[Pomp-commits] r1210 - in pkg/pompExamples: . R inst/examples tests
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jun 17 14:56:45 CEST 2015
Author: kingaa
Date: 2015-06-17 14:56:44 +0200 (Wed, 17 Jun 2015)
New Revision: 1210
Modified:
pkg/pompExamples/DESCRIPTION
pkg/pompExamples/R/pertussis.R
pkg/pompExamples/inst/examples/bbp.R
pkg/pompExamples/inst/examples/bsflu.R
pkg/pompExamples/inst/examples/bsflu3.R
pkg/pompExamples/inst/examples/budmoth.R
pkg/pompExamples/inst/examples/parus.R
pkg/pompExamples/tests/bbp.Rout.save
pkg/pompExamples/tests/budmoth.Rout.save
pkg/pompExamples/tests/ebola.Rout.save
pkg/pompExamples/tests/parus.Rout.save
pkg/pompExamples/tests/pertussis.R
pkg/pompExamples/tests/pertussis.Rout.save
Log:
- bring pompExamples up to date
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/DESCRIPTION 2015-06-17 12:56:44 UTC (rev 1210)
@@ -16,7 +16,7 @@
person(given=c("Helen"),family="Wearing",role=c("ctb")))
URL: http://pomp.r-forge.r-project.org
Description: More 'pomp' examples.
-Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.58-6)
+Depends: R(>= 3.0.0), stats, graphics, pomp(>= 0.65-1)
Suggests: plyr, reshape2, ggplot2, knitr, markdown
LinkingTo: pomp
Additional_repositories: http://r-forge.r-rproject.org
Modified: pkg/pompExamples/R/pertussis.R
===================================================================
--- pkg/pompExamples/R/pertussis.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/R/pertussis.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -15,117 +15,119 @@
invisible(datasets)
} else {
which <- as.character(substitute(which))
- simulate(
- pomp(
- data=data.frame(time=seq(from=0,to=20,by=1/52),reports=NA),
- times="time",
- t0=-1/52,
- params=switch(
- which,
- SEIR.small=c(
- birthrate=0.02, deathrate=0.02, mean.beta=450, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0, alpha.ratio=1,
- report.prob=0.3, boost.prob=0, polar.prob=0, foi.mod=0,
- popsize=5e+5, noise.sigma=0, tau=0.01,
- S.0=0.0574148031949802, E.0=0.0004081763321755, I.0=0.00067028956509212,
- R1.0=0.941506730907752, R2.0=0),
- SEIR.big=c(
- birthrate=0.02, deathrate=0.02, mean.beta=450, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0, alpha.ratio=1,
- report.prob=0.3, boost.prob=0, polar.prob=0, foi.mod=0,
- popsize=5e+6, noise.sigma=0, tau=0.01,
- S.0=0.0515635231482973, E.0=0.000437143470487014, I.0=0.000734641109212043,
- R1.0=0.947264692272004, R2.0=0),
- SEIRS.small=c(
- birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
- report.prob=0.1, boost.prob=0, polar.prob=0, foi.mod=0,
- popsize=5e+5, noise.sigma=0, tau=0.01,
- S.0=0.157360395940609, E.0=0.000837874318852172, I.0=0.00124181372794081,
- R1.0=0.45913512973054, R2.0=0.381424786282058),
- SEIRS.big=c(
- birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
- report.prob=0.1, boost.prob=0, polar.prob=0, foi.mod=0,
- popsize=5e+6, noise.sigma=0, tau=0.01,
- S.0=0.157398354546347, E.0=0.00132093662562661, I.0=0.0022558671035406,
- R1.0=0.457185201591761, R2.0=0.381839640132725),
- SEIRR.small=c(
- birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
- report.prob=0.11, boost.prob=0.75, polar.prob=0, foi.mod=0.5,
- popsize=5e+5, noise.sigma=0, tau=0.01,
- S.0=0.128943112158304, E.0=0.00068688724266688, I.0=0.00114414648269803,
- R1.0=0.638074319602244, R2.0=0.231151534514087),
- SEIRR.big=c(
- birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
- report.prob=0.11, boost.prob=0.75, polar.prob=0, foi.mod=0.5,
- popsize=5e+6, noise.sigma=0, tau=0.01,
