[Pomp-commits] r1216 - pkg/pomp pkg/pomp/R pkg/pomp/demo pkg/pomp/inst pkg/pomp/man pkg/pomp/tests www/content www/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jun 18 01:26:33 CEST 2015
Author: kingaa
Date: 2015-06-18 01:26:32 +0200 (Thu, 18 Jun 2015)
New Revision: 1216
Modified:
pkg/pomp/DESCRIPTION
pkg/pomp/R/nlf.R
pkg/pomp/R/pomp.R
pkg/pomp/R/spect.R
pkg/pomp/demo/sir.R
pkg/pomp/inst/NEWS
pkg/pomp/inst/NEWS.Rd
pkg/pomp/man/LondonYorke.Rd
pkg/pomp/man/csnippet.Rd
pkg/pomp/tests/ou2-spect.R
pkg/pomp/tests/ou2-spect.Rout.save
www/content/NEWS.html
www/vignettes/getting_started.Rmd
www/vignettes/getting_started.html
www/vignettes/pomp.pdf
Log:
- new global option for location of .c and .so files generated by 'pomp'
- minor fixes in 'nlf' and 'spect' to eliminate warnings by using '.lm.fit' in place of 'lm'
- update man pages
- use new 'pomp.file.dir' option in 'getting started' vignette
Modified: pkg/pomp/DESCRIPTION
===================================================================
--- pkg/pomp/DESCRIPTION 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/DESCRIPTION 2015-06-17 23:26:32 UTC (rev 1216)
@@ -1,7 +1,7 @@
Package: pomp
Type: Package
Title: Statistical Inference for Partially Observed Markov Processes
-Version: 0.67-5
+Version: 0.68-1
Date: 2015-06-17
Authors at R: c(person(given=c("Aaron","A."),family="King",
role=c("aut","cre"),email="kingaa at umich.edu"),
Modified: pkg/pomp/R/nlf.R
===================================================================
--- pkg/pomp/R/nlf.R 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/R/nlf.R 2015-06-17 23:26:32 UTC (rev 1216)
@@ -193,8 +193,7 @@
## find a good epsilon
h <- se.par.frac
- if (verbose)
- cat("h in NLF = ", h, "\n")
+ if (verbose) cat("h in NLF = ", h, "\n")
eps <- rep(h,nfitted)
for (i in seq_len(nfitted)) {
@@ -250,13 +249,12 @@
)
FAILED <- -999999
Fvals[Fvals < FAILED+10] <- NA
- xvals <- c(sqrt(2),1,0,1,sqrt(2))*h*fitted[i]
- c2 <- lm(Fvals~I(xvals^2))$coef[2]
+ xvals <- cbind(1,(c(sqrt(2),1,0,1,sqrt(2))*h*fitted[i])^2)
+ c2 <- .lm.fit(xvals,Fvals)$coefficients[2]
eps[i] <- sqrt(abs(lql.frac/c2))
}
- if (verbose)
- cat("epsilon in NLF =",t(eps), "\n")
+ if (verbose) cat("epsilon in NLF =",t(eps), "\n")
Imat <- matrix(0,npts,nfitted)
for (i in seq_len(nfitted)) {
@@ -279,8 +277,7 @@
verbose=FALSE
)
- if (verbose)
- cat("Fitted param ", i, F.up, mean(f.up2,na.rm=T)," up in ",sQuote("nlf"),"\n")
+ if (verbose) cat("Fitted param ", i, F.up, mean(f.up2,na.rm=T)," up in ",sQuote("nlf"),"\n")
guess.down <- fitted
guess.down[i] <- guess.down[i]-eps[i]
@@ -293,8 +290,7 @@
)
F.down <- mean(f.down,na.rm=T)
- if (verbose)
- cat("Fitted param ",i, F.down," down in ",sQuote("NLF"),"\n")
+ if (verbose) cat("Fitted param ",i, F.down," down in ",sQuote("NLF"),"\n")
Jhat[i,i] <- (F.up + F.down-2*F0)/(eps[i]*eps[i])
Imat[,i] <- (f.up-f.down)/(2*eps[i])
Modified: pkg/pomp/R/pomp.R
===================================================================
--- pkg/pomp/R/pomp.R 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/R/pomp.R 2015-06-17 23:26:32 UTC (rev 1216)
@@ -11,7 +11,9 @@
fromEstimationScale, toEstimationScale,
parameter.transform = NULL, parameter.inv.transform = NULL,
globals, userdata, ...,
- .solibfile, .filename, .filedir,
+ .solibfile = list(),
+ .filename = NULL,
+ .filedir = getOption("pomp.file.dir",NULL),
verbose = getOption("verbose",FALSE)) {
## preliminary error checking
@@ -19,9 +21,6 @@
if (missing(times)) stop(sQuote("times")," is a required argument")
if (missing(t0)) stop(sQuote("t0")," is a required argument")
if (missing(params)) params <- numeric(0)
- if (missing(.solibfile)) .solibfile <- list()
- if (missing(.filename)) .filename <- NULL
- if (missing(.filedir)) .filedir <- NULL
if (missing(userdata)) userdata <- list()
added.userdata <- list(...)
