[Pomp-commits] r934 - in www: content vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Apr 23 21:33:19 CEST 2014
Author: kingaa
Date: 2014-04-23 21:33:18 +0200 (Wed, 23 Apr 2014)
New Revision: 934
Added:
www/vignettes/gompertz-performance.rda
Removed:
www/vignettes/complex-sir-def.rda
www/vignettes/sim-sim.rda
www/vignettes/sir-pomp-def.rda
Modified:
www/content/NEWS.html
www/vignettes/Makefile
www/vignettes/advanced_topics_in_pomp.R
www/vignettes/advanced_topics_in_pomp.Rnw
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-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/plugin-C-code.rda
www/vignettes/plugin-R-code.rda
www/vignettes/pomp.pdf
www/vignettes/vectorized-C-code.rda
www/vignettes/vectorized-R-code.rda
Log:
- update the vignettes to go with version 0.50-1 of 'pomp'
Modified: www/content/NEWS.html
===================================================================
--- www/content/NEWS.html 2014-04-22 16:13:13 UTC (rev 933)
+++ www/content/NEWS.html 2014-04-23 19:33:18 UTC (rev 934)
@@ -1,58 +1,75 @@
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html><head><title>R: News for Package 'pomp'</title>
+<html><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 align="right">R Documentation</td></tr></table>
-<h2>News for Package 'pomp'</h2>
+<h2>News for package ‘pomp’</h2>
-<h3>Changes in pomp version 0.49-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.50-1</h3>
<ul>
-<li><p> A new method, 'probe.match.objfun', constructs objective functions suitable for use in optimizers.
+<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 "Csnippet" function.
+See the ‘sir’ demo for a demonstration.
</p>
</li>
-<li><p> 'pomp' now depends on 'nloptr', which provides a suite of optimization algorithms.
+<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 'to_log_barycentric' and 'from_log_barycentric' are provided in 'pomp.h' to facilitate log-barycentric transformations.
+<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 'periodic.bspline.basis'.
+<li><p> Bug fix in <code>periodic.bspline.basis</code>.
</p>
</li>
-<li><p> Package vignettes are no longer available via 'vignette()' but can be reached from the help index.
+<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 pomp version 0.48-3</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.48-3</h3>
<ul>
-<li><p> Correct a bug in 'abc' to do with parameter transformation.
+<li><p> Correct a bug in <code>abc</code> to do with parameter transformation.
</p>
</li></ul>
-<h3>Changes in pomp version 0.48-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.48-1</h3>
<ul>
-<li><p> Create new 'dprior' and 'rprior' slots for 'pomp' objects.
-These will be used by the Bayesian methods (currently 'abc', 'bsmc', and 'pmcmc').
-The 'hyperparams' argument to these methods has been removed;
+<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> 'bsmc' can now be called so that the particles are drawn from the prior distribution (as set by the 'rpior' slot).
+<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.
@@ -61,91 +78,91 @@
-<h3>Changes in pomp version 0.47-4</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.47-4</h3>
<ul>
-<li><p> Revisit 'dacca' bug. Set negative compartments to zero along with compartments immediately downstream.
+<li><p> Revisit <code>dacca</code> bug. Set negative compartments to zero along with compartments immediately downstream.
</p>
</li></ul>
-<h3>Changes in pomp version 0.47-3</h3>
+<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 'dacca' cholera example.
+<li><p> Fix bug that arises only very occasionally in the <code>dacca</code> cholera example.
</p>
</li>
-<li><p> Modify 'dacca' model so that rare positivity violations are punished in a different way.
+<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 pomp version 0.47-2</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.47-2</h3>
<ul>
-<li><p> By default, 'pompBuilder' now creates all files in the temporary directory.
+<li><p> By default, <code>pompBuilder</code> now creates all files in the temporary directory.
</p>
</li></ul>
-<h3>Changes in pomp version 0.47-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.47-1</h3>
<ul>
-<li><p> 'abc' implements Approximate Bayesian Computation for pomp models.
+<li> <p><code>abc</code> implements Approximate Bayesian Computation for pomp models.
