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PredictiveEcology/SpaDES: v1.3.0

Eliot McIntire; Alex Chubaty; Yong Luo; Sarah Bauduin; Steve Cumming; ygc2l


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    <subfield code="a">Sarah Bauduin</subfield>
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    <subfield code="a">&lt;p&gt;Known issues: &lt;a href="https://github.com/PredictiveEcology/SpaDES/issues"&gt;https://github.com/PredictiveEcology/SpaDES/issues&lt;/a&gt;&lt;/p&gt;
version 1.3.0
&lt;ul&gt;
&lt;li&gt;stricter package version dependencies in Imports and Suggests&lt;/li&gt;
&lt;li&gt;&lt;code&gt;debug&lt;/code&gt; argument in &lt;code&gt;spades()&lt;/code&gt; can now take any expression, character strings. &lt;code&gt;TRUE&lt;/code&gt;/&lt;code&gt;FALSE&lt;/code&gt; changed behavior to show only current event.&lt;/li&gt;
&lt;li&gt;timeunits: when there are parent and grandparent modules, if timeunit is defined, it overrides the "smallest unit" rule. Thus, a parent module can force a timeunit.&lt;/li&gt;
&lt;li&gt;&lt;p&gt;Plot - enhancements and fixes:&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;more robust base plotting and many visual tests on Windows;&lt;/li&gt;
&lt;li&gt;re-add &lt;code&gt;col&lt;/code&gt; arg to &lt;code&gt;Plot&lt;/code&gt; (mimicks &lt;code&gt;cols&lt;/code&gt;). Was lost from version 1.1.2;&lt;/li&gt;
&lt;li&gt;allow any arbitrary function to be used internally to &lt;code&gt;Plot&lt;/code&gt; (&lt;em&gt;e.g.&lt;/em&gt;, barplot, plot, etc.);&lt;/li&gt;
&lt;li&gt;add &lt;code&gt;arr&lt;/code&gt; argument to &lt;code&gt;Plot()&lt;/code&gt;, allowing passing of arrangement;&lt;/li&gt;
&lt;li&gt;allow &lt;code&gt;title&lt;/code&gt; arg in &lt;code&gt;Plot()&lt;/code&gt; to accept character for plot title;&lt;/li&gt;
&lt;li&gt;&lt;code&gt;Plot&lt;/code&gt; can use character passed to &lt;code&gt;title&lt;/code&gt; as a title;&lt;/li&gt;
&lt;li&gt;some additional functionality for plotting of factor rasters, incl. &lt;code&gt;clickValues&lt;/code&gt;, legends correct for wide variety of types;&lt;/li&gt;
&lt;li&gt;change &lt;code&gt;new&lt;/code&gt; arg in &lt;code&gt;Plot()&lt;/code&gt;. Now it does one plot at a time, not whole device. Use &lt;code&gt;clearPlot()&lt;/code&gt; to wipe whole device.&lt;/li&gt;
&lt;/ul&gt;
&lt;/li&gt;
&lt;li&gt;Add &lt;code&gt;modulesGraph&lt;/code&gt;, showing parent and child module relationships.&lt;/li&gt;
&lt;li&gt;Add &lt;code&gt;filesOnly&lt;/code&gt; arg to &lt;code&gt;shine()&lt;/code&gt;. This can be in preparation for publishing to www.shinyapps.io or other pages. Currently still alpha.&lt;/li&gt;
&lt;li&gt;Add POM: Pattern Oriented Modeling (#269). A simple interface to a simList object, allowing fitting parameters to data.&lt;/li&gt;
&lt;li&gt;add &lt;code&gt;.inputObjects&lt;/code&gt; functionality -- function that runs during &lt;code&gt;simInit()&lt;/code&gt; to create default &lt;code&gt;inputObjects&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;add &lt;code&gt;P&lt;/code&gt; as a namespaced shortcut for params: &lt;code&gt;P(sim)&lt;/code&gt; would replace &lt;code&gt;params(sim)$moduleName&lt;/code&gt; when called from within that module&lt;/li&gt;
&lt;li&gt;allow &lt;code&gt;params(sim)&lt;/code&gt; &amp;amp; &lt;code&gt;start(sim)&lt;/code&gt; &amp;amp; others in &lt;code&gt;defineModule()&lt;/code&gt; by changing parse order in module metadata&lt;/li&gt;
&lt;li&gt;add explicit &lt;code&gt;cl&lt;/code&gt; arg to parallel aware functions, for more control&lt;/li&gt;
&lt;li&gt;&lt;code&gt;newModule&lt;/code&gt; gains new arguments &lt;code&gt;type = c("child", "parent")&lt;/code&gt; and &lt;code&gt;children = c()&lt;/code&gt;. See &lt;code&gt;?newModule&lt;/code&gt; (#300).&lt;/li&gt;
&lt;li&gt;module structure now includes an R subfolder for R scripts. These will be parsed during simInit.&lt;/li&gt;
&lt;li&gt;&lt;code&gt;checksums&lt;/code&gt; updated to use faster hashing algorithm (&lt;code&gt;xxhash64&lt;/code&gt;) and now only requires a single hash value per file (#295)&lt;/li&gt;
&lt;li&gt;new Rstudio addin for 'newModule' (#298); requires Import of &lt;code&gt;shiny (&amp;gt;= 0.13)&lt;/code&gt;, &lt;code&gt;miniUI (&amp;gt;= 0.1.1)&lt;/code&gt;, and &lt;code&gt;rstudioapi (&amp;gt;= 0.5)&lt;/code&gt;&lt;/li&gt;
&lt;li&gt;fixed bugs in module template&lt;/li&gt;
&lt;li&gt;fixed bug in &lt;code&gt;cir&lt;/code&gt; (#288, #311)&lt;/li&gt;
&lt;li&gt;improved use of package options; added new option &lt;code&gt;spades.modulesPath&lt;/code&gt;.&lt;/li&gt;
&lt;li&gt;improved &lt;code&gt;downloadModule&lt;/code&gt; to use option &lt;code&gt;spades.modulesPath&lt;/code&gt; (#309)&lt;/li&gt;
&lt;li&gt;improved specification of module inputs and outputs (#189, #214, PR#310)&lt;/li&gt;
&lt;li&gt;remove module version warning (#312)&lt;/li&gt;
&lt;li&gt;other tweaks and fixes&lt;/li&gt;
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