[Pomp-commits] r1092 - in www: content vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Feb 23 15:05:48 CET 2015
Author: kingaa
Date: 2015-02-23 15:05:48 +0100 (Mon, 23 Feb 2015)
New Revision: 1092
Modified:
www/content/NEWS.html
www/vignettes/advanced_topics_in_pomp.R
www/vignettes/advanced_topics_in_pomp.pdf
www/vignettes/bsmc-ricker-flat-prior.rda
www/vignettes/bsmc-ricker-normal-prior.rda
www/vignettes/gompertz-multi-mif.rda
www/vignettes/gompertz-performance.rda
www/vignettes/gompertz-pfilter-guess.rda
www/vignettes/gompertz-trajmatch.rda
www/vignettes/intro_to_pomp.R
www/vignettes/intro_to_pomp.Rnw
www/vignettes/intro_to_pomp.pdf
www/vignettes/nlf-block-boot.rda
www/vignettes/nlf-boot.rda
www/vignettes/nlf-fit-from-truth.rda
www/vignettes/nlf-fits.rda
www/vignettes/nlf-lag-tests.rda
www/vignettes/nlf-multi-short.rda
www/vignettes/plugin-C-code.rda
www/vignettes/plugin-R-code.rda
www/vignettes/pomp.pdf
www/vignettes/ricker-comparison.rda
www/vignettes/ricker-first-probe.rda
www/vignettes/ricker-mif.rda
www/vignettes/ricker-probe-match.rda
www/vignettes/ricker-probe.rda
www/vignettes/vectorized-C-code.rda
www/vignettes/vectorized-R-code.rda
Log:
- bring vignettes up to date
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-02-22 22:49:40 UTC (rev 1091)
+++ www/content/NEWS.html 2015-02-23 14:05:48 UTC (rev 1092)
@@ -8,6 +8,82 @@
<h2>News for package ‘pomp’</h2>
+<h3>Changes in <span class="pkg">pomp</span> version 0.60-1</h3>
+
+
+<ul>
+<li> <p><code>pmcmc</code> and <code>abc</code> can now use arbitrary symmetric proposal distributions via the <code>proposal</code> argument.
+For the moment, these are constrained to be symmetric.
+Two new functions, <code>mvn.diag.rw</code> and <code>mvn.rw</code> generate suitable proposal functions.
+The first generates a multivariate normal random-walk proposal with diagonal variance-covariance matrix; this duplicates the old behavior of both <code>abc</code> and <code>pmcmc</code>.
+The second, <code>mvn.rw</code>, corresponds to a multivariate normal random-walk proposal with arbitrary variance-covariance matrix.
+</p>
+</li>
+<li><p> In <code>pmcmc</code> and <code>abc</code>, the arguments <code>pars</code> and <code>rw.sd</code> are now unneeded and have been deprecated.
+Use of <code>rw.sd</code> will generate a warning and result in behavior equivalent to choosing <code>proposal=mvn.diag.rw(rw.sd)</code>.
+Use of <code>pars</code> will be ignored, with a warning.
+</p>
+</li>
+<li><p> In <code>nlf</code>, the <code>transform.params</code> argument is now deprecated;
+use instead the <code>transform</code> argument, as in the other inference methods.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.59-1</h3>
+
+
+<ul>
+<li><p> A bug in <code>spect.match</code> has been fixed.
+Thanks to Karsten Hempel for finding it and contributing the fix.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.58-1</h3>
+
+
+<ul>
+<li><p> Compiler messages are now suppressed by default when <code>Csnippet</code>s are used in construction of a <code>pomp</code> object.
+These can be enabled by setting <code>options(verbose=TRUE)</code>.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.58-1</h3>
+
+
+<ul>
+<li><p> A <code>pomp</code> object created with <code>Csnippet</code>s or <code>pompBuilder</code> will now remember its associated shared-object file, which can be unloaded and reloaded using the new <code>pompUnload</code> and <code>pompLoad</code> methods.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.57-1</h3>
+
+
+<ul>
+<li> <p><code>simulate</code> has a new argument, <code>include.data</code>, that when used in conjuncion with <code>as.data.frame=TRUE</code> will include the actual data in the resulting data frame along with the simulations.
