[Pomp-commits] r1252 - / www www/content www/graphics
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Jul 7 15:20:45 CEST 2015
Author: kingaa
Date: 2015-07-07 15:20:45 +0200 (Tue, 07 Jul 2015)
New Revision: 1252
Removed:
TODO.md
www/content/Makefile
www/content/NEWS.html
www/content/about.htm
www/content/authors.htm
www/content/ecology.bst
www/content/refs.htm
www/content/refs.tex
www/content/vignettes.htm
www/graphics/NSF_logo.jpg
www/graphics/abstract.gif
www/graphics/cc-by-nc.png
www/graphics/cc0.png
www/graphics/pomp_schematic1.png
www/graphics/pomp_schematic2.png
www/whitestyle.css
Log:
- remove unneeded web content
Deleted: TODO.md
===================================================================
--- TODO.md 2015-07-07 13:16:46 UTC (rev 1251)
+++ TODO.md 2015-07-07 13:20:45 UTC (rev 1252)
@@ -1,10 +0,0 @@
-### pomp to-do list
-
-- documentation on 'mifList', 'pmcmcList', etc.
-- 'transform' argument for pmcmc?
-- 'initializer' -> 'rinit' and perhaps 'dinit'
-- documentation: "regular parameters" instead of "non-IVP"
-- add 'coef' method for 'mifList' objects
-- objective function for spectrum matching
-- one-point SCQL function for possible use in fitting initial conditions
-- save particle filtering variance? Prediction means are optional. Only interesting for end-user if one wants to look at residuals.
Deleted: www/content/Makefile
===================================================================
--- www/content/Makefile 2015-07-07 13:16:46 UTC (rev 1251)
+++ www/content/Makefile 2015-07-07 13:20:45 UTC (rev 1252)
@@ -1,137 +0,0 @@
-INSTALLDIR = $(HOME)
-
-LATEX = latex
-PDFLATEX = pdflatex
-BIBTEX = bibtex
-MAKEIDX = makeindex
-DVIPS = dvips -t letter -Ppdf
-RM = rm -f
-CP = cp
-TAR = tar
-TARFLAGS = zcvf
-PSTOPDF = ps2pdf
-EPSTOPDF = epstopdf
-
-CC = gcc
-CXX = g++
-CFLAGS = -O2 -I. -Wall -static
-LDLIBS = -L. -L/usr/X11/lib
-FC = g77
-FFLAGS = -O2 -fno-underscoring
-AR = ar
-ARFLAGS = rs
-INSTALL = install
-
-AWK = gawk
-L2H = latex2html
-L2HFLAGS = -scalable_fonts -style "whitestyle.css" -short_extn -local_icons -noinfo -split 0 -no_navigation -nosubdir -noaddress -nofootnode
-TIDY = tidy
-F2D = fig2dev
-GZIP = gzip
-ZIP = zip
-
-PSFIX = /usr/local/bin/psfix
-
-GRAPH = graph
-GRAPHFLAGS = -Tfig -K2 --max-line 256 --title-font-name "times-bolditalic" -F"times-bold" -W0.005 -B
-
-TABLES =
-
-FIGS =
-
-EPSFIGS = $(addsuffix .eps, $(FIGS))
-
-PDFFIGS = $(addsuffix .pdf, $(FIGS))
-
-%.ps: %.dvi
- $(DVIPS) $* -o $*.ps
-
-%.dvi: %.tex
- $(LATEX) $*
- -$(BIBTEX) $*
- $(LATEX) $*
- $(LATEX) $*
-
-%.pdf: %.tex
- $(PDFLATEX) $*
- -$(BIBTEX) $*
- $(PDFLATEX) $*
- $(PDFLATEX) $*
-
-%.pdf: %.ps
- $(PSTOPDF) $*.ps $*.pdf
-
-%.idx: %.tex
- -$(LATEX) $*
-
-%.ind: %.idx
- $(MAKEIDX) $*
-
-%.pdf: %.eps
- $(EPSTOPDF) $*.eps --outfile=$*.pdf
-
-%.pdf: %.fig
- $(F2D) -Lpdf $*.fig $@
-
-%.eps: %.fig
- $(F2D) -Leps $*.fig $@
-
-%.gif: %.fig
- $(F2D) -Lgif -t"#ffffff" $*.fig $@
-
-%.png: %.fig
- $(F2D) -Lpng $*.fig $@
-
-%.pdf: %.fig
- $(F2D) -Lpdf $*.fig $@
-
-%.pcx: %.fig
- $(F2D) -Lpcx $*.fig $@
-
-%.htm: %.tex %.pdf
- $(L2H) $(L2HFLAGS) $*
- $(AWK) '{gsub("H2", "H3"); print;}' $*.htm > $*_1.htm
- $(AWK) '{gsub("<BR><HR>", ""); print;}' $*_1.htm > $*_2.htm
- -$(TIDY) -i -w --show-body-only yes $*_2.htm > $*.htm
