NEWS.html

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<table style="width: 100%;"><tr><td>NEWS</td><td style="text-align: right;">R Documentation</td></tr></table>

<h2>News for the <span class="pkg">panelPomp</span> package</h2>

<h3>Changes in <span class="pkg">panelPomp</span> version 1.6.0.0</h3>


<ul>
<li><p>Removed deprecated functions.
</p>
</li>
<li><p>Release matching CRAN version 1.6.0.0
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.5.0.2</h3>


<ul>
<li><p> Created internal functions for in-place modification of <code>pparamArray</code> within the <code>mif2</code> function. When the number of units and particles is large, this change results in substantial improvements in computational speed by avoiding unecessary memory creation and garbage collection.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.5.0.1</h3>


<ul>
<li><p> Removed unused variables.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.5.0.0</h3>


<ul>
<li><p> Streamlined <code>panelPomp-methods</code> documentation.
</p>
</li>
<li><p> Added <code>panelMeasles</code> to <code>panelPomp</code> models documentation family.
</p>
</li>
<li><p> Fixed redirected link in documentation.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.4.1.0</h3>


<ul>
<li><p> Added two new datasets: <code>twentycities</code> and <code>uk_measles</code>. These data contain measles incidence data from 20 UK cities.
</p>
</li>
<li><p> Added a new <code>panelPomp</code> model example: <code>panelMeasles</code>.
</p>
</li>
<li><p> Added Aaron Abkemeier as a package contributor.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.4.0.1</h3>


<ul>
<li><p> Added Jesse Wheeler as one of the package authors in citation file.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.4.0.0</h3>


<ul>
<li><p> Changed package maintainers
</p>
</li>
<li><p> Updated package governance file and website
</p>
</li>
<li><p> Standardized package version numbering system to four point system.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.3.1</h3>


<ul>
<li><p> Fixed broken links in function documentation.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.3.0</h3>


<ul>
<li><p> Changed the default <code>cooling.type</code> argument in the <code>mif2()</code> function to be <code>"geometric"</code> in order to be consistent with the <code>pomp</code> package.
</p>
</li>
<li><p> Added <code>format</code> argument to <code>coef.panelPomp</code> method, with options <code>c("vector", "list")</code>. This functionality makes the <code>pparams</code> function obsolete, so it has been removed from the package in this version.
</p>
</li>
<li><p> Changed the <code>pParams()</code> function name to <code>toParamList()</code>.
</p>
</li>
<li><p> Modified the <code>toVectorPparams()</code> function so that it returns a vector instead of a <code>data.frame</code> object with a single row. The name of the function was also changed to <code>toParamVec()</code>, and is a near inverse of the <code>toParamList()</code> function.
</p>
</li>
<li><p> Updated unit tests and documentation.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.2.0</h3>


<ul>
<li><p> Change the generic <code>unitlogLik</code> to <code>unitLogLik</code> to match camel-case style of package. The original function is deprecated in this version and will be removed in future updates.
</p>
</li>
<li><p> Changed <code>panelPomp</code> S4 object slot name from <code>unit.objects</code> to <code>unit_objects</code> in order to be consistent with <code>pomp</code> pacakge. Corresponding getter and setter methods for this slot have also been changed from <code>unitobjects()</code> to <code>unit_objects()</code>.
</p>
</li>
<li><p> Added generics <code>shared()</code>, <code>shared()&lt;-</code>, <code>specific()</code>, and <code>specific()&lt;-</code>. These generics provide convinient access to parameters of a <code>panelPomp</code> object, but the setter methods also allow for changing a parameter type between shared and unit-specific.
</p>
</li>
<li><p> Added function <code>runif_panel_design()</code>, which is useful for generating design matrices for PanelPOMP models.
</p>
</li>
<li><p> Minor typo fixes to package and function documentation.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.1.0.2</h3>


<ul>
<li><p> Added a type check for the <code>params</code> arguement of the
<code>pfilter</code> function in order to throw more user friendly error.
</p>
</li>
<li><p> A more user friendly error is thrown when the user specifies a
parameter as both shared and unit specific in the <code>mif2</code> function.
</p>
</li>
<li><p> Added a <code>match.arg</code> call in <code>mif2.internal</code>; this will
allow the default option for the <code>cooling.type</code> argument in
<code>mif2</code> to no longer throw an error, and mimics the behaviour of the
<code>mif2</code> function in the <code>pomp</code> package.
</p>
</li>
<li><p> The <code>pParams</code> function no longer changes the order of the unit
specific parameter names; this was causing an error because the
<code>barycentric</code> parameter transformation requires that the parameters
are adjacent to one another in the parameter vector.
</p>
</li>
<li><p> Improved documentation for <code>panel_logmeanexp</code>.
</p>
</li>
<li><p> More robust input checking for the <code>pfilter</code> function with
user friendly error messages.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.1.0</h3>