+</p>
+</li></ul>
+
+
+
+<h3>Changes in <span class="pkg">pomp</span> version 0.56-1</h3>
+
+
+<ul>
+<li><p> Revamped the <code>pompExample</code> function.
+A search path for example directories is now stored in global option "pomp.examples".
+</p>
+</li></ul>
+
+
+
<h3>Changes in <span class="pkg">pomp</span> version 0.55-1</h3>
Modified: www/vignettes/advanced_topics_in_pomp.R
===================================================================
--- www/vignettes/advanced_topics_in_pomp.R 2015-02-22 22:49:40 UTC (rev 1091)
+++ www/vignettes/advanced_topics_in_pomp.R 2015-02-23 14:05:48 UTC (rev 1092)
@@ -1,4 +1,3 @@
-
## ----include=FALSE-------------------------------------------------------
opts_chunk$set(
echo=TRUE,results='markup',
@@ -18,12 +17,10 @@
)
-
## ----include=FALSE-------------------------------------------------------
library(pomp)
set.seed(5384959)
-
## ----pomp-builder-measmod,eval=T-----------------------------------------
## negative binomial measurement model
## E[cases|incid] = rho*incid
@@ -36,7 +33,6 @@
lik = dnbinom_mu(cases,theta,rho*incid,give_log);
'
-
## ----pomp-builder-stepfn,eval=T------------------------------------------
## SIR process model with extra-demographic stochasticity
## and seasonal transmission
@@ -76,7 +72,6 @@
if (beta_sd > 0.0) W += (dW-dt)/beta_sd; // increment has mean = 0, variance = dt
'
-
## ----pomp-builder-skel,eval=T--------------------------------------------
skel <- '
int nrate = 6;
@@ -112,7 +107,6 @@
DW = 0;
'
-
## ----pomp-builder-partrans,eval=T----------------------------------------
## parameter transformations
## note we use barycentric coordinates for the initial conditions
@@ -144,7 +138,6 @@
to_log_barycentric(&TS_0,&S_0,3);
"
-
## ----pomp-builder-covar,eval=T-------------------------------------------
covartab <- data.frame(
time=seq(from=-1/52,to=10+1/52,by=1/26)
@@ -164,7 +157,6 @@
)
-
## ----pomp-builder,eval=F-------------------------------------------------
## pompBuilder(
## name="SIR",
@@ -200,7 +192,6 @@
## }
## ) -> sir
-
## ----pomp-builder-eval,echo=F,eval=T,results='hide'----------------------
if (Sys.getenv("POMP_BUILD_VIGNETTES")=="yes") {
require(pomp)
@@ -239,7 +230,6 @@
) -> sir
}
-
## ----sir-sim,eval=T------------------------------------------------------
coef(sir) <- c(
gamma=26,mu=0.02,iota=0.01,
@@ -253,11 +243,9 @@
sir <- simulate(sir,seed=3493885L)
traj <- trajectory(sir,hmax=1/52)
-
## ----sir-plot,fig=T,echo=F-----------------------------------------------
plot(sir)
-
## ------------------------------------------------------------------------
pompExample(ou2)
true.p <- coef(ou2)
@@ -267,20 +255,17 @@
new.p["x1.0",] <- 1:3
init.state(ou2,params=new.p)
-
## ------------------------------------------------------------------------
x <- rprocess(ou2,xstart=x0,times=time(ou2,t0=T),params=true.p)
dim(x)
x[,,1:5]
-
## ------------------------------------------------------------------------
x <- x[,,-1,drop=F]
y <- rmeasure(ou2,x=x,times=time(ou2),params=true.p)
dim(y)
y[,,1:5]
-
## ------------------------------------------------------------------------
fp <- dprocess(ou2,x=x,times=time(ou2),params=true.p)
dim(fp)
@@ -291,19 +276,15 @@
dim(fm)
fm[,36:40]
-
## ----all-examples,eval=F-------------------------------------------------
## pompExample()
-
