removed final time interval
1 lines of code changed in 1 file:
removed final time interval
45 lines of code changed in 2 files:
Trunk: add xml BSP no clock to compare BEAST 2
238 lines of code changed in 5 files:
Added skeleton class for non-phylogenetic trait model for model comparison
57 lines of code changed in 4 files:
TRUNK: update clock model xmls to compare BEAST 2 results
551 lines of code changed in 2 files:
TRUNK: update yule and birth death xml to compare BEAST 2 results
0 lines of code changed in 4 files:
TRUNK: add xml to compare BEAST 2 results
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Implementing paired virus-antiserum measurements (for when a titre is available for a serum raised against the virus being tested - this will be assume to be drawn from an identical distribution across all such pairs).
44 lines of code changed in 2 files:
Trunk: add xml to compare BEAST 2
232 lines of code changed in 1 file:
Simplified the special buttons down to just -Inf and +Inf for the lower and upper bounds respectively.
40 lines of code changed in 1 file:
Continuing to fix things back up...
46 lines of code changed in 2 files:
Continuing to fix things back up...
4 lines of code changed in 1 file:
Some major refactoring of PriorDialog. Probably horribly broken but at least it compiles.
747 lines of code changed in 11 files:
Fixed a burn-in issue with the path sampling analysis (previous version discards 20% of the samples leading to an incorrect marginal likelihood).
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More fixes...
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Report speed per 10^9 for fast runs
9 lines of code changed in 1 file:
Add first version for exact marginal for the general case of N monophyletic clades
604 lines of code changed in 5 files:
Starting to fix things back up...
28 lines of code changed in 1 file:
Some serious cleaning up of how priors are specified. This allows appropriate prior choices for different 'flavours' of parameters (non-negative, zero-one interval, discrete, HPM, CMTC rates). Truncation of the the prior is now a switch and bounds so can be applied to any prior (although the UI is not in place for this yet).
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Added vector slice functionality to parameter matrices
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Enabling basic hierarchical phylogenetics models by default
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Mostly working hierarchical phylogenetic models
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Merged with latest bug fixed. Also implemented Component insertion points inside of the operatior schedule for specially formated operations.
348 lines of code changed in 10 files:
Cleaned up PriorDialog to better render distributions if possible.
679 lines of code changed in 13 files:
Made validation of RealNumberFields a bit prettier - doesn't report MIN_DOUBLE/MAX_DOUBLE as bounds.
16 lines of code changed in 1 file:
Bug in CompleteHistoryLogger prevented use with single site/data column.
1 lines of code changed in 1 file:
Fixing an error in my last commit
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Transferring my changes from branch 1.6 to trunk:
Changes to LogNormalDistributionModel to allow for the stdev value to also not
be in log space (r3774)
Changes to UncorrelatedRelaxedClockTest due to changes in
LogNormalDistributionModel in r3774 (r3775)
Minor change in MixtureModelBranchRates to fix an issue caused by changes in
revision 3735 (r3773)
Bug fix for AncestralSequenceAnnotator plus added a window to select
input/output files (r3819)
Fixed spelling for GeneralSubstitutionModelTest (r3833)
Fixed a RuntimeException for AncestralStateTreeLikelihood (r3957)
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Added support for multiple rate categories in ancestral sequence reconstruction
16 lines of code changed in 1 file:
Reads text based files which map repeated assays to antisera and viruses to corresponding antisera (these will be assumed to be drawn from an independent distribution independent of location).
103 lines of code changed in 1 file:
63 lines of code changed in 2 files:
TRUNK: update my tool for exponetial growth vs bdss
60 lines of code changed in 1 file:
Trunk: update my tool adding exp
321 lines of code changed in 1 file:
Intermediate work on implementing Hierarchical Phylogenetics Models in BEAUti
424 lines of code changed in 11 files:
Major work on AncestralSequenceAnnotator. Mostly generalization for different models and datatypes. Added MakeAncestralSequenceAnnotatedTree, which takes BAli-Phy output and turns it into a BEAST compatible format
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Update SplitBySiteTraitLogger to work with sequence traits
37 lines of code changed in 2 files:
Added (approx.) conditional reference prior for overall substitution rate scalar into BEAUti
135 lines of code changed in 10 files:
Fixed bug in Procrustes and added UnitTest.
116 lines of code changed in 5 files:
Further tweaks to Procrustes
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Can now apply the configured procrustes transformation to other vectors (say, coordinates at internal nodes of the tree).
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Procrustination is working I think.
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Added the as yet untested procrustination into AntigenicPlotter.
9 lines of code changed in 2 files:
TRUNK: update my tool adding combined trees
295 lines of code changed in 1 file:
Work on porting procrustes.r
62 lines of code changed in 1 file:
36 lines of code changed in 2 files:
Added translational hints about R code
13 lines of code changed in 1 file:
Start of a port of the R procrustination function
60 lines of code changed in 1 file:
Trunk: update my tool
116 lines of code changed in 1 file:
LogCombiner now writes all the attributes of the tree (not just the lnP).
