[Pomp-commits] r1119 - pkg/pomp/R pkg/pomp/inst pkg/pomp/inst/examples pkg/pomp/man pkg/pomp/tests www/content www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Sun Mar 1 04:40:57 CET 2015
Author: kingaa
Date: 2015-03-01 04:40:56 +0100 (Sun, 01 Mar 2015)
New Revision: 1119
Removed:
pkg/pomp/inst/examples/verhulst.R
pkg/pomp/man/verhulst.Rd
pkg/pomp/tests/verhulst.R
pkg/pomp/tests/verhulst.Rout.save
Modified:
pkg/pomp/R/pomp-methods.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/man/example.Rd
pkg/pomp/tests/steps.R
pkg/pomp/tests/steps.Rout.save
www/content/NEWS.html
www/vignettes/Makefile
www/vignettes/index.html
Log:
- fix bug in partrans
- remove 'verhulst' example
- remove reference to 'advanced topics' vignette from webpage
Modified: pkg/pomp/R/pomp-methods.R
===================================================================
--- pkg/pomp/R/pomp-methods.R 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/R/pomp-methods.R 2015-03-01 03:40:56 UTC (rev 1119)
@@ -28,8 +28,11 @@
partrans.internal <- function (object, params, dir = c("forward","inverse"),
.getnativesymbolinfo = TRUE, ...) {
if (!object at has.trans) return(params)
+ pompLoad(object)
dir <- switch(match.arg(dir),forward=1L,inverse=-1L)
- .Call(do_partrans,object,params,dir,.getnativesymbolinfo)
+ rv <- .Call(do_partrans,object,params,dir,.getnativesymbolinfo)
+ pompUnload(object)
+ rv
}
setMethod("partrans","pomp",
@@ -310,4 +313,3 @@
invisible(NULL)
}
)
-
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/inst/NEWS 2015-03-01 03:40:56 UTC (rev 1119)
@@ -1,5 +1,12 @@
_N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_2-_2:
+
+ • Bug fix in ‘partrans’ when transformations are implemented
+ using ‘Csnippet’s.
+
+ • Remove the ‘verhulst’ example.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_2-_1:
• ‘mif’ now has the default value ‘var.factor=1’. Since
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/inst/NEWS.Rd 2015-03-01 03:40:56 UTC (rev 1119)
@@ -1,5 +1,11 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.62-2}{
+ \itemize{
+ \item Bug fix in \code{partrans} when transformations are implemented using \code{Csnippet}s.
+ \item Remove the \code{verhulst} example.
+ }
+}
\section{Changes in \pkg{pomp} version 0.62-1}{
\itemize{
\item \code{mif} now has the default value \code{var.factor=1}.
Deleted: pkg/pomp/inst/examples/verhulst.R
===================================================================
--- pkg/pomp/inst/examples/verhulst.R 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/inst/examples/verhulst.R 2015-03-01 03:40:56 UTC (rev 1119)
@@ -1,1052 +0,0 @@
-require(pomp)
-
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-'
-
-pomp(
- data=read.csv2(text=dat),
- times="time",
- t0=0,
- params=c(n.0=10000,K=10000,r=0.9,sigma=0.4,tau=0.1),
- rprocess=euler.sim(
- step.fun=function(x,t,params,delta.t,...){
- r <- params["r"]
- K <- params["K"]
- sigma <- params["sigma"]
- n <- x["n"]
- rnorm(
- n=1,
- mean=n+r*n*(1-n/K)*delta.t,
- sd=sigma*n*sqrt(delta.t)
- )
- },
- delta.t=0.01
- ),
- dprocess=onestep.dens(
- dens.fun=function(x1,x2,t1,t2,params,log,...){
- delta.t <- t2-t1
- r <- params["r"]
- K <- params["K"]
- sigma <- params["sigma"]
- n <- x1["n"]
- dnorm(
- x=x2["n"],
- mean=n+r*n*(1-n/K)*delta.t,
- sd=sigma*n*sqrt(delta.t),
- log=log
- )
- }
- ),
- measurement.model=obs~lnorm(meanlog=log(n),sdlog=log(1+tau)),
- skeleton.type="vectorfield",
- skeleton=function(x,t,params,...){
- r <- params["r"]
- K <- params["K"]
- n <- x["n"]
- f <- r*n*(1-n/K)
- names(f) <- "n"
- f
- }
- ) -> verhulst
-
-c("verhulst")
Modified: pkg/pomp/man/example.Rd
===================================================================
--- pkg/pomp/man/example.Rd 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/man/example.Rd 2015-03-01 03:40:56 UTC (rev 1119)
@@ -46,7 +46,7 @@
\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{bbs}}
}
\keyword{models}
\keyword{datasets}
Deleted: pkg/pomp/man/verhulst.Rd
===================================================================
--- pkg/pomp/man/verhulst.Rd 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/man/verhulst.Rd 2015-03-01 03:40:56 UTC (rev 1119)
@@ -1,29 +0,0 @@
-\name{verhulst}
-\alias{verhulst}
-\docType{data}
-\title{Simple Verhulst-Pearl (logistic) model.}
-\description{
- \code{verhulst} is a \code{pomp} object encoding a univariate stochastic logistic model with measurement error.