## ----example-sources,eval=F----------------------------------------------
## list.files(system.file("examples",package="pomp"))
-
## ----demos,eval=F--------------------------------------------------------
## demo(package='pomp')
-
## ----plugin-R-code,echo=T,eval=T-----------------------------------------
pompExample(ou2)
ou2.dat <- as.data.frame(ou2)
@@ -343,7 +324,6 @@
save(etime.Rplug,n.Rplug,file=binary.file,compress='xz')
}
-
## ----vectorized-R-code,eval=F--------------------------------------------
## ou2.Rvect.rprocess <- function (xstart, times, params, ...) {
## nrep <- ncol(xstart) # number of realizations
@@ -378,11 +358,9 @@
## x
## }
-
## ----vectorized-R-pomp,eval=F--------------------------------------------
## ou2.Rvect <- pomp(ou2.Rplug,rprocess=ou2.Rvect.rprocess)
-
## ----theta,eval=F--------------------------------------------------------
## theta <- c(
## x1.0=-3, x2.0=4,
@@ -447,15 +425,12 @@
save(etime.Rvect,n.Rvect,file=binary.file,compress='xz')
}
-
## ----view-ou2-source,eval=F----------------------------------------------
## file.show(file=system.file("examples/ou2.c",package="pomp"))
-
## ----view-pomp.h,eval=F,results='hide'-----------------------------------
## file.show(file=system.file("include/pomp.h",package="pomp"))
-
## ----plugin-C-code,eval=F------------------------------------------------
## ou2.Cplug <- pomp(
## ou2.Rplug,
@@ -498,11 +473,9 @@
save(n.Cplug,etime.Cplug,speedup,file=binary.file,compress='xz')
}
-
## ----eval=F,results='hide'-----------------------------------------------
## file.show(file=system.file("examples/ou2.c",package="pomp"))
-
## ----vectorized-C-code---------------------------------------------------
ou2.Cvect.rprocess <- function (xstart, times, params, ...) {
nvar <- nrow(xstart)
@@ -522,7 +495,6 @@
)
}
-
## ----vectorized-C-code-pomp----------------------------------------------
ou2.Cvect <- pomp(
ou2.Rplug,
@@ -555,4 +527,3 @@
save(n.Cvect,etime.Cvect,speedup,file=binary.file,compress='xz')
}
-
Modified: www/vignettes/advanced_topics_in_pomp.pdf
===================================================================
(Binary files differ)
Modified: www/vignettes/bsmc-ricker-flat-prior.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/bsmc-ricker-normal-prior.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/gompertz-multi-mif.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/gompertz-performance.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/gompertz-pfilter-guess.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/gompertz-trajmatch.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/intro_to_pomp.R
===================================================================
--- www/vignettes/intro_to_pomp.R 2015-02-22 22:49:40 UTC (rev 1091)
+++ www/vignettes/intro_to_pomp.R 2015-02-23 14:05:48 UTC (rev 1092)
@@ -1,4 +1,3 @@
-
## ----include=FALSE-------------------------------------------------------
opts_chunk$set(
echo=TRUE,results='markup',
@@ -18,11 +17,9 @@
)
-
## ----set-opts,echo=F,results='hide'--------------------------------------
set.seed(5384959L)
-
## ----gompertz-proc-sim-def-----------------------------------------------
require(pomp)
@@ -42,7 +39,6 @@
}
-
## ----gompertz-meas-sim-def-----------------------------------------------
gompertz.meas.sim <- function (x, t, params, ...) {
## unpack the parameters:
@@ -55,7 +51,6 @@
}
-
## ----first-pomp-construction,eval=F--------------------------------------
## gompertz <- pomp(
## data=data.frame(
@@ -72,11 +67,9 @@
## )
##
-
## ----set-params----------------------------------------------------------
theta <- c(r=0.1,K=1,sigma=0.1,tau=0.1,X.0=1)
-
## ----gompertz-first-simulation,eval=F------------------------------------
## gompertz <- simulate(gompertz,params=theta)
@@ -95,11 +88,9 @@
)
coef(gompertz) <- theta
-
## ----gompertz-plot,echo=F------------------------------------------------
plot(gompertz,variables=c("Y"))
-
## ----second-pomp-construction--------------------------------------------
gompertz.meas.dens <- function (y, x, t, params, log, ...) {
## unpack the parameters:
@@ -118,7 +109,6 @@
dmeasure=gompertz.meas.dens
)
-
## ----gompertz-pfilter-truth,eval=F---------------------------------------
## pf <- pfilter(gompertz,params=theta,Np=1000)
## loglik.truth <- logLik(pf)
@@ -130,15 +120,12 @@
loglik.truth <- logLik(pf)
loglik.truth
-
## ----gompertz-pfilter-truth-alt1,eval=F----------------------------------
## pf <- pfilter(gompertz,params=coef(gompertz),Np=1000)
-
## ----gompertz-pfilter-truth-alt2,eval=F----------------------------------
## pf <- pfilter(gompertz,Np=1000)
-
## ----gompertz-pfilter-guess,eval=F---------------------------------------
## theta.true <- coef(gompertz)
## theta.guess <- theta.true
@@ -160,7 +147,6 @@
save(theta.true,theta.guess,loglik.guess,file=binary.file,compress='xz')
}
-
## ----kalman-filter-def---------------------------------------------------
kalman.filter <- function (Y, X0, r, K, sigma, tau) {
ntimes <- length(Y)
@@ -192,7 +178,6 @@
)
}
-
## ----kalman-filter-run---------------------------------------------------
y <- obs(gompertz)
x0 <- init.state(gompertz)
@@ -205,45 +190,36 @@
## ----kalman-likelihood-correction,echo=F---------------------------------
loglik.kalman <- kf$loglik
-
## ----eval=F--------------------------------------------------------------
## as(gompertz,"data.frame")
-
## ----eval=F--------------------------------------------------------------
## obs(gompertz)
## obs(gompertz,"Y")
## time(gompertz)
-
## ----eval=F--------------------------------------------------------------
## time(gompertz) <- 1:10
-
## ----eval=F--------------------------------------------------------------
## timezero(gompertz)
## timezero(gompertz) <- -10
-
## ----eval=F--------------------------------------------------------------
## time(gompertz,t0=TRUE)
## time(gompertz,t0=T) <- seq(from=0,to=10,by=1)
-
## ----eval=F--------------------------------------------------------------
## window(gompertz,start=3,end=20)
-
## ----eval=F--------------------------------------------------------------
## coef(gompertz)
## coef(gompertz,c("sigma","tau")) <- c(1,0)
-
## ----eval=F--------------------------------------------------------------
## states(gompertz)
## states(gompertz,"X")
-
## ----snippet-gomp-pomp,results='hide'------------------------------------
gomp2 <- pomp(
data=subset(as(gompertz,"data.frame"),select=c(time,Y)),
@@ -269,7 +245,6 @@
)
-