Modified: pkg/pomp/R/spect.R
===================================================================
--- pkg/pomp/R/spect.R 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/R/spect.R 2015-06-17 23:26:32 UTC (rev 1216)
@@ -36,12 +36,13 @@
type,
mean=tseries-mean(tseries),
linear={
- x <- seq_along(tseries)
- lm(tseries~x)$residuals
+ m <- cbind(1,seq_along(tseries))
+ .lm.fit(m,tseries)$residuals
},
quadratic={
x <- seq_along(tseries)
- lm(tseries~x+I(x^2))$residuals
+ m <- cbind(1,x,x*x)
+ .lm.fit(m,tseries)$residuals
},
tseries
)
Modified: pkg/pomp/demo/sir.R
===================================================================
--- pkg/pomp/demo/sir.R 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/demo/sir.R 2015-06-17 23:26:32 UTC (rev 1216)
@@ -114,8 +114,6 @@
to_log_barycentric(&TS_0,&S_0,3);
"
-data(LondonYorke)
-
cbind(
time=seq(from=1928,to=1934,by=0.01),
as.data.frame(
Modified: pkg/pomp/inst/NEWS
===================================================================
--- pkg/pomp/inst/NEWS 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/inst/NEWS 2015-06-17 23:26:32 UTC (rev 1216)
@@ -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_8-_1:
+
+ • When using ‘Csnippet’s, by default, the C codes and
+ shared-object files are stored in the R session's temporary
+ directory. One can override this behavior by setting the
+ global ‘pomp.file.dir’ option.
+
_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _0._6_7-_1:
• A 'pomp' object's initializer can now be specified as a
Modified: pkg/pomp/inst/NEWS.Rd
===================================================================
--- pkg/pomp/inst/NEWS.Rd 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/inst/NEWS.Rd 2015-06-17 23:26:32 UTC (rev 1216)
@@ -1,5 +1,11 @@
\name{NEWS}
\title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 0.68-1}{
+ \itemize{
+ \item When using \code{Csnippet}s, by default, the C codes and shared-object files are stored in the R session's temporary directory.
+ One can override this behavior by setting the global \code{pomp.file.dir} option.
+ }
+}
\section{Changes in \pkg{pomp} version 0.67-1}{
\itemize{
\item A 'pomp' object's initializer can now be specified as a Csnippet.
Modified: pkg/pomp/man/LondonYorke.Rd
===================================================================
--- pkg/pomp/man/LondonYorke.Rd 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/man/LondonYorke.Rd 2015-06-17 23:26:32 UTC (rev 1216)
@@ -6,11 +6,9 @@
\code{LondonYorke} is a data-frame containing the monthly number of reported cases of chickenpox, measles, and mumps from two American cities (Baltimore and New York) in the mid-20th century (1928--1972).
}
\usage{
-data(LondonYorke)
+LondonYorke
}
\examples{
-data(LondonYorke)
-
plot(cases~time,data=LondonYorke,subset=disease=="measles",type='n',main="measles",bty='l')
lines(cases~time,data=LondonYorke,subset=disease=="measles"&town=="Baltimore",col="red")
lines(cases~time,data=LondonYorke,subset=disease=="measles"&town=="New York",col="blue")
Modified: pkg/pomp/man/csnippet.Rd
===================================================================
--- pkg/pomp/man/csnippet.Rd 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/man/csnippet.Rd 2015-06-17 23:26:32 UTC (rev 1216)
@@ -21,6 +21,8 @@
Furnishing one or more \code{Csnippet}s as arguments to the \code{pomp} constructor causes them to be written to a C file stored in the \R session's temporary directory, which is then compiled (via \code{\link[=SHLIB]{R CMD SHLIB}}) into a dynamically loadable shared object file.
This is then loaded as needed.
+ One can choose to store these files in a different directory by setting the global option \code{pomp.file.dir}, e.g.: \preformatted{options(pomp.file.dir=getwd())}.
+
\strong{Note to Windows and Mac users:}
By default, your \R installation may not support \code{\link[=SHLIB]{R CMD SHLIB}}.
Have a look at the tutorials on the package website for instructions on enabling this powerful feature of \R.