- S.0=0.127128689912424, E.0=0.00126497004491763, I.0=0.00216092385991776,
- R1.0=0.639879739889535, R2.0=0.229565676293206),
- full.small=c(
- birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
- report.prob=0.1, boost.prob=0.75, polar.prob=0.1, foi.mod=0.5,
- popsize=5e+5, noise.sigma=0.01, tau=0.01,
- S.0=0.132553922599906, E.0=0.0010539075727066, I.0=0.00166100642162314,
- R1.0=0.641737544956371, R2.0=0.222993618449393),
- full.big=c(
- birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
- imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
- report.prob=0.1, boost.prob=0.75, polar.prob=0.1, foi.mod=0.5,
- popsize=5e+6, noise.sigma=0.01, tau=0.01,
- S.0=0.130980596244438, E.0=0.00115096693013597, I.0=0.0018994251960431,
- R1.0=0.643957103848235, R2.0=0.222011907781148),
- stop("unrecognized dataset ",sQuote(which),call.=FALSE)
- ),
- rprocess = euler.sim(
- step.fun="pertussis_sveirr_EM",
- delta.t=1/52/7, # Euler stepsize
- PACKAGE="pompExamples"
- ),
- skeleton.type="vectorfield",
- skeleton="pertussis_sveirr_skel",
- PACKAGE="pompExamples",
- paramnames=c(
- "birthrate","deathrate","mean.beta","ampl.beta",
- "imports","sigma","gamma","alpha","alpha.ratio",
- "report.prob","boost.prob","polar.prob",
- "foi.mod","noise.sigma","popsize","tau",
- "S.0","E.0","I.0","R1.0","R2.0"
- ),
- statenames=c("S","E","I","R1","R2","cases","W","err","simpop"),
- zeronames=c("cases","err"),
- ivps=c("S.0","E.0","I.0","R1.0","R2.0"),
- comp.names=c("S","E","I","R1","R2"),
- rmeasure = "negbin_rmeasure",
- dmeasure = "negbin_dmeasure",
- parameter.inv.transform="pertussis_par_untrans",
- parameter.transform="pertussis_par_trans",
- varnames=c("S","E","I","R1","R2","cases","W","err","simpop"),
- initializer = function (params, t0, varnames, comp.names, ivps, ...) {
- states <- numeric(length(varnames))
- names(states) <- varnames
- ## translate fractions into initial conditions
- frac <- params[ivps]
- states[comp.names] <- round(params['popsize']*frac/sum(frac))
- states["simpop"] <- params["popsize"]
- states
- }
- ),
- seed=switch(
- which,
- SEIR.small=1831650124L,
- SEIR.big=908022490L,
- SEIRS.small=1111340406L,
- SEIRS.big=1751228386L,
- SEIRR.small=350421545L,
- SEIRR.big=748454784L,
- full.small=581894515L,
- full.big=301057392L,
- stop("unrecognized dataset ",sQuote(which),call.=FALSE)
- )
- )
+ suppressMessages(
+ simulate(
+ pomp(
+ data=data.frame(time=seq(from=0,to=20,by=1/52),reports=NA),
+ times="time",
+ t0=-1/52,
+ params=switch(
+ which,
+ SEIR.small=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=450, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0, alpha.ratio=1,
+ report.prob=0.3, boost.prob=0, polar.prob=0, foi.mod=0,
+ popsize=5e+5, noise.sigma=0, tau=0.01,
+ S.0=0.0574148031949802, E.0=0.0004081763321755, I.0=0.00067028956509212,
+ R1.0=0.941506730907752, R2.0=0),
+ SEIR.big=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=450, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0, alpha.ratio=1,
+ report.prob=0.3, boost.prob=0, polar.prob=0, foi.mod=0,
+ popsize=5e+6, noise.sigma=0, tau=0.01,
+ S.0=0.0515635231482973, E.0=0.000437143470487014, I.0=0.000734641109212043,
+ R1.0=0.947264692272004, R2.0=0),
+ SEIRS.small=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
+ report.prob=0.1, boost.prob=0, polar.prob=0, foi.mod=0,
+ popsize=5e+5, noise.sigma=0, tau=0.01,
+ S.0=0.157360395940609, E.0=0.000837874318852172, I.0=0.00124181372794081,
+ R1.0=0.45913512973054, R2.0=0.381424786282058),
+ SEIRS.big=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
