[Pomp-commits] r803 - pkg/pomp/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 9 23:56:49 CET 2013
Author: kingaa
Date: 2013-01-09 23:56:49 +0100 (Wed, 09 Jan 2013)
New Revision: 803
Modified:
pkg/pomp/man/blowflies.Rd
pkg/pomp/man/dacca.Rd
pkg/pomp/man/example.Rd
pkg/pomp/man/gompertz.Rd
pkg/pomp/man/init.state-pomp.Rd
pkg/pomp/man/ou2.Rd
pkg/pomp/man/parmat.Rd
pkg/pomp/man/probe.Rd
pkg/pomp/man/ricker.Rd
pkg/pomp/man/rw2.Rd
pkg/pomp/man/simulate-pomp.Rd
pkg/pomp/man/sir.Rd
pkg/pomp/man/spect.Rd
pkg/pomp/man/traj-match.Rd
pkg/pomp/man/trajectory-pomp.Rd
pkg/pomp/man/verhulst.Rd
Log:
- improved 'pompExample'
Modified: pkg/pomp/man/blowflies.Rd
===================================================================
--- pkg/pomp/man/blowflies.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/blowflies.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -8,7 +8,7 @@
\code{blowflies1} and \code{blowflies2} are \code{pomp} objects encoding stochastic delay-difference models.
}
\examples{
-pompExample("blowflies")
+pompExample(blowflies)
plot(blowflies1)
plot(blowflies2)
}
Modified: pkg/pomp/man/dacca.Rd
===================================================================
--- pkg/pomp/man/dacca.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/dacca.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -16,7 +16,7 @@
parameters that are naturally unbounded or take integer values are not transformed.
}
\examples{
-pompExample("dacca")
+pompExample(dacca)
plot(dacca)
#MLEs on the natural scale
coef(dacca)
Modified: pkg/pomp/man/example.Rd
===================================================================
--- pkg/pomp/man/example.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/example.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -9,7 +9,7 @@
}
\arguments{
\item{example}{
- character; name of the example to load.
+ example to load given as a name or literal character string.
Evoked without an argument, \code{pompExample} lists all available examples.
}
}
@@ -19,5 +19,6 @@
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
pompExample()
- pompExample("euler.sir")
+ pompExample(euler.sir)
+ pompExample("gompertz")
}
Modified: pkg/pomp/man/gompertz.Rd
===================================================================
--- pkg/pomp/man/gompertz.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/gompertz.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -12,7 +12,7 @@
The \code{pomp} object includes parameter transformations that log-transform the parameters for estimation purposes.
}
\examples{
-pompExample("gompertz")
+pompExample(gompertz)
plot(gompertz)
coef(gompertz)
coef(gompertz,transform=TRUE)
Modified: pkg/pomp/man/init.state-pomp.Rd
===================================================================
--- pkg/pomp/man/init.state-pomp.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/init.state-pomp.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -25,11 +25,11 @@
Returns a matrix of initial states (with rownames).
}
\examples{
-pompExample("ou2")
+pompExample(ou2)
coef(ou2)
init.state(ou2)
-pompExample("euler.sir")
+pompExample(euler.sir)
coef(euler.sir)
init.state(euler.sir)
}
Modified: pkg/pomp/man/ou2.Rd
===================================================================
--- pkg/pomp/man/ou2.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/ou2.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -15,7 +15,7 @@
This object is demonstrated in the vignette "Advanced topics in pomp".
}
\examples{
-pompExample("ou2")
+pompExample(ou2)
plot(ou2)
coef(ou2)
x <- simulate(ou2)
Modified: pkg/pomp/man/parmat.Rd
===================================================================
--- pkg/pomp/man/parmat.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/parmat.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -21,7 +21,7 @@
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
## generate a bifurcation diagram for the Ricker map
- pompExample("ricker")
+ pompExample(ricker)
p <- parmat(coef(ricker),nrep=500)
p["r",] <- exp(seq(from=1.5,to=4,length=500))
x <- trajectory(ricker,times=seq(from=1000,to=2000,by=1),params=p)
Modified: pkg/pomp/man/probe.Rd
===================================================================
--- pkg/pomp/man/probe.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/probe.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -166,7 +166,7 @@
Aaron A. King (kingaa at umich dot edu)
}
\examples{
-pompExample("ou2")
+pompExample(ou2)
good <- probe(
ou2,
probes=list(
Modified: pkg/pomp/man/ricker.Rd
===================================================================
--- pkg/pomp/man/ricker.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/ricker.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -10,7 +10,7 @@
The observed variables \eqn{y_t}{y[t]} are distributed as \eqn{\mathrm{Poisson}(\phi N_t)}{Poisson(phi N[t])}.