Modified: pkg/pomp/tests/ou2-spect.R
===================================================================
--- pkg/pomp/tests/ou2-spect.R 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/tests/ou2-spect.R 2015-06-17 23:26:32 UTC (rev 1216)
@@ -1,12 +1,18 @@
library(pomp)
pompExample(ou2)
+set.seed(362083261L)
+
+pdf(file="ou2-spect.pdf")
+
gm1 <- spect.match(ou2,
kernel.width=3,
detrend="mean",
nsim=50,
est=c("alpha.1","alpha.4"),
method="Nelder-Mead")
+gm1 at value
+plot(gm1)
gm2 <- spect.match(ou2,
kernel.width=3,
@@ -14,3 +20,25 @@
nsim=49,
est=c("alpha.1","alpha.4"),
method="Nelder-Mead")
+gm2 at value
+plot(gm2)
+
+gm3 <- spect.match(ou2,
+ kernel.width=3,
+ detrend="linear",
+ nsim=50,
+ est=c("alpha.1","alpha.4"),
+ method="Nelder-Mead")
+gm3 at value
+plot(gm3)
+
+gm4 <- spect.match(ou2,
+ kernel.width=3,
+ detrend="quadratic",
+ nsim=50,
+ est=c("alpha.1","alpha.4"),
+ method="Nelder-Mead")
+gm4 at value
+plot(gm4)
+
+dev.off()
Modified: pkg/pomp/tests/ou2-spect.Rout.save
===================================================================
--- pkg/pomp/tests/ou2-spect.Rout.save 2015-06-17 20:15:19 UTC (rev 1215)
+++ pkg/pomp/tests/ou2-spect.Rout.save 2015-06-17 23:26:32 UTC (rev 1216)
@@ -20,12 +20,19 @@
newly created object(s):
ou2
>
+> set.seed(362083261L)
+>
+> pdf(file="ou2-spect.pdf")
+>
> gm1 <- spect.match(ou2,
+ kernel.width=3,
+ detrend="mean",
+ nsim=50,
+ est=c("alpha.1","alpha.4"),
+ method="Nelder-Mead")
+> gm1 at value
+[1] 64.89552
+> plot(gm1)
>
> gm2 <- spect.match(ou2,
+ kernel.width=3,
@@ -33,7 +40,34 @@
+ nsim=49,
+ est=c("alpha.1","alpha.4"),
+ method="Nelder-Mead")
+> gm2 at value
+[1] 73.42989
+> plot(gm2)
>
+> gm3 <- spect.match(ou2,
++ kernel.width=3,
++ detrend="linear",
++ nsim=50,
++ est=c("alpha.1","alpha.4"),
++ method="Nelder-Mead")
+> gm3 at value
+[1] 60.4426
+> plot(gm3)
+>
+> gm4 <- spect.match(ou2,
++ kernel.width=3,
++ detrend="quadratic",
++ nsim=50,
++ est=c("alpha.1","alpha.4"),
++ method="Nelder-Mead")
+> gm4 at value
+[1] 66.11778
+> plot(gm4)
+>
+> dev.off()
+null device
+ 1
+>
> proc.time()
user system elapsed
- 16.957 0.040 17.048
+ 40.234 0.068 40.591
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-06-17 20:15:19 UTC (rev 1215)
+++ www/content/NEWS.html 2015-06-17 23:26:32 UTC (rev 1216)
@@ -7,6 +7,17 @@
<h2>News for package ‘pomp’</h2>
+<h3>Changes in <span class="pkg">pomp</span> version 0.68-1</h3>
+
+
+<ul>
+<li><p> When using <code>Csnippet</code>s, by default, the C codes and shared-object files are stored in the R session's temporary directory.
+One can override this behavior by setting the global <code>pomp.file.dir</code> option.
+</p>
+</li></ul>
+
+
+
<h3>Changes in <span class="pkg">pomp</span> version 0.67-1</h3>
Modified: www/vignettes/getting_started.Rmd
===================================================================
--- www/vignettes/getting_started.Rmd 2015-06-17 20:15:19 UTC (rev 1215)
+++ www/vignettes/getting_started.Rmd 2015-06-17 23:26:32 UTC (rev 1216)
@@ -40,6 +40,7 @@
dev='png',
dev.args=list(bg='transparent')
)
+options(pomp.file.dir="cache/")
```
Modified: www/vignettes/getting_started.html
===================================================================
--- www/vignettes/getting_started.html 2015-06-17 20:15:19 UTC (rev 1215)
+++ www/vignettes/getting_started.html 2015-06-17 23:26:32 UTC (rev 1216)
@@ -90,7 +90,7 @@
</div>
<p>Licensed under the <a href="http://creativecommons.org/licenses/by-nc/3.0">Creative Commons attribution-noncommercial license</a>. Please share and remix noncommercially, mentioning its origin.<br /><img src="data:image/png;base64,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" alt="CC-BY_NC" /></p>
-<p>This document was produced using <code>pomp</code> version 0.66.6.</p>
+<p>This document was produced using <code>pomp</code> version 0.68.1.</p>
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<p>This tutorial aims to help you get started using <code>pomp</code> as a suite of tools for analysis of time series data based on dynamical systems models. First, we give some conceptual background regarding the class of models—partially observed Markov processes—that <code>pomp</code> handles. We then discuss some preliminaries: installing the package and so on. Next, using a basic question about ecological population regulation as an example, we load some data and implement some models as <code>R</code> objects of class <code>pomp</code>. Finally, we illustrate some of the package’s capabilities by using its algorithms to fit and compare the models using various inference methods.</p>
@@ -174,7 +174,7 @@
geom_line()+geom_point()+
expand_limits(y=0)+
theme_classic()</code></pre>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 1216
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