- $(RM) $*_1.htm $*_2.htm
-
-%.ps: %.nb.ps
- $(PSFIX) $*.nb.ps > $@
-
-%.gz: %
- $(GZIP) < $* > $*.gz
-
-%.tgz: %
- $(TAR) $(TARFLAGS) $*.tgz $*
-
-%: %.c
- $(CC) $(CFLAGS) $*.c $(LDLIBS) -o $*
-
-%: %.cc
- $(CXX) $(CFLAGS) $*.cc $(LDLIBS) -o $*
-
-%: %.f
- $(FC) $(FFLAGS) $*.f $(LDLIBS) -o $*
-
-(%.o): %.c
- $(CC) -c $(CFLAGS) $*.c -o $*.o
- $(AR) $(ARFLAGS) $@ $*.o
- $(RM) $*.o
-
-(%.o): %.cc
- $(CXX) -c $(CFLAGS) $*.cc -o $*.o
- $(AR) $(ARFLAGS) $@ $*.o
- $(RM) $*.o
-
-(%.o): %.f
- $(FC) -c $(FFLAGS) $*.f -o $*.o
- $(AR) $(ARFLAGS) $@ $*.o
- $(RM) $*.o
-
-$(LIB): $(LIB)($(addsuffix .o, $(basename $(SRC))))
-
-clean:
- $(RM) *.log *.blg *.ilg *.aux *.lof *.lot *.toc *.idx *.ttt *.fff *.out internals.pl labels.pl
-
-fresh: clean
- $(RM) *.bbl *.ind *.dvi *.ps
Deleted: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2015-07-07 13:16:46 UTC (rev 1251)
+++ www/content/NEWS.html 2015-07-07 13:20:45 UTC (rev 1252)
@@ -1,1622 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: News for package 'pomp'</title>
-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-<link rel="stylesheet" type="text/css" href="R.css" />
-</head><body>
-
-<table width="100%" summary="page for NEWS"><tr><td>NEWS</td><td style="text-align: right;">R Documentation</td></tr></table>
-
-<h2>News for package ‘pomp’</h2>
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.69-2</h3>
-
-
-<ul>
-<li><p> Measles data from England and Wales, kindly provided by Ben Bolker, are now included as <code>ewmeas</code> and <code>ewcitmeas</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.68-2</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.cache</code> option.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.67-1</h3>
-
-
-<ul>
-<li><p> A 'pomp' object's initializer can now be specified as a Csnippet.
-</p>
-</li>
-<li><p> The default initializer is now considerably faster.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.66-4</h3>
-
-
-<ul>
-<li><p> A full-featured version of IF2, an improved iterated filtering algorithm, is now available as <code>mif2</code>.
-This allows a more general structure for the random perturbations applied to parameters and is generally more efficient and stable than IF1.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.65-2</h3>
-
-
-<ul>
-<li><p> In the <code>pomp</code> constructor, unrecognized arguments are stored internally for use with user-supplied model functions.
-As of this version, an informative message is generated when this happens.
-Previously, this silent behavior was a source of confusion for some users.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.65-1</h3>
-
-
-<ul>
-<li><p> The unfortunately named <code>pomp</code> arguments <code>parameter.transform</code> and <code>parameter.inv.transform</code> have been deprecated in favor of the more mnemonic <code>toEstimationScale</code> and <code>fromEstimationScale</code>.
-Using the old arguments will result in the same behavior as previously, but a warning will be generated.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.64-1</h3>
-
-
-<ul>
-<li><p> The <code>mif</code> option <code>cooling.fraction</code> has been replaced by the more descriptive <code>cooling.fraction.50</code>.