+ report.prob=0.1, boost.prob=0, polar.prob=0, foi.mod=0,
+ popsize=5e+6, noise.sigma=0, tau=0.01,
+ S.0=0.157398354546347, E.0=0.00132093662562661, I.0=0.0022558671035406,
+ R1.0=0.457185201591761, R2.0=0.381839640132725),
+ SEIRR.small=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
+ report.prob=0.11, boost.prob=0.75, polar.prob=0, foi.mod=0.5,
+ popsize=5e+5, noise.sigma=0, tau=0.01,
+ S.0=0.128943112158304, E.0=0.00068688724266688, I.0=0.00114414648269803,
+ R1.0=0.638074319602244, R2.0=0.231151534514087),
+ SEIRR.big=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
+ report.prob=0.11, boost.prob=0.75, polar.prob=0, foi.mod=0.5,
+ popsize=5e+6, noise.sigma=0, tau=0.01,
+ S.0=0.127128689912424, E.0=0.00126497004491763, I.0=0.00216092385991776,
+ R1.0=0.639879739889535, R2.0=0.229565676293206),
+ full.small=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
+ report.prob=0.1, boost.prob=0.75, polar.prob=0.1, foi.mod=0.5,
+ popsize=5e+5, noise.sigma=0.01, tau=0.01,
+ S.0=0.132553922599906, E.0=0.0010539075727066, I.0=0.00166100642162314,
+ R1.0=0.641737544956371, R2.0=0.222993618449393),
+ full.big=c(
+ birthrate=0.02, deathrate=0.02, mean.beta=150, ampl.beta=0.15,
+ imports=10, sigma=46, gamma=26, alpha=0.1, alpha.ratio=1,
+ report.prob=0.1, boost.prob=0.75, polar.prob=0.1, foi.mod=0.5,
+ popsize=5e+6, noise.sigma=0.01, tau=0.01,
+ S.0=0.130980596244438, E.0=0.00115096693013597, I.0=0.0018994251960431,
+ R1.0=0.643957103848235, R2.0=0.222011907781148),
+ stop("unrecognized dataset ",sQuote(which),call.=FALSE)
+ ),
+ rprocess = euler.sim(
+ step.fun="pertussis_sveirr_EM",
+ delta.t=1/52/7, # Euler stepsize
+ PACKAGE="pompExamples"
+ ),
+ skeleton.type="vectorfield",
+ skeleton="pertussis_sveirr_skel",
+ PACKAGE="pompExamples",
+ paramnames=c(
+ "birthrate","deathrate","mean.beta","ampl.beta",
+ "imports","sigma","gamma","alpha","alpha.ratio",
+ "report.prob","boost.prob","polar.prob",
+ "foi.mod","noise.sigma","popsize","tau",
+ "S.0","E.0","I.0","R1.0","R2.0"
+ ),
+ statenames=c("S","E","I","R1","R2","cases","W","err","simpop"),
+ zeronames=c("cases","err"),
+ ivps=c("S.0","E.0","I.0","R1.0","R2.0"),
+ comp.names=c("S","E","I","R1","R2"),
+ rmeasure = "negbin_rmeasure",
+ dmeasure = "negbin_dmeasure",
+ toEstimationScale="pertussis_par_untrans",
+ fromEstimationScale="pertussis_par_trans",
+ varnames=c("S","E","I","R1","R2","cases","W","err","simpop"),
+ initializer = function (params, t0, varnames, comp.names, ivps, ...) {
+ states <- numeric(length(varnames))
+ names(states) <- varnames
+ ## translate fractions into initial conditions
+ frac <- params[ivps]
+ states[comp.names] <- round(params['popsize']*frac/sum(frac))
+ states["simpop"] <- params["popsize"]
+ states
+ }
+ ),
+ seed=switch(
+ which,
+ SEIR.small=1831650124L,
+ SEIR.big=908022490L,
+ SEIRS.small=1111340406L,
+ SEIRS.big=1751228386L,
+ SEIRR.small=350421545L,
+ SEIRR.big=748454784L,
+ full.small=581894515L,
+ full.big=301057392L,
+ stop("unrecognized dataset ",sQuote(which),call.=FALSE)
+ )
+ )
+ )
}
}
Modified: pkg/pompExamples/inst/examples/bbp.R
===================================================================
--- pkg/pompExamples/inst/examples/bbp.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/inst/examples/bbp.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -87,12 +87,12 @@
### dmeasure=Csnippet("lik=dnbinom_mu(deaths,theta,ratio*exp(y),give_log);"),
logvar=c("beta","delta","ratio","sigma","theta","mu"),
logitvar=c("y0"),