</p>
</li></ul>
-<h3>Changes in pomp version 0.46-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.46-1</h3>
<ul>
-<li><p> 'pompExample' now has an optional argument, 'envir', determining which environment the pomp object will be loaded into.
+<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> 'logmeanexp' now has an optional argument, 'se', allowing for computation of an approximate standard error.
+<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 pomp version 0.45-8</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-8</h3>
<ul>
-<li><p> bug fix in 'gompertz' example.
+<li><p> bug fix in <code>gompertz</code> example.
</p>
</li></ul>
-<h3>Changes in pomp version 0.45-7</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-7</h3>
<ul>
-<li><p> bug fix in 'pmcmc': Metropolis-Hastings ratio was incorrect except for flat priors!
+<li><p> bug fix in <code>pmcmc</code>: Metropolis-Hastings ratio was incorrect except for flat priors!
</p>
</li></ul>
-<h3>Changes in pomp version 0.45-6</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-6</h3>
<ul>
-<li><p> a fix so that 'pompBuilder' will find 'pomp.h' header file on Windows machines. Thanks to Dave Hayman for finding the problem.
+<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 'logmeanexp' function.
+<li><p> new <code>logmeanexp</code> function.
</p>
</li>
<li><p> some reorganization of the source package structure.
@@ -154,74 +171,74 @@
-<h3>Changes in pomp version 0.45-4</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-4</h3>
<ul>
-<li><p> changes in the way 'reulermultinom', 'deulermultinom', 'dot_product' are exported to other packages. Rather than just being exported as linkables, these are now also defined as static inline functions in the 'pomp.h' header.
+<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 pomp version 0.45-3</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-3</h3>
<ul>
-<li><p> fix bug with 'continue' and method 'mif2'
+<li><p> Fix bug with <code>continue</code> and method <code>"mif2"</code>.
</p>
</li></ul>
-<h3>Changes in pomp version 0.45-2</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-2</h3>
<ul>
-<li><p> new method to coerce 'pfilterd.pomp' objects to data-frames.
+<li><p> new method to coerce <code>pfilterd.pomp</code> objects to data-frames.
</p>
</li></ul>
-<h3>Changes in pomp version 0.45-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.45-1</h3>
<ul>
-<li><p> 'profileDesign' can now handle variables of mixed type.
+<li> <p><code>profileDesign</code> can now handle variables of mixed type.
</p>
</li></ul>
-<h3>Changes in pomp version 0.44-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.44-1</h3>
<ul>
-<li><p> New 'mif2' option for 'mif'.
+<li><p> New <code>"mif2"</code> option for <code>mif</code>.
</p>
</li>
-<li><p> The default behavior for 'mif' and 'pfilter' with respect to filtering failures has been changed.
-Before, the default behavior has been to stop with an error on the first filtering failure ('max.fail=0').
-Now, the default is 'max.fail=Inf', i.e., an error is never triggered.
+<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 'type' and a 'fraction'.
-Currently, supported 'cooling.type's include 'geometric' (the old behavior) and 'hyperbolic', i.e., a 1/(1+n) schedule.
-The 'cooling.fraction' argument specifies the cooling at 50 iterations.
-That is, if s is the intensity of the random-walk perturbation to parameters at the first iteration ('rw.sd'), then the intensity at iteration 50 is s*cooling.fraction.
+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 data()-loadable pomp objects.
-To load the prebuilt example pomp objects from previous versions, use the new 'pompExample' function.
-E.g., instead of 'data(euler.sir)', do 'pompExample("euler.sir")'.
+<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 pomp version 0.43-4</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.43-4</h3>
<ul>
@@ -231,69 +248,69 @@
-<h3>Changes in pomp version 0.43-3</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.43-3</h3>
<ul>
-<li><p> Fix bug in 'pompBuilder' on mac.
+<li><p> Fix bug in <code>pompBuilder</code> on mac.
</p>
</li>
-<li><p> Fix bug in 'dmeasure' when log=TRUE. Bug located by R. Reiner.
+<li><p> Fix bug in <code>dmeasure</code> when <code>log=TRUE</code>. Bug located by R. Reiner.