-Recall that this parameter specifies the fraction of random-walk remaining after 50 <code>mif</code> iterations.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.63-6</h3>
-
-
-<ul>
-<li><p> Fixed bug arising when using <code>pomp</code> with <code>Csnippets</code> under windows.
-Thanks to Hamish McCallum for reporting it.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.63-3</h3>
-
-
-<ul>
-<li><p> Improvements to documentation.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.63-1</h3>
-
-
-<ul>
-<li><p> The optimization packages <span class="pkg">nloptr</span> and <span class="pkg">subplex</span> are no longer dependencies of <span class="pkg">pomp</span> that will be loaded at the time <span class="pkg">pomp</span> is.
-Instead, they are imported as needed.
-</p>
-</li></ul>
-
-
-
-<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>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.62-1</h3>
-
-
-<ul>
-<li> <p><code>mif</code> now has the default value <code>var.factor=1</code>.
-Since <code>var.factor</code> has long been a required parameter, this change is backward compatible.
-</p>
-</li>
-<li><p> The long-deprecated <code>cooling.factor</code> option to <code>mif</code> has now been removed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.61-3</h3>
-
-
-<ul>
-<li> <p><code>mif</code>'s <code>pars</code> argument, which is redundant, is now deprecated.
-In a future release, this argument will be removed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.61-1</h3>
-
-
-<ul>
-<li><p> When using <code>Csnippet</code>s or <code>pompBuilder</code>, it is no longer necessary to manually load and unload the dynamically loadable library.
-This is now handled automatically.
-Accordingly, the <code>link</code> argument of <code>pompBuilder</code> has been removed.
-The <code>pompLoad</code> and <code>pompUnload</code> functions introduced in 0.58-1 remain available, though they should rarely be needed.
-</p>
-</li></ul>
-
-
-
-<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>
-
-
-<ul>
-<li><p> New <code>values</code> method extracts simulated probe values on <code>probed.pomp</code> object.
-</p>
-</li>
-<li><p> Better documentation in the ‘<span class="file">pomp.h</span>’ header file.
-</p>
-</li>
-<li><p> Vignettes now feature <code>bsmc2</code> instead of <code>bsmc</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.54-1</h3>
-
-
-<ul>
-<li><p> A modified version of the Liu and West (2001) algorithm is included as <code>bsmc2</code>.
-</p>
-</li>
-<li><p> By default, when <code>B</code> is of class <code>bsmcd.pomp</code>, <code>plot(B)</code> ignores fixed parameters.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.53-6</h3>
-
-
-<ul>
-<li><p> A bug having to do with paths to the temporary C files, encountered when using <code>Csnippet</code>s under windows, has been fixed.
-</p>
-</li>
-<li><p> Package demos are now checked by <code>R CMD check</code> on all platforms.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.53-1</h3>
-
-
-<ul>
-<li> <p><code>nlf</code> now returns an S4 object of class <code>nlfd.pomp</code> with a <code>logLik</code> method for extracting the log quasi likelihood and a <code>$</code> method for extracting arbitrary components.
-</p>
-</li>
-<li><p> The <code>transform</code> argument (for providing a function to transform the data) has been removed in favor of <code>transform.data</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.52-1</h3>
-
-
-<ul>
-<li><p> The new <code>mifList</code> class facilitates approaches based on multiple <code>mif</code> runs.
-The <code>c</code> method constructs <code>mifList</code>s from <code>mif</code>s.
-The <code>plot</code> method produces diagnostic plots.
-</p>
-</li>
-<li> <p><code>compare.mif</code> is now deprecated in favor of <code>plot</code> applied to a <code>mif</code> or <code>mifList</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.51-3</h3>
-
-
-<ul>
-<li> <p><code>transform</code> argument for <code>pmcmc</code> and <code>abc</code> has been removed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.51-2</h3>
-
-
-<ul>
-<li><p> More informative error messages are generated when a needed variable cannot be found.
-</p>
-</li>
-<li><p> Features that facilitate multiple ABC chains have been added.
-There is a <code>c</code> method to combine <code>abc</code> objects into an <code>abcList</code> object and to combine <code>abcList</code> objects.
