June 2011 Commit Log

Number of Commits:
87
Number of Active Developers:
8
alexei.drummond 2011-06-30 22:40 Rev.: 4081

removed final time interval

1 lines of code changed in 1 file:

alexei.drummond 2011-06-30 22:32

removed final time interval

45 lines of code changed in 2 files:

dong.w.xie 2011-06-29 15:22 Rev.: 4078

Trunk: add xml BSP no clock to compare BEAST 2

238 lines of code changed in 5 files:

msuchard 2011-06-29 15:07 Rev.: 4077

Added skeleton class for non-phylogenetic trait model for model comparison

57 lines of code changed in 4 files:

dong.w.xie 2011-06-29 11:34 Rev.: 4076

TRUNK: update clock model xmls to compare BEAST 2 results

551 lines of code changed in 2 files:

dong.w.xie 2011-06-28 14:50 Rev.: 4075

TRUNK: update yule and birth death xml to compare BEAST 2 results

0 lines of code changed in 4 files:

dong.w.xie 2011-06-28 13:00 Rev.: 4074

TRUNK: add xml to compare BEAST 2 results

0 lines of code changed in 3 files:

rambaut 2011-06-28 04:17 Rev.: 4073

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:

dong.w.xie 2011-06-27 17:39 Rev.: 4072

Trunk: add xml to compare BEAST 2

232 lines of code changed in 1 file:

rambaut 2011-06-25 11:13 Rev.: 4071

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:

rambaut 2011-06-25 11:00 Rev.: 4070

Continuing to fix things back up...

46 lines of code changed in 2 files:

rambaut 2011-06-25 07:44 Rev.: 4069

Continuing to fix things back up...

4 lines of code changed in 1 file:

rambaut 2011-06-25 04:09 Rev.: 4068

Some major refactoring of PriorDialog. Probably horribly broken but at least it compiles.

747 lines of code changed in 11 files:

baele.guy@gmail.com 2011-06-25 01:32 Rev.: 4067

Fixed a burn-in issue with the path sampling analysis (previous version discards 20% of the samples leading to an incorrect marginal likelihood).

2 lines of code changed in 1 file:

rambaut 2011-06-24 22:29 Rev.: 4066

More fixes...

2 lines of code changed in 1 file:

jheled@gmail.com 2011-06-24 21:43 Rev.: 4065

Report speed per 10^9 for fast runs

9 lines of code changed in 1 file:

jheled@gmail.com 2011-06-24 21:33 Rev.: 4064

Add first version for exact marginal for the general case of N monophyletic clades

604 lines of code changed in 5 files:

rambaut 2011-06-24 21:31 Rev.: 4063

Starting to fix things back up...

28 lines of code changed in 1 file:

rambaut 2011-06-24 20:49 Rev.: 4062

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).

731 lines of code changed in 34 files:

msuchard 2011-06-23 08:11 Rev.: 4061

Added vector slice functionality to parameter matrices

131 lines of code changed in 3 files:

msuchard 2011-06-23 04:41 Rev.: 4060

Enabling basic hierarchical phylogenetics models by default

20 lines of code changed in 4 files:

msuchard 2011-06-22 17:04 Rev.: 4059

Mostly working hierarchical phylogenetic models

278 lines of code changed in 6 files:

msuchard 2011-06-22 06:54 Rev.: 4058

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:

rambaut 2011-06-22 01:40 Rev.: 4057

Cleaned up PriorDialog to better render distributions if possible.

679 lines of code changed in 13 files:

rambaut 2011-06-22 01:37 Rev.: 4056

Made validation of RealNumberFields a bit prettier - doesn't report MIN_DOUBLE/MAX_DOUBLE as bounds.

16 lines of code changed in 1 file:

rambaut 2011-06-22 00:39 Rev.: 4055

Bug in CompleteHistoryLogger prevented use with single site/data column.