## ----gompertz-perform,eval=F,echo=T--------------------------------------
## tic <- Sys.time()
## sim1 <- simulate(gompertz,nsim=1000,seed=5676868L,obs=TRUE)
@@ -327,15 +302,12 @@
save(g1sim,g2sim,g1pf,g2pf,file=binary.file,compress='xz')
}
-
## ----eval=F--------------------------------------------------------------
## demo(gompertz)
-
## ----eval=F--------------------------------------------------------------
## system.file("examples",package="pomp")
-
## ----loggomp-pomp-construction,eval=T------------------------------------
gompertz <- pomp(
gompertz,
@@ -347,28 +319,22 @@
}
)
-
## ----eval=T--------------------------------------------------------------
coef(gompertz) <- c(r=0.1,K=1,tau=0.1,sigma=0.1,X.0=1)
-
## ----eval=T--------------------------------------------------------------
coef(gompertz)
-
## ----eval=T--------------------------------------------------------------
coef(gompertz,transform=TRUE) <- c(r=log(0.1),K=0,tau=log(0.1),
sigma=log(0.1),X.0=0)
-
## ----eval=T--------------------------------------------------------------
coef(gompertz,transform=TRUE)
-
## ----eval=T--------------------------------------------------------------
coef(gompertz)
-
## ----par-trans-inverse-test,results='markup'-----------------------------
# use parameter.inv.transform:
theta <- coef(gompertz,transform=TRUE)
@@ -380,7 +346,6 @@
all.equal(coef(gompertz),coef(g2))
-
## ----echo=F,results='hide'-----------------------------------------------
pompExample(gompertz)
theta <- coef(gompertz)
@@ -418,7 +383,6 @@
## list(mif=m1,ll=ll)
## }
-
## ----gompertz-post-mif,eval=F,echo=F-------------------------------------
## theta.true <- coef(gompertz)
## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,Np=10000)))
@@ -429,7 +393,6 @@
## theta.mif <- theta.mif[best,]
## loglik.mif <- loglik.mif[best,]
-
## ----gompertz-multi-mif-eval,echo=F,results='hide'-----------------------
binary.file <- "gompertz-multi-mif.rda"
if (file.exists(binary.file)) {
@@ -500,7 +463,6 @@
truth=c(signif(theta.true[estpars],3),loglik=round(loglik.true,2))
) -> results.table
-
## ----eval=F--------------------------------------------------------------
## theta.true <- coef(gompertz)
## loglik.true <- replicate(n=10,logLik(pfilter(gompertz,Np=10000)))
@@ -511,7 +473,6 @@
## theta.mif <- theta.mif[best,]
## loglik.mif <- loglik.mif[best,]
-
## ----multi-mif-plot,echo=F,eval=F----------------------------------------
## op <- par(mfrow=c(4,1),mar=c(3,3,0,0),mgp=c(2,1,0),bty='l')
## loglik <- sapply(mf,function(x)conv.rec(x$mif,"loglik"))
@@ -524,7 +485,6 @@
## matplot(log.tau,type='l',lty=1,xlab="MIF iteration",ylab=expression(log~tau))
## par(op)
-
## ----mif-plot,echo=F-----------------------------------------------------
op <- par(mfrow=c(4,1),mar=c(3,3,0,0),mgp=c(2,1,0),bty='l')
loglik <- sapply(mf,function(x)conv.rec(x$mif,"loglik"))
@@ -537,11 +497,9 @@
matplot(log.tau,type='l',lty=1,xlab="MIF iteration",ylab=expression(log~tau))
par(op)
-
## ----first-mif-results-table,echo=F--------------------------------------
print(results.table)
-
## ----gompertz-skeleton-def,echo=T----------------------------------------
gompertz.skel <- function (x, t, params, ...) {
r <- params["r"]
@@ -552,7 +510,6 @@
return(xnew)
}
-