}
\examples{
-pompExample("ricker")
+pompExample(ricker)
plot(ricker)
coef(ricker)
}
Modified: pkg/pomp/man/rw2.Rd
===================================================================
--- pkg/pomp/man/rw2.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/rw2.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -9,7 +9,7 @@
The random-walk process is fully but noisily observed.
}
\examples{
-pompExample("rw2")
+pompExample(rw2)
plot(rw2)
x <- simulate(rw2,nsim=10,seed=20348585L,params=c(x1.0=0,x2.0=0,s1=1,s2=3,tau=1))
plot(x[[1]])
Modified: pkg/pomp/man/simulate-pomp.Rd
===================================================================
--- pkg/pomp/man/simulate-pomp.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/simulate-pomp.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -61,7 +61,7 @@
This makes it possible for the user to write highly optimized code for these potentially expensive computations.
}
\examples{
-pompExample("ou2")
+pompExample(ou2)
x <- simulate(ou2,seed=3495485,nsim=10)
x <- simulate(ou2,seed=3495485,nsim=10,states=TRUE,obs=TRUE)
}
Modified: pkg/pomp/man/sir.Rd
===================================================================
--- pkg/pomp/man/sir.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/sir.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -21,17 +21,17 @@
The boarding school influenza outbreak is described in Anonymous (1978).
}
\examples{
-pompExample("euler.sir")
+pompExample(euler.sir)
plot(euler.sir)
plot(simulate(euler.sir,seed=20348585))
coef(euler.sir)
-pompExample("gillespie.sir")
+pompExample(gillespie.sir)
plot(gillespie.sir)
plot(simulate(gillespie.sir,seed=20348585))
coef(gillespie.sir)
-pompExample("bbs")
+pompExample(bbs)
plot(bbs)
coef(bbs)
}
Modified: pkg/pomp/man/spect.Rd
===================================================================
--- pkg/pomp/man/spect.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/spect.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -154,7 +154,7 @@
Aaron A. King (kingaa at umich dot edu)
}
\examples{
-pompExample("ou2")
+pompExample(ou2)
good <- spect(
ou2,
vars=c("y1","y2"),
Modified: pkg/pomp/man/traj-match.Rd
===================================================================
--- pkg/pomp/man/traj-match.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/traj-match.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -111,7 +111,7 @@
\code{traj.match.objfun} returns a function suitable for use as an objective function in an \code{\link{optim}}-like optimizer.
}
\examples{
- pompExample("ou2")
+ pompExample(ou2)
true.p <- c(
alpha.1=0.9,alpha.2=0,alpha.3=-0.4,alpha.4=0.99,
sigma.1=2,sigma.2=0.1,sigma.3=2,
@@ -137,11 +137,11 @@
lines(x1~time,data=as(res,"data.frame"),col='blue')
lines(x2~time,data=as(res,"data.frame"),col='red')
- pompExample("ricker")
+ pompExample(ricker)
ofun <- traj.match.objfun(ricker,est=c("r","phi"),transform=TRUE)
optim(fn=ofun,par=c(2,0),method="BFGS")
- pompExample("bbs")
+ pompExample(bbs)
ofun <- traj.match.objfun(bbs,est=c("beta","gamma"),transform=TRUE,hmax=0.001)
optim(fn=ofun,par=c(0,-1),method="Nelder-Mead")
}
Modified: pkg/pomp/man/trajectory-pomp.Rd
===================================================================
--- pkg/pomp/man/trajectory-pomp.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/trajectory-pomp.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -48,7 +48,7 @@
}
\author{Aaron A. King \email{kingaa at umich dot edu}}
\examples{
-pompExample("euler.sir")
+pompExample(euler.sir)
x <- trajectory(euler.sir)
plot(time(euler.sir),x["I",1,],type='l',xlab='time',ylab='I')
lines(time(euler.sir),x["cases",1,],col='red')
Modified: pkg/pomp/man/verhulst.Rd
===================================================================
--- pkg/pomp/man/verhulst.Rd 2013-01-09 20:22:08 UTC (rev 802)
+++ pkg/pomp/man/verhulst.Rd 2013-01-09 22:56:49 UTC (rev 803)
@@ -10,7 +10,7 @@
It is implemented using the \code{\link{euler.sim}} plug-in.
}
\examples{
-pompExample("verhulst")
+pompExample(verhulst)
plot(verhulst)
coef(verhulst)
params <- cbind(
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