-Running <code>conv.rec</code> on an <code>abc</code> or <code>abcList</code> object produces <span class="pkg">coda</span> <code>mcmc</code> and <code>mcmc.list</code> objects, respectively.
-Diagnostic plots are produced by running <code>plot</code> on such objects.
-</p>
-</li>
-<li><p> Basic structure of <code>pmcmcList</code> and <code>abcList</code> objects is changed: these objects now inherit directly from <code>list</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.51-1</h3>
-
-
-<ul>
-<li><p> Package <span class="pkg">coda</span> is now a dependency of <span class="pkg">pomp</span>.
-This package provides various generic MCMC diagnostics.
-</p>
-</li>
-<li><p> Features that facilitate multiple PMCMC chains have been added.
-There is a <code>c</code> method to combine <code>pmcmc</code> objects into a <code>pmcmcList</code> object and to combine <code>pmcmcList</code> objects.
-Running <code>conv.rec</code> on a <code>pmcmc</code> or <code>pmcmcList</code> object now produces <span class="pkg">coda</span> <code>mcmc</code> and <code>mcmc.list</code> objects, respectively.
-Diagnostic plots are produced by running <code>plot</code> on such objects.
-</p>
-</li>
-<li><p> The <code>compare.pmcmc</code> and <code>compare.abc</code> methods have been removed as obsolete.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-9</h3>
-
-
-<ul>
-<li><p> Fix bug in <code>compare.pmcmc</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-8</h3>
-
-
-<ul>
-<li><p> Introduced new <code>compare.pmcmc</code> and <code>compare.abc</code> functions, comparable to <code>compare.mif</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-6</h3>
-
-
-<ul>
-<li><p> The package manual and tutorials are no longer included with the package source.
-Instead, links are provided to the <span class="pkg">pomp</span> website.
-</p>
-</li>
-<li><p> The package help pages have been revisited for accuracy and completeness.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.50-1</h3>
-
-
-<ul>
-<li> <p><code>pomp</code> can now take snippets of C code directly as definitions of the various basic functions.
-This is accomplished through the use of a new <code>Csnippet</code> function.
-See the ‘sir’ demo for a demonstration.
-</p>
-</li>
-<li><p> It is now possible to specify global variables and typedefs using the <code>globals</code> argument to <code>pompBuilder</code> and <code>pomp</code>.
-See the ‘sir’ demo for a demonstration.
-Thanks to Carl Pearson for the suggestion.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.49-1</h3>
-
-
-<ul>
-<li><p> A new method, <code>probe.match.objfun</code>, constructs objective functions suitable for use in optimizers.
-</p>
-</li>
-<li> <p><code>pomp</code> now depends on <code>nloptr</code>, which provides a suite of optimization algorithms.
-This package can now be used in various methods for optimization of an objective function.
-</p>
-</li>
-<li><p> New inline C functions <code>to_log_barycentric</code> and <code>from_log_barycentric</code> are provided in ‘<span class="file">pomp.h</span>’ to facilitate log-barycentric transformations.
-These have proven very useful in dealing with parameters constrained to sum to one (e.g., initial conditions of compartmental models).
-</p>
-</li>
-<li><p> Bug fix in <code>periodic.bspline.basis</code>.
-</p>
-</li>
-<li><p> Package vignettes are no longer available via <code>vignette()</code> but can be reached from the help index.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.48-3</h3>
-
-
-<ul>
-<li><p> Correct a bug in <code>abc</code> to do with parameter transformation.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.48-1</h3>
-
-
-<ul>
-<li><p> Create new <code>dprior</code> and <code>rprior</code> slots for <code>pomp</code> objects.
-These will be used by the Bayesian methods (currently <code>abc</code>, <code>bsmc</code>, and <code>pmcmc</code>).
-The <code>hyperparams</code> argument to these methods has been removed;
-hyperparameters are now treated just as any others.
-</p>
-</li>
-<li> <p><code>bsmc</code> can now be called so that the particles are drawn from the prior distribution (as set by the <code>rprior</code> slot).
-</p>
-</li>
-<li><p> Some of the longer tests will only be run if an environment variable is set.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-4</h3>
-
-
-<ul>
-<li><p> Revisit <code>dacca</code> bug. Set negative compartments to zero along with compartments immediately downstream.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-3</h3>
-
-
-<ul>
-<li><p> Fix bug that arises only very occasionally in the <code>dacca</code> cholera example.