## ----gomp3-pomp----------------------------------------------------------
gomp3 <- simulate(
pomp(
@@ -566,7 +523,6 @@
seed=88737400L
)
-
## ----gompertz-trajmatch-calc,eval=F--------------------------------------
## tm <- traj.match(
## gomp3,
@@ -595,14 +551,12 @@
save(tm,file=binary.file,compress="xz")
}
-
## ----trajmatch-plot,echo=F,eval=T,fig.height=4,fig.width=6---------------
op <- par(mfrow=c(1,1),mar=c(3,3,0,0),mgp=c(2,1,0),bty='l')
plot(time(tm),obs(tm,"Y"),xlab="time",ylab=expression(X,Y),type='o')
lines(time(tm),states(tm,"X"),lwd=2)
par(op)
-
## ----ricker-map-defn-----------------------------------------------------
ricker.sim <- function (x, t, params, delta.t, ...) {
e <- rnorm(n=1,mean=0,sd=params["sigma"])
@@ -615,14 +569,12 @@
)
}
-
## ----ricker-sim-C-def----------------------------------------------------
ricker.sim <- Csnippet('
e = rnorm(0,sigma);
N = r*N*exp(-N+e);
')
-
## ----ricker-pomp,results='hide'------------------------------------------
ricker <- pomp(
data=data.frame(time=seq(0,50,by=1),y=NA),
@@ -644,11 +596,9 @@
)
ricker <- simulate(ricker,seed=73691676L)
-
## ----get-ricker,echo=T,eval=T,results='hide'-----------------------------
pompExample(ricker)
-
## ----probe-list----------------------------------------------------------
plist <- list(
probe.marginal("y",ref=obs(ricker),transform=sqrt),
@@ -657,7 +607,6 @@
transform=sqrt)
)
-
## ----first-probe,eval=F,echo=T-------------------------------------------
## pb.truth <- probe(ricker,probes=plist,nsim=1000,seed=1066L)
## guess <- c(r=20,sigma=1,phi=20,N.0=7,e.0=0)
@@ -674,14 +623,12 @@
save(pb.truth,pb.guess,guess,file=binary.file,compress='xz')
}
-
## ----first-probe-plot,eval=F---------------------------------------------
## summary(pb.truth)
## summary(pb.guess)
## plot(pb.truth)
## plot(pb.guess)
-
## ----ricker-probe-plot,echo=F,results='hide'-----------------------------
binary.file <- "ricker-probe.rda"
if (file.exists(binary.file)) {
@@ -701,7 +648,6 @@
}
plot(pb)
-
## ----ricker-probe-match-calc,eval=F--------------------------------------
## pm <- probe.match(
## pb.guess,
@@ -715,7 +661,6 @@
## )
## summary(pm)
-
## ----ricker-probe.match-eval,echo=F,eval=T,results='hide'----------------
binary.file <- "ricker-probe-match.rda"
if (file.exists(binary.file)) {
@@ -735,7 +680,6 @@
save(pm,file=binary.file,compress="xz")
}
-
## ----ricker-mif-calc,eval=F----------------------------------------------
## mf <- mif(
## ricker,
@@ -752,7 +696,6 @@
## )
## mf <- continue(mf,Nmif=500,max.fail=20)
-
## ----ricker-mif-eval,echo=F,eval=T,results='hide'------------------------
binary.file <- "ricker-mif.rda"
if (file.exists(binary.file)) {
@@ -775,7 +718,6 @@
save(mf,file=binary.file,compress="xz")
}
-
## ----ricker-comparison,eval=F,echo=T-------------------------------------
## pf.truth <- pfilter(ricker,Np=1000,max.fail=50,seed=1066L)
## pf.guess <- pfilter(ricker,params=guess,Np=1000,max.fail=50,seed=1066L)
@@ -817,18 +759,16 @@
## ----ricker-comparison-show----------------------------------------------
print(res,digits=3)
-
## ----first-nlf,eval=T,results='hide'-------------------------------------
pompExample(gompertz)
out <- nlf(
gompertz,
start=c(r=1,K=2,sigma=0.5,tau=0.5,X.0=1),
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=c(1,2)
)