</p>
</li>
-<li><p> Add 'eff.sample.size' and 'cond.logLik' methods for 'pfilterd.pomp' objects.
+<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 pomp version 0.43-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.43-1</h3>
<ul>
-<li><p> Modify 'traj.match.objfun' to allow arbitrary parameters to be passed to the ODE integrator.
+<li><p> Modify <code>traj.match.objfun</code> to allow arbitrary parameters to be passed to the ODE integrator.
</p>
</li>
-<li><p> Add 'params' argument to 'pomp' so that parameters can be specified at the time the pomp object is created.
+<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 pomp version 0.42-6</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.42-6</h3>
<ul>
-<li><p> Improve error checking in 'pomp'.
+<li><p> Improve error checking in <code>pomp</code>.
</p>
</li>
-<li><p> Add support for covariates to 'pompBuilder'.
+<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 'lookup_table' so that warnings are not generated unless true extrapolation is performed (i.e., eliminate the warnings at the boundary).
+<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 'pomp.h' header file.
+<li><p> Some small modifications to the ‘<span class="file">pomp.h</span>’ header file.
</p>
</li></ul>
-<h3>Changes in pomp version 0.42-4</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.42-4</h3>
<ul>
-<li><p> When 'trajectory' calls 'ode', there is a need to preserve information across calls to the vectorfield-evaluating function.
+<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 pomp version 0.42-2</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.42-2</h3>
<ul>
@@ -304,92 +321,92 @@
-<h3>Changes in pomp version 0.42-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.42-1</h3>
<ul>
-<li><p> An EXPERIMENTAL facility for constructing pomp objects out of native C routines is now included (pompBuilder).
+<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 'userdata' slot of a pomp object from compiled 'rprocess', 'rmeasure', 'dprocess', 'dmeasure', 'skeleton', and 'partrans' codes is now available.
-Calls to the new C routines 'get_pomp_userdata', 'get_pomp_userdata_int', and 'get_pomp_userdata_double' allow retrieval of these elements.
+<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 data()-loadable examples have been reworked to make use of the above facility.
+<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 data()-loadable examples may be broken.
+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 pomp version 0.41-8</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-8</h3>
<ul>
-<li><p> A demonstration of 'pompBuilder' has been put into the 'advanced topics' vignette.
+<li><p> A demonstration of <code>pompBuilder</code> has been put into the “advanced topics” vignette.
</p>
</li></ul>
-<h3>Changes in pomp version 0.41-7</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-7</h3>
<ul>
-<li><p> A bug in the 'blowflies' example has been fixed.
+<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 pomp version 0.41-6</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-6</h3>
<ul>
-<li><p> The 'gompertz' example parameter transformations have been changed.
+<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 'euler.sir' and 'gillespie.sir' examples have been changed.
-The transmission rate beta(t) is now the arithmetic sum of the seasonality basis functions.
+<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.
-R0 is now given by the arithmetic average of the beta parameters divided by (gamma+mu).
+<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 pomp version 0.41-5</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-5</h3>
<ul>
-<li><p> An experimental facility for constructing pomp objects with native C routines is now included.
+<li><p> An experimental facility for constructing <code>pomp</code> objects with native C routines is now included.
</p>
</li></ul>
-<h3>Changes in pomp version 0.41-4</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-4</h3>
<ul>
-<li><p> The 'blowflies', 'euler.sir', 'gillespie.sir', 'bbs', and 'ricker' data()-loadable examples have been changed to make the parameterization simpler and more natural.
+<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 pomp version 0.41-3</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-3</h3>
<ul>
-<li><p> In 'trajectory', all vectorfield and map evaluation is now done in C for speed.
+<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>
@@ -399,163 +416,163 @@
-<h3>Changes in pomp version 0.41-2</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-2</h3>
<ul>
-<li><p> A segfault bug in 'bbs' example has been fixed.
+<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 'params' slot of the 'bsmcd.pomp' object.
