +1,5 @@
-R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -21,7 +21,7 @@
Loading required package: deSolve
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
>
> set.seed(64857673L)
@@ -282,4 +282,4 @@
>
> proc.time()
user system elapsed
- 12.416 0.084 12.654
+ 12.152 0.060 12.353
Modified: pkg/pomp/tests/ou2-mif2.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-mif2.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-mif2.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -1,7 +1,6 @@
-R version 2.15.3 (2013-03-01) -- "Security Blanket"
+R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -22,7 +21,7 @@
Loading required package: deSolve
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
>
> pdf(file="ou2-mif2.pdf")
@@ -130,4 +129,4 @@
>
> proc.time()
user system elapsed
- 49.343 0.076 49.753
+ 51.519 0.044 51.909
Modified: pkg/pomp/tests/ou2-nlf.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-nlf.Rout.save 2014-01-10 19:50:48 UTC (rev 878)
+++ pkg/pomp/tests/ou2-nlf.Rout.save 2014-01-10 19:51:10 UTC (rev 879)
@@ -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 3.0.2 (2013-09-25) -- "Frisbee Sailing"
+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.
@@ -24,7 +23,7 @@
> set.seed(594861940L)
>
> pompExample(ou2)
-newly created pomp objects:
+newly created pomp object(s):
ou2
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 879
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