-
## ----nlf-gompertz-starts,eval=F------------------------------------------
## # pick 5 random starting parameter values
## starts <- replicate(n=5,
@@ -841,7 +781,6 @@
## simplify=FALSE
## )
-
## ----nlf-gompertz-fits,eval=F--------------------------------------------
## out <- list()
## ## Do the fitting.
@@ -851,7 +790,7 @@
## gompertz,
## start=starts[[j]],
## transform.data=log,
-## transform.params=TRUE,
+## transform=TRUE,
## est=c("K","r"),
## lags=c(1,2),
## seed=7639873L,
@@ -886,7 +825,7 @@
gompertz,
start=starts[[j]],
transform.data=log,
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=c(1,2),
seed=7639873L,
@@ -900,16 +839,13 @@
save(starts,out,fits,file=binary.file,compress="xz")
}
-
## ----eval=T--------------------------------------------------------------
fits
-
## ----nlf-my-pomp,eval=T--------------------------------------------------
long.gomp <- simulate(gompertz,times=1:1000)
theta <- coef(long.gomp)
-
## ----nlf-lag-test-log.r,eval=F-------------------------------------------
## lags <- list(1,2,c(1,2),c(2,3))
## r.vals <- theta["r"]*exp(seq(-0.69,0.69,length=25))
@@ -990,7 +926,6 @@
save(theta,lags,r.vals,K.vals,fvals,fvals2,file=binary.file,compress="xz")
}
-
## ----nlf-gompertz-plot,fig.height=4,fig.width=6,echo=F-------------------
fvals <- scale(fvals,center=apply(fvals,2,max),scale=FALSE)
fvals2 <- scale(fvals2,center=apply(fvals2,2,max),scale=FALSE)
@@ -1021,7 +956,6 @@
abline(v=theta["K"],col="blue")
par(op)
-
## ----nlf-multi-short,eval=F----------------------------------------------
## nreps <- 100
## ndata <- 60
@@ -1066,15 +1000,13 @@
save(lags,nreps,ndata,fvals,file=binary.file,compress="xz")
}
-
## ----eval=T--------------------------------------------------------------
apply(fvals,2,function(x)sd(x)/mean(x))
-
## ----nlf-fit-from-truth,eval=F-------------------------------------------
## true.fit <- nlf(
## gompertz,
-## transform.params=TRUE,
+## transform=TRUE,
## est=c("K","r"),
## lags=2,
## seed=7639873,
@@ -1090,7 +1022,7 @@
} else {
true.fit <- nlf(
gompertz,
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=2,
seed=7639873,
@@ -1101,7 +1033,6 @@
save(true.fit,file=binary.file,compress="xz")
}
-
## ----echo=F--------------------------------------------------------------
set.seed(32329L)
@@ -1116,7 +1047,7 @@
## fit <- nlf(
## gompertz,
## start=coef(gompertz),
-## transform.params=TRUE,
+## transform=TRUE,
## est=c("K","r"),
## lags=lags,
## seed=7639873,
@@ -1146,7 +1077,7 @@
fit <- nlf(
gompertz,
start=coef(gompertz),
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=lags,
seed=7639873,
@@ -1166,12 +1097,10 @@
## ------------------------------------------------------------------------
apply(pars,2,sd)
-
## ----block-bootsamp,eval=F-----------------------------------------------
## bootsamp <- replicate(n=nreps,sample(nboot,size=floor(nboot/3),replace=TRUE))
## bootsamp <- rbind(bootsamp,bootsamp+1,bootsamp+2)
-
## ----nlf-block-boot,eval=F,echo=F----------------------------------------
## lags <- 2
## ndata <- length(obs(gompertz))
@@ -1186,7 +1115,7 @@
## for (j in seq_len(nreps)) {
## fit <- nlf(
## gompertz,
-## transform.params=TRUE,
+## transform=TRUE,
## est=c("K","r"),
## lags=lags,
## seed=7639873L,
@@ -1201,7 +1130,6 @@
## }
## colnames(pars) <- c("r","K")
-
## ----nlf-block-boot-eval,eval=T,echo=F,results='hide'--------------------
binary.file <- "nlf-block-boot.rda"
if (file.exists(binary.file)) {
@@ -1220,7 +1148,7 @@
for (j in seq_len(nreps)) {
fit <- nlf(
gompertz,
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=lags,
seed=7639873L,
@@ -1237,7 +1165,6 @@
save(pars,file=binary.file,compress="xz")
}
-
## ----bsmc-example-flat-prior-1,echo=T,eval=T,results='hide'--------------
pompExample(ricker)
@@ -1250,7 +1177,6 @@
}
)
-
## ----bsmc-example-flat-prior-3,eval=F------------------------------------
## fit1 <- bsmc2(ricker,Np=10000,transform=TRUE,
## est=c("r","sigma"),smooth=0.2,
@@ -1277,15 +1203,12 @@
save(fit1,file=binary.file,compress="xz")
}
-
## ----bsmc-example-flat-prior-coef----------------------------------------
signif(coef(fit1),digits=2)
-