- parameter.inv.transform=function (params, logvar, logitvar, ...) {
+ toEstimationScale=function (params, logvar, logitvar, ...) {
params[logvar] <- log(params[logvar])
params[logitvar] <- qlogis(params[logitvar])
params
},
- parameter.transform=function (params, logvar, logitvar, ...) {
+ fromEstimationScale=function (params, logvar, logitvar, ...) {
params[logvar] <- exp(params[logvar])
params[logitvar] <- plogis(params[logitvar])
params
Modified: pkg/pompExamples/inst/examples/bsflu.R
===================================================================
--- pkg/pompExamples/inst/examples/bsflu.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/inst/examples/bsflu.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -89,8 +89,8 @@
skeleton.type="map",
rmeasure=Csnippet(rmeas),
dmeasure=Csnippet(dmeas),
- parameter.transform=Csnippet(partrans),
- parameter.inv.transform=Csnippet(paruntrans),
+ fromEstimationScale=Csnippet(partrans),
+ toEstimationScale=Csnippet(paruntrans),
obsnames = c("confined","convalescent"),
statenames=c("S","I","R","C"),
paramnames=c(
Modified: pkg/pompExamples/inst/examples/bsflu3.R
===================================================================
--- pkg/pompExamples/inst/examples/bsflu3.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/inst/examples/bsflu3.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -97,8 +97,8 @@
skeleton.type="map",
rmeasure=Csnippet(rmeas),
dmeasure=Csnippet(dmeas),
- parameter.transform=Csnippet(partrans),
- parameter.inv.transform=Csnippet(paruntrans),
+ fromEstimationScale=Csnippet(partrans),
+ toEstimationScale=Csnippet(paruntrans),
obsnames = c("confined","convalescent"),
statenames=c("S","I","R1","R2","R3","C"),
paramnames=c(
Modified: pkg/pompExamples/inst/examples/budmoth.R
===================================================================
--- pkg/pompExamples/inst/examples/budmoth.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/inst/examples/budmoth.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -77,13 +77,13 @@
"g","delta","a","w","sig.a","beta1","sigQobs",
"sigNobs", "sigSobs","N.0"
),
- parameter.transform=function (params, logitvar,
+ fromEstimationScale=function (params, logitvar,
logvar, ...) {
params[logitvar] <- plogis(params[logitvar])
params[logvar] <- exp(params[logvar])
params
},
- parameter.inv.transform=function (params, logitvar,
+ toEstimationScale=function (params, logitvar,
logvar, ...) {
params[logitvar] <- qlogis(params[logitvar])
params[logvar] <- log(params[logvar])
Modified: pkg/pompExamples/inst/examples/parus.R
===================================================================
--- pkg/pompExamples/inst/examples/parus.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/inst/examples/parus.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -91,10 +91,10 @@
paramnames=c("r","K","sigma","theta"),
statenames=c("N"),
obsnames=c("pop"),
- parameter.transform=function(params,...){
+ fromEstimationScale=function(params,...){
exp(params)
},
- parameter.inv.transform=function(params,...){
+ toEstimationScale=function(params,...){
log(params)
},
PACKAGE="pompExamples"
Modified: pkg/pompExamples/tests/bbp.Rout.save
===================================================================
--- pkg/pompExamples/tests/bbp.Rout.save 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/tests/bbp.Rout.save 2015-06-17 12:56:44 UTC (rev 1210)
@@ -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 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+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.
