Version 1.4.0 for BEAST2.7

New release with BEAST2.7-related updates.
All templates removed.

PhyDyn version 1.3.8

This release incorporates all changes introduced by all version 1.3.7 patches.
In particular, it adds:

• Option to run trajectory from root.
• Covariate Likelihood.

PhyDyn version 1.3.7

This release incorporates all changes introduced by all version 1.3.6 patches.
New patches:
Patch 1: (7/04/2021)

• Added option to run trajectory from root.
• Prototype for seroprevalence likelihood

Patch 2: (19/04/2021)

• Seroprevalence Likelihood data now accepts a 'sigma' column.

Patch 3: (06/07/2021)

• Added CovariateLikelihood

PhyDyn first subtemplate (patch 10)

Includes first subtemplate for seirExog model.

patch 5:

• STreeLikelihoodODE: 'solvePL' deprecated in favour of 'equations'. If equations is not explicitly used, the default equations='PL' is used.
• STreeRootLogger: bug fix. Error when ancestral='false' (default)

patch 6:

• STreeInterval: force restore().
• TrajectoryLogger: last line output wasn't showing rate matrix values (logrates option)

patch 7:

• t1 is set during initAndValidate(). mapNodesToStates is now only called once.
• Added exception to init check: model variable must be initialised by TrajectoryParameters.

patch 8:

• extended TrajectoryLogger's logrates functionality

patch 9:

• Efficient calculation of PopModeloODE
• Added splitIndex and splitSymbol to extract deme names from taxa.

patch 10:

• New default value of stepSize = 0.001

PhyDyn v1.3.5

Minor bug fix: removed repeated Input<> declaration in TrajectoryLogger.

v1.3.4

Compiled against BEASTv2.6.0 pre-release (beast2-2.5.3pre)

PhyDyn v1.3.3

• XMLGenerator now uses BEAST's XML code generator.
• Added sir2Master.xml to examples/SIR2
• STreeIntervals: Node sorting is performed with the aid of a Comparator object.
• Problem with STreeRootLogger fixed.

PhyDyn v1.3.2

Updates/Fixes:

• Simplified version of Tree Intervals. Problem with node order when zero branch lengths fixed.
• STreeRootLogger bug fixed.

Version 1.3.1 (BEAST2.5)

• Changed default STreeLikelihoodODE equations parameter to PL2.
• Added gc parameter STreeLikelihoodODE to control calls to garbage collector in case of poor memory performance.
• Basic model parameters MCMC code generation.

Version 1.3 (BEAST 2.5)

Version 1.3 will start providing XML generation functionality.
Currently, the XMLGenerator class generates XML for a basic case: Structured Tree likelihood given a newick tree file and a population model.