-</p>
-</li>
-<li><p> Modify <code>dacca</code> model so that rare positivity violations are punished in a different way.
-This modifies the formal model slightly.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-2</h3>
-
-
-<ul>
-<li><p> By default, <code>pompBuilder</code> now creates all files in the temporary directory.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.47-1</h3>
-
-
-<ul>
-<li> <p><code>abc</code> implements Approximate Bayesian Computation for pomp models.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.46-1</h3>
-
-
-<ul>
-<li> <p><code>pompExample</code> now has an optional argument, <code>envir</code>, determining which environment the <code>pomp</code> object will be loaded into.
-</p>
-</li>
-<li> <p><code>logmeanexp</code> now has an optional argument, <code>se</code>, allowing for computation of an approximate standard error.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-8</h3>
-
-
-<ul>
-<li><p> bug fix in <code>gompertz</code> example.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-7</h3>
-
-
-<ul>
-<li><p> bug fix in <code>pmcmc</code>: Metropolis-Hastings ratio was incorrect except for flat priors!
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-6</h3>
-
-
-<ul>
-<li><p> a fix so that <code>pompBuilder</code> will find ‘<span class="file">pomp.h</span>’ header file on Windows machines. Thanks to Dave Hayman for finding the problem.
-</p>
-</li>
-<li><p> new <code>logmeanexp</code> function.
-</p>
-</li>
-<li><p> some reorganization of the source package structure.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-4</h3>
-
-
-<ul>
-<li><p> changes in the way <code>reulermultinom</code>, <code>deulermultinom</code>, <code>dot_product</code> are exported to other packages. Rather than just being exported as linkables, these are now also defined as static inline functions in the ‘<span class="file">pomp.h</span>’ header.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-3</h3>
-
-
-<ul>
-<li><p> Fix bug with <code>continue</code> and method <code>"mif2"</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-2</h3>
-
-
-<ul>
-<li><p> new method to coerce <code>pfilterd.pomp</code> objects to data-frames.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.45-1</h3>
-
-
-<ul>
-<li> <p><code>profileDesign</code> can now handle variables of mixed type.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.44-1</h3>
-
-
-<ul>
-<li><p> New <code>"mif2"</code> option for <code>mif</code>.
-</p>
-</li>
-<li><p> The default behavior for <code>mif</code> and <code>pfilter</code> with respect to filtering failures has been changed.
-Before, the default behavior has been to stop with an error on the first filtering failure (<code>max.fail=0</code>).
-Now, the default is <code>max.fail=Inf</code>, i.e., an error is never triggered.
-</p>
-</li>
-<li><p> The implementation of MIF cooling schedules has been changed to make it more general.
-The cooling schedule is now specified by a <code>type</code> and a <code>fraction</code>.
-Currently, supported <code>cooling.type</code>s include <code>geometric</code> (the old behavior) and <code>hyperbolic</code>, i.e., a <i>1/(1+n)</i> schedule.
-The <code>cooling.fraction</code> argument specifies the cooling at 50 iterations.
-That is, if <code>s</code> is the intensity of the random-walk perturbation to parameters at the first iteration (<code>rw.sd</code>), then the intensity at iteration 50 is <code>s*cooling.fraction</code>.
-</p>
-</li>
-<li><p> Remove all <code>data()</code>-loadable <code>pomp</code> objects.
-To load the prebuilt example <code>pomp</code> objects from previous versions, use the new <code>pompExample</code> function.
-E.g., instead of <code>data(euler.sir)</code>, do <code>pompExample("euler.sir")</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.43-4</h3>
-
-
-<ul>
-<li><p> Clean up tests.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.43-3</h3>
-
-
-<ul>
-<li><p> Fix bug in <code>pompBuilder</code> on mac.
-</p>
-</li>
-<li><p> Fix bug in <code>dmeasure</code> when <code>log=TRUE</code>. Bug located by R. Reiner.
-</p>
-</li>
-<li><p> Add <code>eff.sample.size</code> and <code>cond.logLik</code> methods for <code>pfilterd.pomp</code> objects.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.43-1</h3>
-
-
-<ul>
-<li><p> Modify <code>traj.match.objfun</code> to allow arbitrary parameters to be passed to the ODE integrator.