@@ -17,12 +17,11 @@
> library(pompExamples)
Loading required package: pomp
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(47575684L)
>
> pompExample(bbp)
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'logvar','logitvar'
newly created object(s):
bbp
> pf <- pfilter(simulate(bbp),Np=100,max.fail=Inf)
@@ -30,4 +29,4 @@
>
> proc.time()
user system elapsed
- 0.575 0.045 0.608
+ 0.633 0.026 0.636
Modified: pkg/pompExamples/tests/budmoth.Rout.save
===================================================================
--- pkg/pompExamples/tests/budmoth.Rout.save 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/tests/budmoth.Rout.save 2015-06-17 12:56:44 UTC (rev 1210)
@@ -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 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+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.
@@ -17,12 +17,14 @@
> library(pompExamples)
Loading required package: pomp
-Loading required package: subplex
-Loading required package: nloptr
>
> all <- c("food","para1","para2","tri")
>
> bm <- pompExample(budmoth,envir=NULL)
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'logitvar','logvar'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'logitvar','logvar'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'logitvar','logvar'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'logitvar','logvar'
>
> names(bm)
[1] "food" "para1" "para2" "tri"
@@ -127,4 +129,4 @@
>
> proc.time()
user system elapsed
- 0.626 0.053 0.668
+ 0.653 0.042 0.680
Modified: pkg/pompExamples/tests/ebola.Rout.save
===================================================================
--- pkg/pompExamples/tests/ebola.Rout.save 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/tests/ebola.Rout.save 2015-06-17 12:56:44 UTC (rev 1210)
@@ -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 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+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.
@@ -17,8 +17,6 @@
> library(pompExamples)
Loading required package: pomp
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(47575684L)
>
@@ -28,16 +26,19 @@
newly created object(s):
ebolaModel
> ebolaModel(country="Guinea") -> po
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nstageE'
> pf <- pfilter(simulate(po),Np=100)
> tj <- trajectory(po)
>
> ebolaModel(country="SierraLeone",na.rm=TRUE,type='cum') -> po
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nstageE'
> pf <- pfilter(simulate(po),Np=100)
> tj <- trajectory(po)
> dd <- simulate(po,as.data.frame=TRUE,obs=TRUE)
> dd$week <- dd$time
> po <- ebolaModel(data=subset(dd,select=c(week,cases,deaths)))
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'nstageE'
>
> proc.time()
user system elapsed
- 1.837 0.246 2.034
+ 1.824 0.321 2.121
Modified: pkg/pompExamples/tests/parus.Rout.save
===================================================================
--- pkg/pompExamples/tests/parus.Rout.save 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/tests/parus.Rout.save 2015-06-17 12:56:44 UTC (rev 1210)
@@ -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 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+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.