-}
-\details{
- The model is written as an Ito diffusion, \deqn{dn = r n \left(1-\frac{n}{K}\right) dt + \sigma n dW}{dn = r n (1-n/K) dt + sigma n dW}, where \eqn{W} is a Wiener process.
- It is implemented using the \code{\link{euler.sim}} plug-in.
-}
-\examples{
-pompExample(verhulst)
-plot(verhulst)
-coef(verhulst)
-params <- cbind(
- c(n.0=100,K=10000,r=0.2,sigma=0.4,tau=0.1),
- c(n.0=1000,K=11000,r=0.1,sigma=0.4,tau=0.1)
- )
-x <- simulate(verhulst,params=params,states=TRUE)
-matplot(time(verhulst),t(x['n',,]),type='l')
-y <- trajectory(verhulst,params=params)
-matlines(time(verhulst),t(y['n',,]),type='l',lwd=2)
-}
-\seealso{
- \code{\link{pomp}}
-}
-\keyword{models}
-\keyword{datasets}
Modified: pkg/pomp/tests/steps.R
===================================================================
--- pkg/pomp/tests/steps.R 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/tests/steps.R 2015-03-01 03:40:56 UTC (rev 1119)
@@ -9,9 +9,8 @@
y <- simulate(ricker,times=tm,states=TRUE)["N",,]
stopifnot(identical(x,y))
-pompExample(verhulst)
-coef(verhulst,c("n.0","sigma")) <- c(15,0)
+pompExample(euler.sir)
tm <- sort(runif(n=100,max=1))
-x <- trajectory(verhulst,times=tm)["n",,]
-y <- simulate(verhulst,times=tm,states=TRUE)["n",,]
+x <- trajectory(euler.sir,times=tm)["I",,]
+y <- simulate(euler.sir,times=tm,states=TRUE)["I",,]
table(cut(x-y,breaks=c(-Inf,seq(-0.2,0.2,by=0.01),Inf),ordered=T))
Modified: pkg/pomp/tests/steps.Rout.save
===================================================================
--- pkg/pomp/tests/steps.Rout.save 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/tests/steps.Rout.save 2015-03-01 03:40:56 UTC (rev 1119)
@@ -30,17 +30,16 @@
> y <- simulate(ricker,times=tm,states=TRUE)["N",,]
> stopifnot(identical(x,y))
>
-> pompExample(verhulst)
+> pompExample(euler.sir)
newly created object(s):
- verhulst
-> coef(verhulst,c("n.0","sigma")) <- c(15,0)
+ euler.sir
> tm <- sort(runif(n=100,max=1))
-> x <- trajectory(verhulst,times=tm)["n",,]
-> y <- simulate(verhulst,times=tm,states=TRUE)["n",,]
+> x <- trajectory(euler.sir,times=tm)["I",,]
+> y <- simulate(euler.sir,times=tm,states=TRUE)["I",,]
> table(cut(x-y,breaks=c(-Inf,seq(-0.2,0.2,by=0.01),Inf),ordered=T))
(-Inf,-0.2] (-0.2,-0.19] (-0.19,-0.18] (-0.18,-0.17] (-0.17,-0.16]
- 0 0 0 0 0
+ 96 0 0 0 0
(-0.16,-0.15] (-0.15,-0.14] (-0.14,-0.13] (-0.13,-0.12] (-0.12,-0.11]
0 0 0 0 0
(-0.11,-0.1] (-0.1,-0.09] (-0.09,-0.08] (-0.08,-0.07] (-0.07,-0.06]
@@ -48,16 +47,16 @@
(-0.06,-0.05] (-0.05,-0.04] (-0.04,-0.03] (-0.03,-0.02] (-0.02,-0.01]
0 0 0 0 0
(-0.01,0] (0,0.01] (0.01,0.02] (0.02,0.03] (0.03,0.04]
- 0 13 11 11 8
+ 0 0 0 0 0
(0.04,0.05] (0.05,0.06] (0.06,0.07] (0.07,0.08] (0.08,0.09]