-</p>
-</li>
-<li><p> Add <code>params</code> argument to <code>pomp</code> so that parameters can be specified at the time the <code>pomp</code> object is created.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-6</h3>
-
-
-<ul>
-<li><p> Improve error checking in <code>pomp</code>.
-</p>
-</li>
-<li><p> Add support for covariates to <code>pompBuilder</code>.
-</p>
-</li>
-<li><p> Add native parameter transformation routines to the demos.
-</p>
-</li>
-<li><p> Change the warning behavior in <code>lookup_table</code> so that warnings are not generated unless true extrapolation is performed (i.e., eliminate the warnings at the boundary).
-</p>
-</li>
-<li><p> Some small modifications to the ‘<span class="file">pomp.h</span>’ header file.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-4</h3>
-
-
-<ul>
-<li><p> When <code>trajectory</code> calls <code>ode</code>, there is a need to preserve information across calls to the vectorfield-evaluating function.
-The code has been modified to do this in a cleaner way.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-2</h3>
-
-
-<ul>
-<li><p> Several minor bugs have been fixed.
-See the ChangeLog for details.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.42-1</h3>
-
-
-<ul>
-<li><p> An EXPERIMENTAL facility for constructing <code>pomp</code> objects out of native C routines is now included (pompBuilder).
-This facility is being actively developed and future changes may not be backward compatible.
-</p>
-</li>
-<li><p> A new facility allowing access to the <code>userdata</code> slot of a <code>pomp</code> object from compiled <code>rprocess</code>, <code>rmeasure</code>, <code>dprocess</code>, <code>dmeasure</code>, <code>skeleton</code>, and <code>partrans</code> codes is now available.
-Calls to the new C routines <code>get_pomp_userdata</code>, <code>get_pomp_userdata_int</code>, and <code>get_pomp_userdata_double</code> allow retrieval of these elements.
-</p>
-</li>
-<li><p> Some of the <code>data()</code>-loadable examples have been reworked to make use of the above facility.
-The parameterization of these examples has changed.
-These changes are not backward compatible: codes that depend on the <code>data()</code>-loadable examples may be broken.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-8</h3>
-
-
-<ul>
-<li><p> A demonstration of <code>pompBuilder</code> has been put into the “advanced topics” vignette.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-7</h3>
-
-
-<ul>
-<li><p> A bug in the <code>blowflies</code> example has been fixed.
-Thanks to Greg Minshall for discovering it.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-6</h3>
-
-
-<ul>
-<li><p> The <code>gompertz</code> example parameter transformations have been changed.
-No longer are the names of the parameter vector changed in the transformation.
-This change is not backward-compatible, but only codes using this example are affected.
-</p>
-</li>
-<li><p> The <code>euler.sir</code> and <code>gillespie.sir</code> examples have been changed.
-The transmission rate <i>β(t)</i> is now the arithmetic sum of the seasonality basis functions.
-Before, it was the geometric sum.
-<i>R_0</i> is now given by the arithmetic average of the <i>β</i> parameters divided by <i>γ+μ</i>.
-This change is not backward-compatible, but only codes using these examples are affected.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-5</h3>
-
-
-<ul>
-<li><p> An experimental facility for constructing <code>pomp</code> objects with native C routines is now included.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-4</h3>
-
-
-<ul>
-<li><p> The <code>blowflies</code>, <code>euler.sir</code>, <code>gillespie.sir</code>, <code>bbs</code>, and <code>ricker</code> <code>data()</code>-loadable examples have been changed to make the parameterization simpler and more natural.
-This change is not backward-compatible, but only codes using this example are affected.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-3</h3>
-
-
-<ul>
-<li><p> In <code>trajectory</code>, all vectorfield and map evaluation is now done in C for speed.
-For continuous-time dynamical systems, this gives an approximately 4-fold speedup.
-</p>
-</li>
-<li><p> Demos have been created to show some examples.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-2</h3>
-
-
-<ul>
-<li><p> A segfault bug in <code>bbs</code> example has been fixed.
-</p>
-</li>
-<li><p> The posterior medians (not means) are now stored in the <code>params</code> slot of the <code>bsmcd.pomp</code> object.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.41-1</h3>
-
-
-<ul>
-<li><p> New arguments in <code>mif</code>, <code>nlf</code>, <code>bsmc</code>, <code>pmcmc</code>, <code>probe-match</code>, and <code>traj-match</code> allow the estimation to be done on a transformed parameter space.