+<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 pomp version 0.41-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.41-1</h3>
<ul>
-<li><p> New arguments in 'mif', 'nlf', 'bsmc', 'pmcmc', 'probe-match', and 'traj-match' allow the estimation to be done on a transformed parameter space.
-When 'transform=TRUE' in these commands ('transform.params=TRUE' for 'nlf'), estimation is performed on the transformed parameter space.
-This is described and demonstrated in the 'intro_to_pomp' vignette.
+<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 data()-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 'rprocess', 'dprocess', 'rmeasure', 'dmeasure', 'skeleton', and 'initializer' codes.
-This change is not backward-compatible, but only codes using these data()-loadable example are affected.
+<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 'bsmc' now returns not a list but an object of class 'bsmcd.pomp'.
-An experimental 'plot' method for objects of this class now exists.
-Also, the parameter posterior means are now stored in the 'params' slot of the 'bsmcd.pomp' object:
-access them with the 'coef' command as usual.
+<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 'data(bbs)' to load it.
+Do <code>data(bbs)</code> to load it.
</p>
</li></ul>
-<h3>Changes in pomp version 0.40-9</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-9</h3>
<ul>
-<li><p> Setting the new argument 'as.data.frame' to 'TRUE' in 'simulate' and 'trajectory' causes the results to be returned as a data-frame.
+<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 pomp version 0.40-8</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-8</h3>
<ul>
-<li><p> A new method 'partrans' allows transformation of vectors or matrices of parameters.
+<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 'has.trans' has been introduced into the 'pomp' class, and the types of slots 'par.trans' and 'par.untrans' have changed.
+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 pomp version 0.40-7</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-7</h3>
<ul>
-<li><p> 'parmat' now gracefully handles the case when 'params' is already a matrix.
+<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 'pfilter' repaired.
+<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 'data(blowflies)'.
+<li><p> Improvements in the documentation of the Nicholson blowflies data <code>data(blowflies)</code>.
</p>
</li></ul>
-<h3>Changes in pomp version 0.40-6</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-6</h3>
<ul>
-<li><p> When a pomp object is updated using 'pomp', the 'params' slot will now be copied over (appropriately transformed).
+<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 'gillespie.sir' example has been changed to make the reporting rate equal to 'rho'.
+<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 'probe' and 'probe.match' for the case nsim < nprobes.
+<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 pomp version 0.40-5</h3>
+<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 'weighted' argument to 'mif' and 'continue' is now deprecated in favor of a new argument 'method'.
-The old 'weighted=T' corresponds to 'method="mif"' while the old 'weighted=F' corresponds to 'method="unweighted"'.
+<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 pomp version 0.40-4</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-4</h3>
<ul>
-<li><p> New functions 'traj.match.objfun' and 'probe.match.objfun' have been added.
-These functions construct functions of one argument suitable for use as objective functions in 'optim'-like optimizers (iincluding 'subplex' and 'sannbox').
+<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.
-This allows the user much greater flexibility in choice of optimization algorithm than is afforded by 'traj.match' and 'probe.match'.
+This allows the user much greater flexibility in choice of optimization algorithm than is afforded by <code>traj.match</code> and <code>probe.match</code>.
</p>
</li>
-<li><p> The 'sannbox' optimizer, which performs simulated annealing with box constraints, is now exported and available for general use.
+<li><p> The <code>sannbox</code> optimizer, which performs simulated annealing with box constraints, is now exported and available for general use.
</p>
</li></ul>
-<h3>Changes in pomp version 0.40-3</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-3</h3>
<ul>
-<li><p> The 'bsmc' method has been improved, due to the contributions of Pierre Jacob.
-Specifically, 'bsmc' no longer reports a log-likelihood (which it never actually computed anyway) but a log-evidence.
+<li><p> The <code>bsmc</code> method has been improved, due to the contributions of Pierre Jacob.
+Specifically, <code>bsmc</code> no longer reports a log-likelihood (which it never actually computed anyway) but a log-evidence.
The latter computation was supplied by Pierre Jacob.
</p>
</li>
-<li><p> A new helper function, 'exp2geom_rate_correction' has been added to the 'pomp.h' file.