24 lines of code changed in 1 file:
Changed the BEAGLE defaults in the BEAST dialog to 'prefer CPU' and 'prefer Double'
3 lines of code changed in 1 file:
Extended complete histories for multiple sites
147 lines of code changed in 3 files:
Logger to get data likelihood easily from a MarkovJumpsTreeLikelihood
67 lines of code changed in 2 files:
Adding TreeAnnonator parsing ability for MarkovJumps processes with multiple sites. To be used in Markov-modulated substitution models with Chris Simon.
151 lines of code changed in 6 files:
Removed an erroneously repeated command line option.
0 lines of code changed in 1 file:
TRUNK: update my tool and BDSS log transf
12 lines of code changed in 2 files:
Trunk: update my tool
48 lines of code changed in 1 file:
Trunk: a small correction of TraceAnalysis
3 lines of code changed in 1 file:
Added a SigmoidIntegrator which allows taking small sampling steps towards the edges of the integration interval (see Lepage et al., 2007). An example of how to use this new integrator was added to examples/release/testTreePathSampling.xml.
32 lines of code changed in 1 file:
Added a section to the xml to illustrate usage of the sigmoid integration approach for the beta values when using thermodynamic integration.
26 lines of code changed in 1 file:
Trunk: allow to select directory
1 lines of code changed in 1 file:
Trunk: add log transformation into BDSS
32 lines of code changed in 2 files:
Added a "beta quantile integrator" (see Xie et al., 2010 and Fan et al., 2011) as an alternative path scheme for the beta values in the thermodynamic integration framework. See examples/release/testTreePathSampling.xml for an example on how to use this integrator.
22 lines of code changed in 1 file:
Adjusted certain output files so that the entire xml file can be performed in a single run (the previous version gave parsing errors). The second marginal likelihood estimator now uses beta quantiles to define the path of the beta values in the thermodynamic integration approach (see Xie et al., 2010 and Fan et al., 2011).
11 lines of code changed in 1 file:
Placed two unused (deprecated) methods into comment
19 lines of code changed in 1 file:
Re-organize calibration code. add experimental "approximate" marginal.
405 lines of code changed in 7 files:
Trunk: update TraceAnalysis
79 lines of code changed in 5 files:
add some expectations
32 lines of code changed in 12 files:
Small correction to the GeometricIntegrator
1 lines of code changed in 1 file:
add a few calibration test files
722 lines of code changed in 7 files:
add all worked out closed form calibration marginals: parent of clade, two nested clades, clade and root.
168 lines of code changed in 5 files:
Visual tweaks.
95 lines of code changed in 5 files:
Trace type buttons weren't working...
12 lines of code changed in 1 file:
Didn't mean to remove the category labels
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Working towards Tracer 1.6. Switched trace 'types' (in the GUI) to 'real', 'integer' and 'categorical' as the previous ones were in programmers' jargon. These buttons also are now disabled when no trace is selected. Also disabled the confirmation box for setting types - if you press the button, then you probably intended to do it (this is a static switch at the top of the TracerFrame.java).
Cleaned up some issues with the generification of 'Variate' - in particular some methods in the plotting were not being overridden.
In 'distribution' tab, for real traces, KDEs are now the default. Histogram estimates can also be shown.
Options for plotting are now stored for specific traces (for example, if you set a manual range for a trace it is now remembered and used for this trace only).
Cleaned up some odd code in Skyline plotting (causing an erroneous warning box to appear).
Removed a few exclamation marks from dialog box messages and cleaned up the text.
750 lines of code changed in 60 files:
TRUNK: update my tool
59 lines of code changed in 1 file:
Added secret way to output all times for density estimation.
26 lines of code changed in 1 file:
Some bug fixes in JumpHistoryAnalyser
32 lines of code changed in 1 file:
Initial work on implementing hierarchical priors into BEAUti
554 lines of code changed in 5 files:
Implemented ascertainment correction for continous, integrated diffusion models
370 lines of code changed in 7 files:
Preliminary work on Markov modulated hidden class reporting
72 lines of code changed in 4 files:
Trunk: update my tool
1 lines of code changed in 1 file:
Trunk: fix another trick bug of BDSS
15 lines of code changed in 3 files:
Improved flexibility of JumpHistoryAnalyser - you can now ask it to iterate over from states or to states to give individual counts (either over the specified sets of states or all states).
213 lines of code changed in 1 file:
Finished up JumpHistoryAnalyser. Command line options allow you to limit the 'from' states and 'to' states to be summarized.
139 lines of code changed in 1 file:
Trunk: correct a bug
9 lines of code changed in 1 file:
Trunk: more updates for GetDateFromTree and LogAnalyser
134 lines of code changed in 4 files:
Improved error checking in CompleteHistoryLogger
25 lines of code changed in 1 file:
May 2011 »