1 lines of code changed in 1 file:

sibon.li 2011-06-21 12:59 Rev.: 4054

Fixing an error in my last commit

0 lines of code changed in 1 file:

sibon.li 2011-06-21 12:46 Rev.: 4053

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)

217 lines of code changed in 13 files:

msuchard 2011-06-21 10:34 Rev.: 4052

Added support for multiple rate categories in ancestral sequence reconstruction

16 lines of code changed in 1 file:

rambaut 2011-06-21 03:41 Rev.: 4051

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:

rambaut 2011-06-21 02:54 Rev.: 4050

63 lines of code changed in 2 files:

dong.w.xie 2011-06-20 22:03 Rev.: 4049

TRUNK: update my tool for exponetial growth vs bdss

60 lines of code changed in 1 file:

dong.w.xie 2011-06-20 19:33 Rev.: 4048

Trunk: update my tool adding exp

321 lines of code changed in 1 file:

msuchard 2011-06-20 16:21 Rev.: 4047

Intermediate work on implementing Hierarchical Phylogenetics Models in BEAUti

424 lines of code changed in 11 files:

sibon.li 2011-06-20 08:44 Rev.: 4046

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

1109 lines of code changed in 2 files:

msuchard 2011-06-20 05:43 Rev.: 4045

Update SplitBySiteTraitLogger to work with sequence traits

37 lines of code changed in 2 files:

msuchard 2011-06-19 15:55 Rev.: 4044

Added (approx.) conditional reference prior for overall substitution rate scalar into BEAUti

135 lines of code changed in 10 files:

msuchard 2011-06-19 05:46 Rev.: 4043

Fixed bug in Procrustes and added UnitTest.

116 lines of code changed in 5 files:

rambaut 2011-06-19 01:17 Rev.: 4042

Further tweaks to Procrustes

43 lines of code changed in 2 files:

rambaut 2011-06-19 00:38 Rev.: 4041

Can now apply the configured procrustes transformation to other vectors (say, coordinates at internal nodes of the tree).

41 lines of code changed in 1 file:

rambaut 2011-06-18 23:55 Rev.: 4040

Procrustination is working I think.

19 lines of code changed in 2 files:

rambaut 2011-06-18 22:43 Rev.: 4039

Added the as yet untested procrustination into AntigenicPlotter.

9 lines of code changed in 2 files:

dong.w.xie 2011-06-18 18:10 Rev.: 4038

TRUNK: update my tool adding combined trees

295 lines of code changed in 1 file:

rambaut 2011-06-18 09:56 Rev.: 4037

Work on porting procrustes.r

62 lines of code changed in 1 file:

rambaut 2011-06-18 08:03 Rev.: 4036

36 lines of code changed in 2 files:

msuchard 2011-06-18 01:56 Rev.: 4035

Added translational hints about R code

13 lines of code changed in 1 file:

rambaut 2011-06-17 23:42 Rev.: 4034

Start of a port of the R procrustination function

60 lines of code changed in 1 file:

dong.w.xie 2011-06-17 19:18 Rev.: 4033

Trunk: update my tool

116 lines of code changed in 1 file:

rambaut 2011-06-17 08:32 Rev.: 4032

LogCombiner now writes all the attributes of the tree (not just the lnP).

24 lines of code changed in 1 file:

rambaut 2011-06-17 07:19 Rev.: 4031

Changed the BEAGLE defaults in the BEAST dialog to 'prefer CPU' and 'prefer Double'

3 lines of code changed in 1 file:

msuchard 2011-06-16 07:58 Rev.: 4030

Extended complete histories for multiple sites

147 lines of code changed in 3 files:

msuchard 2011-06-16 05:00 Rev.: 4029

Logger to get data likelihood easily from a MarkovJumpsTreeLikelihood

67 lines of code changed in 2 files:

msuchard 2011-06-16 04:29 Rev.: 4028

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:

rambaut 2011-06-14 03:58 Rev.: 4027

Removed an erroneously repeated command line option.