-This function computes the rate r such that if N ~ geometric(prob=1-exp(-r*dt)) and T ~ exponential(rate=R), then E[N*dt] = E[T].
+<li><p> A new helper function, <code>exp2geom_rate_correction</code> has been added to the ‘<span class="file">pomp.h</span>’ file.
+This function computes the rate <i>r</i> such that if <i>N \sim geometric(prob=1-\exp(-r dt))</i> and <i>T \sim exponential(rate=R)</i>, then <i>E[N dt] = E[T]</i>.
This is useful in approximating a continuous-time death process by a discrete time (Euler) process.
-In particular, in such a case, T is the waiting time to death in the former and N*dt is the waiting time to death in the latter.
-An Euler binomial or multinomial process with rate r=exp2geom_rate_correction(R,dt) will have the same mean waiting time as the exponential process with rate R.
+In particular, in such a case, <code>T</code> is the waiting time to death in the former and <code>N*dt</code> is the waiting time to death in the latter.
+An Euler binomial or multinomial process with rate <code>r=exp2geom_rate_correction(R,dt)</code> will have the same mean waiting time as the exponential process with rate <code>R</code>.
Thanks to Sebastien Ballesteros for suggesting this.
</p>
</li>
-<li><p> A new helper function, 'rgammawn' has been added, with both R and C interfaces.
+<li><p> A new helper function, <code>rgammawn</code> has been added, with both R and C interfaces.
This function draws an increment of a Gamma white-noise process with a given intensity.
-Specifically, dw=rgammwn(sigma,dt) is Gamma distributed with mean dt and variance sigma^2*dt.
-In this case, mu*dw/dt is suitable for use as a random rate in an Euler-multinomial process.
+Specifically, <code>dw=rgammwn(sigma,dt)</code> is Gamma distributed with mean <code>dt</code> and variance <code>sigma^2*dt</code>.
+In this case, <code>mu*dw/dt</code> is suitable for use as a random rate in an Euler-multinomial process.
Thanks to Sebastien Ballesteros for suggesting this.
</p>
</li></ul>
-<h3>Changes in pomp version 0.40-2</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-2</h3>
<ul>
@@ -566,111 +583,111 @@
-<h3>Changes in pomp version 0.40-1</h3>
+<h3>Changes in <span class="pkg">pomp</span> version 0.40-1</h3>
<ul>
<li><p> It is now possible for discrete-time determistic skeletons to have a general step-size.
Before, the stepsize was always forced to be 1.
-The new argument 'skelmap.delta.t' in 'pomp' (default value 1) sets this step-size.
-NB: in implementing this feature, a new slot has been added to the basic 'pomp' class.
-'pomp' objects created with versions <0.40-1 will not therefore work with this version and must be re-created.
+The new argument <code>skelmap.delta.t</code> in <code>pomp</code> (default value 1) sets this step-size.
+NB: in implementing this feature, a new slot has been added to the basic <code>pomp</code> class.
+<code>pomp</code> objects created with versions <0.40-1 will not therefore work with this version and must be re-created.
</p>
</li>
-<li><p> The deterministic skeleton trajectory functions now look for variables named in 'zeronames' and treat these variables as accumulators.
-This brings the behavior of the deterministic skeleton functions into line with 'rprocess'.
-A new section of the "advanced topics" vignette discusses accumulator variables and 'zeronames'.
+<li><p> The deterministic skeleton trajectory functions now look for variables named in <code>zeronames</code> and treat these variables as accumulators.
+This brings the behavior of the deterministic skeleton functions into line with <code>rprocess</code>.
+A new section of the “advanced topics” vignette discusses accumulator variables and <code>zeronames</code>.
</p>
</li>
<li><p> Include the user manual PDF among the vignettes.
</p>
</li>
-<li><p> The new function 'parmat' creates a suitable matrix of parameters in one line.
+<li><p> The new function <code>parmat</code> creates a suitable matrix of parameters in one line.
</p>
</li></ul>
-<h3>Changes in pomp version 0.39-5</h3>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/pomp -r 934
More information about the pomp-commits
mailing list