@@ -17,8 +17,6 @@
> library(pompExamples)
Loading required package: pomp
-Loading required package: subplex
-Loading required package: nloptr
>
> set.seed(47575684L)
>
@@ -45,4 +43,4 @@
>
> proc.time()
user system elapsed
- 0.575 0.033 0.596
+ 0.576 0.024 0.580
Modified: pkg/pompExamples/tests/pertussis.R
===================================================================
--- pkg/pompExamples/tests/pertussis.R 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/tests/pertussis.R 2015-06-17 12:56:44 UTC (rev 1210)
@@ -21,7 +21,7 @@
pttest <- function (po, digits = 15) {
identical(
signif(coef(po),digits=digits),
- signif(partrans(po,partrans(po,coef(po),dir='inv'),dir='for'),digits=digits)
+ signif(partrans(po,partrans(po,coef(po),dir='to'),dir='from'),digits=digits)
)
}
@@ -30,7 +30,7 @@
pttest <- function (po, digits = 15) {
identical(
signif(coef(po,trans=T),digits=digits),
- signif(partrans(po,partrans(po,coef(po,trans=T),dir='f'),dir='inv'),digits=digits)
+ signif(partrans(po,partrans(po,coef(po,trans=T),dir='from'),dir='to'),digits=digits)
)
}
Modified: pkg/pompExamples/tests/pertussis.Rout.save
===================================================================
--- pkg/pompExamples/tests/pertussis.Rout.save 2015-06-17 12:56:41 UTC (rev 1209)
+++ pkg/pompExamples/tests/pertussis.Rout.save 2015-06-17 12:56:44 UTC (rev 1210)
@@ -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 3.1.3 (2015-03-09) -- "Smooth Sidewalk"
+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.
@@ -17,12 +17,18 @@
> library(pompExamples)
Loading required package: pomp
-Loading required package: subplex
-Loading required package: nloptr
>
> all <- c("SEIR.small","SEIR.big","SEIRS.small","SEIRS.big","SEIRR.small","SEIRR.big","full.small","full.big")
>
> sapply(all,function(n)eval(bquote(pertussis.sim(.(n))))) -> pt
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
>
> names(pt)
[1] "SEIR.small" "SEIR.big" "SEIRS.small" "SEIRS.big" "SEIRR.small"
@@ -111,6 +117,7 @@
>
> x <- simulate(pertussis.sim(full.big),seed=395885L,as.data.frame=TRUE)
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
> tail(x)
time reports S E I R1 R2 cases W err
1036 19.90385 432 662434 5677 9458 3201351 1118149 4831 -0.4801610 7
@@ -128,6 +135,7 @@
1041 4997213 1
>
> y <- trajectory(pertussis.sim(SEIRS.small),as.data.frame=TRUE)
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
> tail(y)
S E I R1 R2 cases W err simpop
1036 81409.73 558.4599 942.3100 227353.0 189736.5 487.2963 0 0 5e+05
@@ -145,13 +153,14 @@
1041 20.00000 1
>
> pf <- pfilter(pertussis.sim(full.small),seed=3445886L,Np=1000)
+In 'pomp': the following unrecognized argument(s) will be stored for use by user-defined functions: 'ivps','comp.names','varnames'
> logLik(pf)
[1] -3829.33
>
> pttest <- function (po, digits = 15) {
+ identical(
+ signif(coef(po),digits=digits),
-+ signif(partrans(po,partrans(po,coef(po),dir='inv'),dir='for'),digits=digits)
++ signif(partrans(po,partrans(po,coef(po),dir='to'),dir='from'),digits=digits)
+ )
+ }
>
@@ -160,7 +169,7 @@
> pttest <- function (po, digits = 15) {
+ identical(
+ signif(coef(po,trans=T),digits=digits),
-+ signif(partrans(po,partrans(po,coef(po,trans=T),dir='f'),dir='inv'),digits=digits)
++ signif(partrans(po,partrans(po,coef(po,trans=T),dir='from'),dir='to'),digits=digits)
+ )
+ }
>
@@ -168,4 +177,4 @@
>
> proc.time()
user system elapsed
- 23.862 0.074 23.943
+ 23.602 0.053 23.659
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