- 13 13 8 3 3
+ 0 0 0 0 0
(0.09,0.1] (0.1,0.11] (0.11,0.12] (0.12,0.13] (0.13,0.14]
- 11 6 0 0 0
+ 0 0 0 0 0
(0.14,0.15] (0.15,0.16] (0.16,0.17] (0.17,0.18] (0.18,0.19]
0 0 0 0 0
(0.19,0.2] (0.2, Inf]
- 0 0
+ 0 4
>
> proc.time()
user system elapsed
- 0.632 0.044 0.697
+ 0.570 0.030 0.587
Deleted: pkg/pomp/tests/verhulst.R
===================================================================
--- pkg/pomp/tests/verhulst.R 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/tests/verhulst.R 2015-03-01 03:40:56 UTC (rev 1119)
@@ -1,11 +0,0 @@
-library(pomp)
-
-pompExample(verhulst)
-
-tail(as(verhulst,"data.frame"))
-tail(as.data.frame(verhulst))
-
-coef(verhulst,c("n.0","sigma")) <- c(100,0.2)
-time(verhulst) <- 1:100
-
-tail(as.data.frame(simulate(verhulst,seed=1066L)))
Deleted: pkg/pomp/tests/verhulst.Rout.save
===================================================================
--- pkg/pomp/tests/verhulst.Rout.save 2015-03-01 03:40:12 UTC (rev 1118)
+++ pkg/pomp/tests/verhulst.Rout.save 2015-03-01 03:40:56 UTC (rev 1119)
@@ -1,57 +0,0 @@
-
-R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
-Copyright (C) 2014 The R Foundation for Statistical Computing
-Platform: x86_64-unknown-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
-> library(pomp)
-Loading required package: subplex
-Loading required package: nloptr
->
-> pompExample(verhulst)
-newly created object(s):
- verhulst
->
-> tail(as(verhulst,"data.frame"))
- time obs
-995 99.5 14051.372
-996 99.6 10764.397
-997 99.7 8359.591
-998 99.8 8337.105
-999 99.9 8322.998
-1000 100.0 8327.300
-> tail(as.data.frame(verhulst))
- time obs
-995 99.5 14051.372
-996 99.6 10764.397
-997 99.7 8359.591
-998 99.8 8337.105
-999 99.9 8322.998
-1000 100.0 8327.300
->
-> coef(verhulst,c("n.0","sigma")) <- c(100,0.2)
-> time(verhulst) <- 1:100
->
-> tail(as.data.frame(simulate(verhulst,seed=1066L)))
- time obs n
-95 95 11528.048 10993.019
-96 96 7829.730 9218.963
-97 97 9483.337 9642.360
-98 98 9819.607 8914.544
-99 99 8753.751 9082.258
-100 100 9202.150 9452.477
->
-> proc.time()
- user system elapsed
- 0.696 0.044 0.755
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-03-01 03:40:12 UTC (rev 1118)
+++ www/content/NEWS.html 2015-03-01 03:40:56 UTC (rev 1119)
@@ -8,6 +8,19 @@
<h2>News for package ‘pomp’</h2>
+<h3>Changes in <span class="pkg">pomp</span> version 0.62-2</h3>
+
+
+<ul>
+<li><p> Bug fix in <code>partrans</code> when transformations are implemented using <code>Csnippet</code>s.
+</p>
+</li>
+<li><p> Remove the <code>verhulst</code> example.
+</p>
+</li></ul>
+
+
+
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1119
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