0 lines of code changed in 1 file:

dong.w.xie 2011-06-13 21:27 Rev.: 4026

TRUNK: update my tool and BDSS log transf

12 lines of code changed in 2 files:

dong.w.xie 2011-06-10 18:38 Rev.: 4025

Trunk: update my tool

48 lines of code changed in 1 file:

dong.w.xie 2011-06-10 10:33 Rev.: 4024

Trunk: a small correction of TraceAnalysis

3 lines of code changed in 1 file:

baele.guy@gmail.com 2011-06-10 07:17 Rev.: 4023

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:

baele.guy@gmail.com 2011-06-10 07:15 Rev.: 4022

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:

dong.w.xie 2011-06-09 17:13 Rev.: 4021

Trunk: allow to select directory

1 lines of code changed in 1 file:

dong.w.xie 2011-06-09 17:13 Rev.: 4020

Trunk: add log transformation into BDSS

32 lines of code changed in 2 files:

baele.guy@gmail.com 2011-06-09 04:29 Rev.: 4019

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:

baele.guy@gmail.com 2011-06-09 04:27 Rev.: 4018

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:

baele.guy@gmail.com 2011-06-08 22:24 Rev.: 4017

Placed two unused (deprecated) methods into comment

19 lines of code changed in 1 file:

jheled 2011-06-08 18:24 Rev.: 4016


Re-organize calibration code. add experimental "approximate" marginal.

405 lines of code changed in 7 files:

dong.w.xie 2011-06-07 11:55 Rev.: 4015

Trunk: update TraceAnalysis

79 lines of code changed in 5 files:

jheled 2011-06-07 11:24 Rev.: 4014

add some expectations

32 lines of code changed in 12 files:

baele.guy@gmail.com 2011-06-06 21:23 Rev.: 4013

Small correction to the GeometricIntegrator

1 lines of code changed in 1 file:

jheled 2011-06-06 17:10 Rev.: 4012

add a few calibration test files

722 lines of code changed in 7 files:

jheled 2011-06-06 13:56 Rev.: 4011

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:

rambaut 2011-06-06 11:32 Rev.: 4010

Visual tweaks.

95 lines of code changed in 5 files:

rambaut 2011-06-06 05:53 Rev.: 4009

Trace type buttons weren't working...

12 lines of code changed in 1 file:

rambaut 2011-06-06 05:48 Rev.: 4008

Didn't mean to remove the category labels

2 lines of code changed in 1 file:

rambaut 2011-06-06 05:44 Rev.: 4007

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:

dong.w.xie 2011-06-05 20:01 Rev.: 4006

TRUNK: update my tool

59 lines of code changed in 1 file:

msuchard 2011-06-05 14:13 Rev.: 4005

Added secret way to output all times for density estimation.

26 lines of code changed in 1 file:

msuchard 2011-06-04 11:48 Rev.: 4004

Some bug fixes in JumpHistoryAnalyser

32 lines of code changed in 1 file:

msuchard 2011-06-04 04:19 Rev.: 4003

Initial work on implementing hierarchical priors into BEAUti

554 lines of code changed in 5 files:

msuchard 2011-06-04 04:01 Rev.: 4002

Implemented ascertainment correction for continous, integrated diffusion models

370 lines of code changed in 7 files:

msuchard 2011-06-04 03:58 Rev.: 4001

Preliminary work on Markov modulated hidden class reporting

72 lines of code changed in 4 files:

dong.w.xie 2011-06-03 19:08 Rev.: 4000

Trunk: update my tool

1 lines of code changed in 1 file:

dong.w.xie 2011-06-03 11:06 Rev.: 3999

Trunk: fix another trick bug of BDSS

15 lines of code changed in 3 files:

rambaut 2011-06-03 01:40 Rev.: 3998

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:

rambaut 2011-06-02 23:12 Rev.: 3997

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:

dong.w.xie 2011-06-02 18:45 Rev.: 3996

Trunk: correct a bug

9 lines of code changed in 1 file:

dong.w.xie 2011-06-01 17:30 Rev.: 3995

Trunk: more updates for GetDateFromTree and LogAnalyser

134 lines of code changed in 4 files:

msuchard 2011-06-01 07:08 Rev.: 3994

Improved error checking in CompleteHistoryLogger

25 lines of code changed in 1 file:

May 2011 »

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