<ul>
<li><p> Improved documentation and tests.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 1.0.0</h3>


<ul>
<li><p> Submitted to CRAN.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.18.0</h3>


<ul>
<li><p> Fixed bug in <code>fromVectorPparams()</code> to make it a true inverse of <code>toVectorPparams()</code>.
</p>
</li>
<li><p> Homogenized documentation; added examples.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.15.0</h3>


<ul>
<li><p> New coercion to <code>pompList</code> and update to list.
</p>
</li>
<li> <p><code>panelGompertzLikelihood</code> replaces <code>kalman_gompertz.R</code>.
</p>
</li>
<li><p> expunged <code>panelPompExample</code>.
</p>
</li>
<li><p> Names added to plot; <code>pfilter</code> matches units by name.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.14.0</h3>


<ul>
<li><p> New <code>simulate</code> function.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.13.0</h3>


<ul>
<li><p> New <code>panelRandomWalk</code> example.
</p>
</li>
<li> <p><code>panelPompExample</code> is now deprecated and will be removed in the
near future.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.12.0</h3>


<ul>
<li><p> New <code>plot</code> method for <code>panelPomp</code> objects.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.11.0</h3>


<ul>
<li><p> Additional functions implementing Kalman filtering to panels and to the Gompertz model.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.10.2.0</h3>


<ul>
<li><p> Minor improvements to the interface.
</p>
</li>
<li><p> Additional examples: <span class="pkg">contacts()</span> and <span class="pkg">panelGompertz()</span>.
</p>
</li>
<li><p> The minimum version of <span class="pkg">pomp</span> supported is now <code>2.7</code>.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.9.1</h3>


<ul>
<li><p> The minimum version of <span class="pkg">pomp</span> supported is now <code>2.1</code>. While
this is likely to imply substantial changes in <span class="pkg">pomp</span> objects (on which
<span class="pkg">panelPomp</span> objects rely) there are only three fundamental changes that
break panelPomp's backwards compatibility:
</p>
</li>
<li><p> The first argument <code>pfilter(object, ...)</code> changes to <code>data</code>.
</p>
</li>
<li><p> The first argument <code>mif2(object, ...)</code> changes to <code>data</code>.
</p>
</li>
<li><p> The ‘conv.rec’ method has been deprecated, replaced by the new
‘traces’ method.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.8.3</h3>


<ul>
<li><p> Improvements to the interface.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.7</h3>


<ul>
<li><p> A new <code>conv.rec</code> method.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.6</h3>


<ul>
<li><p> Many improvements to the interface.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.5.6</h3>


<ul>
<li> <p><code>panelPompExamples()</code> now allows creating <code>panelPomp</code> objects that come with the package.
</p>
</li>
<li><p> New documentation and tests.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.5.5</h3>


<ul>
<li><p> New documentation and tests.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.5.4</h3>


<ul>
<li><p> New documentation and tests.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.5.3</h3>


<ul>
<li><p> New documentation and additional tests.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.5</h3>


<ul>
<li><p> New documentation and additional tests and coverage.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.4</h3>


<ul>
<li><p> New tests added.
</p>
</li>
<li><p> New methods.
</p>
</li>
<li><p> A bug in <code>pfilter</code> and <code>mif2</code> has been fixed (<code>pomp</code>'s default filtering tolerance <code>tol=1e-17</code> was used instead of values specified by the user). Thanks to Aaron King for finding it.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.2</h3>


<ul>
<li><p> New tests added.
</p>
</li>
<li><p> Eliminate need to protect <code>rw.sd</code> from being evaluated.
</p>
</li></ul>


<h3>Changes in <span class="pkg">panelPomp</span> version 0.1</h3>


<ul>
<li><p> Unused variable purged.
</p>
</li>
<li> <p><code>pPfilter.internal</code> streamlined.
</p>
</li>
<li><p> Test for reproducibility of pfilter calculations added.
</p>
</li></ul>


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