## ----bsmc-example-flat-prior-plot,fig.height=6,fig.width=6,echo=F--------
plot(fit1,pars=c("r","sigma"),thin=5000)
-
## ----bsmc-example-normal-prior,eval=F,echo=T-----------------------------
## ricker <- pomp(ricker,
## rprior=function (params, ...) {
@@ -1323,7 +1246,6 @@
## ----bsmc-example-normal-prior-show,echo=T,eval=T------------------------
signif(coef(fit2),digits=2)
-
## ----sir-step-R----------------------------------------------------------
require(pomp)
@@ -1352,7 +1274,6 @@
x
}
-
## ----sir-step-C----------------------------------------------------------
sir.step <- '
double rate[6]; // transition rates
@@ -1380,7 +1301,6 @@
'
-
## ----sir-pomp-def,eval=T,echo=T,results='hide'---------------------------
rmeas <- '
cases = rnbinom_mu(theta,rho*incid);
@@ -1425,17 +1345,14 @@
simulate(sir,seed=1914679908L) -> sir
-
## ----sir-plot,echo=F-----------------------------------------------------
plot(sir,var=c("cases","incid","S","I"))
-
## ----seas-basis----------------------------------------------------------
tbasis <- seq(-1,21,by=1/52)
basis <- periodic.bspline.basis(tbasis,nbasis=3,degree=2,period=1,
names="seas%d")
-
## ----complex-sir-def,echo=T,eval=T,results='hide'------------------------
seas.sir.step <- '
double rate[6]; // transition rates
@@ -1472,7 +1389,6 @@
incid += trans[3]; // incidence is cumulative recoveries
'
-
## ----other-codes,results='hide'------------------------------------------
seas.sir.skel <- '
double rate[6]; // transition rates
@@ -1572,7 +1488,6 @@
) -> complex.sir
-
## ----seas-basis-plot,echo=F,fig.height=4,fig.width=6---------------------
op <- par(mar=c(5,5,1,5))
matplot(tbasis,basis,xlim=c(0,2),type='l',lwd=2,bty='u',
@@ -1594,8 +1509,6 @@
par(op)
-
## ----complex-sir-plot,echo=F---------------------------------------------
plot(complex.sir)
-
Modified: www/vignettes/intro_to_pomp.Rnw
===================================================================
--- www/vignettes/intro_to_pomp.Rnw 2015-02-22 22:49:40 UTC (rev 1091)
+++ www/vignettes/intro_to_pomp.Rnw 2015-02-23 14:05:48 UTC (rev 1092)
@@ -1181,7 +1181,7 @@
out <- nlf(
gompertz,
start=c(r=1,K=2,sigma=0.5,tau=0.5,X.0=1),
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=c(1,2)
)
@@ -1214,7 +1214,7 @@
gompertz,
start=starts[[j]],
transform.data=log,
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=c(1,2),
seed=7639873L,
@@ -1390,7 +1390,7 @@
<<nlf-fit-from-truth,eval=F>>=
true.fit <- nlf(
gompertz,
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=2,
seed=7639873,
@@ -1435,7 +1435,7 @@
fit <- nlf(
gompertz,
start=coef(gompertz),
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=lags,
seed=7639873,
@@ -1488,7 +1488,7 @@
for (j in seq_len(nreps)) {
fit <- nlf(
gompertz,
- transform.params=TRUE,
+ transform=TRUE,
est=c("K","r"),
lags=lags,
seed=7639873L,
Modified: www/vignettes/intro_to_pomp.pdf
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-block-boot.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-boot.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-fit-from-truth.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-fits.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-lag-tests.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/nlf-multi-short.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/plugin-C-code.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/plugin-R-code.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/pomp.pdf
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-comparison.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-first-probe.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-mif.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-probe-match.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/ricker-probe.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/vectorized-C-code.rda
===================================================================
(Binary files differ)
Modified: www/vignettes/vectorized-R-code.rda
===================================================================
(Binary files differ)
More information about the pomp-commits
mailing list