-When <code>transform=TRUE</code> in these commands (<code>transform.params=TRUE</code> for <code>nlf</code>), estimation is performed on the transformed parameter space.
-This is described and demonstrated in the “intro_to_pomp” vignette.
-</p>
-</li>
-<li><p> The <code>data()</code>-loadable examples have been re-implemented to make use of the above-mentioned facility.
-Note that this new functionality makes it unnecessary to un-transform model parameters within the user-specified <code>rprocess</code>, <code>dprocess</code>, <code>rmeasure</code>, <code>dmeasure</code>, <code>skeleton</code>, and <code>initializer</code> codes.
-This change is not backward-compatible, but only codes using these <code>data()</code>-loadable example are affected.
-</p>
-</li>
-<li><p> The Bayesian sequential Monte Carlo command <code>bsmc</code> now returns not a list but an object of class <code>bsmcd.pomp</code>.
-An experimental <code>plot</code> method for objects of this class now exists.
-Also, the parameter posterior means are now stored in the <code>params</code> slot of the <code>bsmcd.pomp</code> object:
-access them with the <code>coef</code> command as usual.
-</p>
-</li>
-<li><p> A new example, using data from an influenza outbreak in a British boarding school and an SIR model, has been included.
-Do <code>data(bbs)</code> to load it.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-9</h3>
-
-
-<ul>
-<li><p> Setting the new argument <code>as.data.frame</code> to <code>TRUE</code> in <code>simulate</code> and <code>trajectory</code> causes the results to be returned as a data-frame.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-8</h3>
-
-
-<ul>
-<li><p> A new method <code>partrans</code> allows transformation of vectors or matrices of parameters.
-The parameter transformations have been pushed into C for speed.
-It is possible to specify native parameter transformation routines in addition to C functions, but this last facility has not yet been extensively tested.
-A new slot <code>has.trans</code> has been introduced into the <code>pomp</code> class, and the types of slots <code>par.trans</code> and <code>par.untrans</code> have changed.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-7</h3>
-
-
-<ul>
-<li> <p><code>parmat</code> now gracefully handles the case when <code>params</code> is already a matrix.
-</p>
-</li>
-<li><p> Error in the documentation of <code>pfilter</code> repaired.
-Thanks to Alex Smith for pointing this out.
-</p>
-</li>
-<li><p> Improvements in the documentation of the Nicholson blowflies data <code>data(blowflies)</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-6</h3>
-
-
-<ul>
-<li><p> When a <code>pomp</code> object is updated using <code>pomp</code>, the <code>params</code> slot will now be copied over (appropriately transformed).
-Before, it was simply dropped.
-</p>
-</li>
-<li><p> The <code>gillespie.sir</code> example has been changed to make the reporting rate equal to <code>rho</code>.
-Before, it was fixed at 10%.
-</p>
-</li>
-<li><p> A new error-trap has been put into <code>probe</code> and <code>probe.match</code> for the case <code>nsim < nprobes</code>.
-Thanks to Dani Jonas for finding this error.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-5</h3>
-
-
-<ul>
-<li><p> More informative error messages when dimension of state space or data space disagree internally.
-</p>
-</li>
-<li><p> The <code>weighted</code> argument to <code>mif</code> and <code>continue</code> is now deprecated in favor of a new argument <code>method</code>.
-The old <code>weighted=TRUE</code> corresponds to <code>method="mif"</code> while the old <code>weighted=FALSE</code> corresponds to <code>method="unweighted"</code>.
-</p>
-</li></ul>
-
-
-
-<h3>Changes in <span class="pkg">pomp</span> version 0.40-4</h3>
-
-
-<ul>
-<li><p> New functions <code>traj.match.objfun</code> and <code>probe.match.objfun</code> have been added.
-These functions construct functions of one argument suitable for use as objective functions in <code>optim</code>-like optimizers (iincluding <code>subplex</code> and <code>sannbox</code>).
-Minimizing these functions solves the trajectory-matching problem and probe-matching problem, respectively.
[TRUNCATED]
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svnlook diff /svnroot/pomp -r 1252
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