Trunk: fix JUnit
3 lines of code changed in 1 file:
Trunk: solve Issue 435: UniformIntegerOperator did not include upper in the value:
int newValue = MathUtils.nextInt(upper - lower) + lower;
Because nextInt(n) gives value [0, n-1], if upper = 2 then newValue cannot have 2.
The correct code should be
int newValue = MathUtils.nextInt(upper - lower + 1) + lower;
47 lines of code changed in 3 files:
Trunk: make Integer Parameter to allow to pass Variable<Integer>.
534 lines of code changed in 14 files:
Added a test and an error to avoid a type casting error when -beagle_instances is used in conjunction with codon partitioning.
3 lines of code changed in 1 file:
Add chs, log and exp tp RPN calculator
Add Tree height statistic parser tp .properties
Special calibration cases use RPN expression.
170 lines of code changed in 7 files:
Adding -/N/+ classification to DnDsPerSiteAnalysis
52 lines of code changed in 1 file:
Improvements to the Guess Dates Dialog to allow for parsing of calendar dates.
301 lines of code changed in 2 files:
A bit of a hack but if the RegEx function of DateGuesser doesn't like the number it tries to parse it as a calendar date.
27 lines of code changed in 2 files:
Added an alternative Continous Tree KML generator (TreeKMLGenerator).
1655 lines of code changed in 12 files:
Trunk: update New Tracer doc, because key word "category" is changed into "categorical".
2 lines of code changed in 4 files:
Added ability to specify a list of HPD densities to add contours for.
71 lines of code changed in 1 file:
Removed -d32 switch from the Mac version's command line script
1 lines of code changed in 2 files:
Cleaned up full evaluation test error reporting.
5 lines of code changed in 1 file:
Started work on caching in ATL
95 lines of code changed in 2 files:
Adding metadata into KML output layers in TimeSlicer
109 lines of code changed in 7 files:
TimeSlicer update for compatibility with Google Earth 5.2 / cartographica
1 lines of code changed in 1 file:
TreeTraitParserUtilities now picks up trait parameters that are either simply called the taxon name or have the trait name appended.
8 lines of code changed in 1 file:
Started to add 'ExtendedData' into the KML output of TimeSlicer. This will be better for use in GIS software, allowing styling by data such as time.
112 lines of code changed in 1 file:
Tweaks to AntigenicTraitLikelihood (consider renaming to MultidimensionalScalingLikelihood) as that class returns finite likelihood. Added default bounds to dimension-changing MatrixParameter.
5 lines of code changed in 2 files:
AntigenicTraitLikelihood runs! Unlikely to work though. Changed MatrixParameter to set dimensions lazily. TreeTraitParserUtility now labels the individual rows of the compound parameter just as taxon labels so that ATL can pick them up.
268 lines of code changed in 5 files:
First implementation of correct calibration density for one monophyletic clade inside a Yule tree.
Allow an "explicit" correction via pre computed coefficients, used when putting additional constraints on the topology
43 lines of code changed in 5 files:
Added AntigenicTraitLikelihood to parser list.
1 lines of code changed in 1 file:
Add release files for Phylogeography tools
143 lines of code changed in 7 files:
Added package building to the phylogeography ant file.
31 lines of code changed in 1 file:
Added argument parsing to ContinuousTreeToKML
117 lines of code changed in 3 files:
Temporary patch for bug in ARG model in which negative branch lengths arise.
18 lines of code changed in 2 files:
Created an ANT file for phylogeography stuff.
543 lines of code changed in 5 files:
Consolidated phylogeography command-line tools in one place.
2127 lines of code changed in 11 files:
Moved command line KML generating phylogenetic tools over from FigTree repository.
3346 lines of code changed in 4 files:
First implementation of correct calibration density for one monophyletic clade inside a Yule tree.
The internal interface it a little clunky since the concept does not fit well with the current classes implementing the various speciation priors.
The XML interface is via an additional 'calibration' element inside
the speciationLikelihood. The element contains the taxa and a distribution for the root of the taxa. For a single taxon list, the distribution is for the parent of the taxon, which has no other constraints.
<speciationLikelihood id="speciationlike">
<model>
<yuleModel idref="yule"/>
</model>
<speciesTree>
<treeModel idref="treeModel"/>
</speciesTree>
<calibration>
<exponentialDistributionModel>
<mean>
<parameter id="mean" value="1"/>
</mean>
</exponentialDistributionModel>
<taxa>
<taxon idref="tip1"/>
<taxon idref="tip2"/>
</taxa>
</calibration>
</speciationLikelihood>
158 lines of code changed in 10 files:
automatic intelliJ minor syntax fixes
8 lines of code changed in 6 files:
add new constructor.
18 lines of code changed in 2 files:
Allows any number of tempratures in command line
92 lines of code changed in 2 files:
Added utility class for reading and handling tabular data and applied it to loading an HI table.
156 lines of code changed in 2 files:
Set default posterior limit in TreeAnnotator dialog box to zero to match commandline behaviour.
1 lines of code changed in 2 files:
More work on AntigenicTraitLikelihood; should now implement the Oh and Raftery sampling density. Priors are still needed.
73 lines of code changed in 1 file:
Trunk: Exception for easy debug.
1 lines of code changed in 1 file:
More work on AntigenicTraitLikelihood
136 lines of code changed in 2 files:
Updated trunk's Laplace Prior Parser to use 'scale' rather than 'stdev' (to match the output of BEAUti and the parser in the 1.6 branch).
3 lines of code changed in 1 file:
Fixed an error loading non-binary trees (i.e., most unrooted trees).
2 lines of code changed in 1 file:
Final tweaks to new version of Pathogen
43 lines of code changed in 3 files:
84 lines of code changed in 1 file:
Pathogen loads Newick tree files now.
35 lines of code changed in 1 file:
Started work on a class for handling antigenic assay data.
70 lines of code changed in 1 file:
Added a 'delta' parameter to the AbstractMultivariateTraitLikelihood. This adds a bit of error to the tip data. This could have been done using a BranchRateModel but I wanted it to be added after rescaling by tree length. The disadvantage of this approach is we can't sample the locations of the tips.
67 lines of code changed in 3 files:
Added model-specitic parameter-maskable model averaging across trees to speciation model framework
347 lines of code changed in 4 files: