[Pomp-commits] r881 - in pkg/pompExamples: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sat Jan 11 19:24:48 CET 2014
Author: kingaa
Date: 2014-01-11 19:24:48 +0100 (Sat, 11 Jan 2014)
New Revision: 881
Modified:
pkg/pompExamples/DESCRIPTION
pkg/pompExamples/R/budmoth.R
pkg/pompExamples/R/pertussis.R
pkg/pompExamples/man/budmoth.Rd
pkg/pompExamples/man/pertussis.Rd
Log:
- small change to pertussis.sim and budmoth.sim
Modified: pkg/pompExamples/DESCRIPTION
===================================================================
--- pkg/pompExamples/DESCRIPTION 2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/DESCRIPTION 2014-01-11 18:24:48 UTC (rev 881)
@@ -1,8 +1,8 @@
Package: pompExamples
Type: Package
Title: Statistical inference for partially observed Markov processes
-Version: 0.22-1
-Date: 2013-11-11
+Version: 0.23-1
+Date: 2014-01-10
Maintainer: Aaron A. King <kingaa at umich.edu>
Authors at R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa at umich.edu"),
person(given=c("Edward","L."),family="Ionides",role=c("aut")),
Modified: pkg/pompExamples/R/budmoth.R
===================================================================
--- pkg/pompExamples/R/budmoth.R 2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/R/budmoth.R 2014-01-11 18:24:48 UTC (rev 881)
@@ -1,9 +1,10 @@
budmoth.sim <- function (which) {
if (missing(which)) {
- cat("available datasets:",
- sQuote(c("food","para1","para2","tri")),"\n")
+ datasets <- c("food","para1","para2","tri")
+ cat("available datasets:",sQuote(datasets),"\n")
+ invisible(datasets)
} else {
- w <- as.character(substitute(which))
+ which <- as.character(substitute(which))
simulate(
pomp(
data=data.frame(
@@ -13,32 +14,36 @@
time="time",
t0=-1,
params=switch(
- w,
+ which,
tri=c(
- alpha=0.5, sig.alpha=0.1, gam=50, lambda=22, sig.lambda=0.25, g=0.08, delta=10,
+ alpha=0.5, sig.alpha=0.1, gam=50, lambda=22,
+ sig.lambda=0.25, g=0.08, delta=10,
a=1.7, sig.a=0.1, w=0.15, beta0=0, beta1=35, u=0.9,
sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
Q.0=0.96, N.0=0.02, S.0=0.22
),
food=c(
- alpha=0.5, sig.alpha=0.1, gam=20, lambda=5, sig.lambda=0.25, g=0.02, delta=10,
+ alpha=0.5, sig.alpha=0.1, gam=20, lambda=5,
+ sig.lambda=0.25, g=0.02, delta=10,
a=1, sig.a=0.1, w=0, beta0=0, beta1=35, u=0.9,
sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
Q.0=0.96, N.0=0.02, S.0=0.22
),
para1=c(
- alpha=0.5, sig.alpha=0.1, gam=50, lambda=22, sig.lambda=0.25, g=0.08, delta=0.5,
+ alpha=0.5, sig.alpha=0.1, gam=50, lambda=22,
+ sig.lambda=0.25, g=0.08, delta=0.5,
a=1.7, sig.a=0.1, w=0.15, beta0=0, beta1=35, u=0.9,
sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
Q.0=0.96, N.0=0.02, S.0=0.22
),
para2=c(
- alpha=0.5, sig.alpha=0.1, gam=50, lambda=10, sig.lambda=5, g=0.08, delta=0.5,
+ alpha=0.5, sig.alpha=0.1, gam=50, lambda=10,
+ sig.lambda=5, g=0.08, delta=0.5,
a=1.7, sig.a=1, w=0.15, beta0=0, beta1=35, u=0.9,
sigQobs=0.03, sigNobs=0.5, sigSobs=0.1,
Q.0=0.96, N.0=0.02, S.0=0.22
),
- stop("unrecognized dataset ",sQuote(w),call.=FALSE)
+ stop("unrecognized dataset ",sQuote(which),call.=FALSE)
),
rprocess=euler.sim(
step.fun="budmoth_map",
@@ -75,24 +80,26 @@
"g","delta","a","w","sig.a","beta1","sigQobs",
"sigNobs", "sigSobs","N.0"
),
- parameter.transform=function (params, logitvar, logvar, ...) {
+ parameter.transform=function (params, logitvar,
+ logvar, ...) {
params[logitvar] <- plogis(params[logitvar])
params[logvar] <- exp(params[logvar])
params
},
- parameter.inv.transform=function (params, logitvar, logvar, ...) {
+ parameter.inv.transform=function (params, logitvar,
+ logvar, ...) {
params[logitvar] <- qlogis(params[logitvar])
params[logvar] <- log(params[logvar])
params
}
),
seed=switch(
- w,
+ which,
tri=1691699385L,
food=1054866677L,
para1=1116757478L,
para2=1361101458L,
- stop("unrecognized dataset ",sQuote(w),call.=FALSE)
+ stop("unrecognized dataset ",sQuote(which),call.=FALSE)
)
)
}
Modified: pkg/pompExamples/R/pertussis.R
===================================================================
--- pkg/pompExamples/R/pertussis.R 2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/R/pertussis.R 2014-01-11 18:24:48 UTC (rev 881)
@@ -4,11 +4,15 @@
pertussis.sim <- function (which) {
if (missing(which)) {
- cat("available datasets:",
- sQuote(c("SEIR.small","SEIR.big",
- "SEIRS.small","SEIRS.big",
- "SEIRR.small","SEIRR.big",
- "full.small","full.big")),"\n")
+ datasets <- c(
+ "SEIR.small","SEIR.big",
+ "SEIRS.small","SEIRS.big",
+ "SEIRR.small","SEIRR.big",
+ "full.small","full.big"
+ )
+
+ cat("available datasets:",sQuote(datasets),"\n")
+ invisible(datasets)
} else {
which <- as.character(substitute(which))
simulate(
Modified: pkg/pompExamples/man/budmoth.Rd
===================================================================
--- pkg/pompExamples/man/budmoth.Rd 2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/man/budmoth.Rd 2014-01-11 18:24:48 UTC (rev 881)
@@ -20,7 +20,7 @@
plot(budmoth.sim(food))
plot(budmoth.sim(para1))
plot(budmoth.sim(para2))
-plot(budmoth.sim(tri))
+plot(budmoth.sim("tri"))
}
\seealso{the \dQuote{budmoth-model} vignette}
\keyword{datasets}
Modified: pkg/pompExamples/man/pertussis.Rd
===================================================================
--- pkg/pompExamples/man/pertussis.Rd 2014-01-10 22:43:03 UTC (rev 880)
+++ pkg/pompExamples/man/pertussis.Rd 2014-01-11 18:24:48 UTC (rev 881)
@@ -18,7 +18,7 @@
plot(pertussis.sim(SEIR.small))
plot(pertussis.sim(SEIRS.big))
plot(pertussis.sim(SEIRR.small))
-plot(pertussis.sim(full.big))
+plot(pertussis.sim("full.big"))
}
\seealso{the \dQuote{pertussis-model} vignette}
\keyword{datasets}
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