November 2007 Commit Log

Number of Commits:
41
Number of Active Developers:
4
msuchard 2007-11-30 06:52 Rev.: 628

There's a bug in the Apache code to calculate Poisson masses. For large integer realizations, 0 gets returned as the probability. Not a good approximation when one is working on the log scale. I hacked in my own logProbability calculator using Alexei's logGamma function.

7 lines of code changed in 1 file:

msuchard 2007-11-29 12:30 Rev.: 627

Started an InhibitionAssayLikelihood class for combining inhibition assay data with phylogenetic reconstruction

711 lines of code changed in 3 files:

msuchard 2007-11-29 05:58 Rev.: 626

Fixed some bugs in DensityPlotter/DensityMap. Added ability of DensityMap to output TIFF graphic slices (for 3D volume rendering in ImageJ). Modifed MultivariateDiffusionModel so that it attributes logged trees with its precision matrix. Matrix will be used by DensityMap to generate processes realizations at arbitrary times. Refactored TreeAttributeProvided into dr.evolution.tree to match Node/BranchAttributeProvider

557 lines of code changed in 6 files:

Michael.DefoinPLatel 2007-11-26 07:10 Rev.: 625

Two missing files added.

0 lines of code changed in 2 files:

rambaut 2007-11-24 09:02 Rev.: 624

Added ability to do 2D 'slices' through time to DensityPlotter.

229 lines of code changed in 2 files:

rambaut 2007-11-23 12:15 Rev.: 623

Created a new standalone application to create density maps from trees (dr.app.tools.DensityPlotter). Moved the code to do this from TreeAnnotator.

356 lines of code changed in 3 files:

Michael.DefoinPLatel 2007-11-23 08:55 Rev.: 622

Numerous changes to BEAUti including: binary data import, binary substitution models (simple and covarion), {estimated, empirical, equal} base frequencies, truncated normal prior, checkbox to optionally remove some operators, all statistics now saved in templates.

946 lines of code changed in 13 files:

rambaut 2007-11-22 05:56 Rev.: 621

Add a few more test files and fixed tree annotator to summarize boolean traits (i.e., 'true', 'false' - treated the same as 1, 0).

877 lines of code changed in 4 files:

rambaut 2007-11-22 04:48 Rev.: 620

Made some efficiency savings when using trait parameters in trees. Previously, these were causing recalculations of the treelikelihood even if this was not necessary. Now an optional (default false) attribute 'fireTreeEvents' controls this behaviour.

896 lines of code changed in 8 files:

jheled 2007-11-21 16:59 Rev.: 619

don't accept bad (0) value as a seed (issue 39)

4 lines of code changed in 1 file:

rambaut 2007-11-20 21:57 Rev.: 618

Fixed up some generification of TreeStatData.

20 lines of code changed in 1 file:

rambaut 2007-11-20 05:10 Rev.: 617

Version number update

1 lines of code changed in 1 file:

jheled 2007-11-18 19:43 Rev.: 616

generify, get rid of warnings

42 lines of code changed in 1 file:

jheled 2007-11-18 19:42 Rev.: 615

cosmetics

5 lines of code changed in 1 file:

jheled 2007-11-18 19:40 Rev.: 614

generify

12 lines of code changed in 1 file:

jheled 2007-11-18 19:40 Rev.: 613

code police

5 lines of code changed in 1 file:

jheled 2007-11-18 19:39 Rev.: 612

replace loop with array copy

3 lines of code changed in 1 file:

jheled 2007-11-18 19:36 Rev.: 611

simplify code

63 lines of code changed in 1 file:

jheled 2007-11-18 19:34 Rev.: 610

Make rule string accuratly reflect min/max number of elements

9 lines of code changed in 1 file:

jheled 2007-11-18 19:32 Rev.: 609

make offset an optional attribute

3 lines of code changed in 1 file:

jheled 2007-11-18 19:30 Rev.: 608

change logic to allow a local file when name starts with './'

46 lines of code changed in 1 file:

jheled 2007-11-18 19:28

generify (java 1.5)

14 lines of code changed in 2 files:

jheled 2007-11-18 19:26 Rev.: 605

java 1.5

1 lines of code changed in 1 file:

jheled 2007-11-18 19:24 Rev.: 604

comment

1 lines of code changed in 1 file:

jheled 2007-11-18 19:23 Rev.: 603

generify

19 lines of code changed in 1 file:

jheled 2007-11-18 19:14 Rev.: 602

get rid of unused argument, generify

4 lines of code changed in 2 files:

jheled 2007-11-18 19:13 Rev.: 601

add comments

45 lines of code changed in 1 file:

jheled 2007-11-18 19:12 Rev.: 600

add a comment

2 lines of code changed in 1 file:

jheled 2007-11-18 18:55 Rev.: 599

use java 5 iterators

11 lines of code changed in 1 file:

jheled 2007-11-18 18:53 Rev.: 598

move HPDInterval here. Create a median(values,indices) version (same as for other statistics in this file)

58 lines of code changed in 1 file:

jheled 2007-11-18 18:49 Rev.: 597

cosmwtic

6 lines of code changed in 1 file:

jheled 2007-11-18 18:46 Rev.: 596

Add comments

15 lines of code changed in 1 file:

jheled 2007-11-18 18:45 Rev.: 595

Reduce number of mathematical operations

36 lines of code changed in 1 file:

jheled 2007-11-18 18:41 Rev.: 594

cosmetic, intellig warning

7 lines of code changed in 1 file:

jheled 2007-11-18 18:39 Rev.: 593

cosmetic

211 lines of code changed in 1 file:

rambaut 2007-11-17 12:07 Rev.: 592

Moved some evolution specific operators from dr.inference.operators to dr.evomodel.operators (all Marc's I think).

0 lines of code changed in 6 files:

rambaut 2007-11-15 12:35 Rev.: 591

Moved some evolution specific operators from dr.inference.operators to dr.evomodel.operators (all Marc's I think).

9 lines of code changed in 2 files:

rambaut 2007-11-15 12:27 Rev.: 590

Moved some evolution specific operators from dr.inference.operators to dr.evomodel.operators (all Marc's I think).

1111 lines of code changed in 5 files:

msuchard 2007-11-13 06:39 Rev.: 584

Rescaling continuous diffusion model so that variance is in terms of the tree height. Fixed *critical* bug in multivariate normal density.

1079 lines of code changed in 10 files:

msuchard 2007-11-12 13:28 Rev.: 583

Started a MultivariateGammaDistribution for specifying pairwise distance-based rates for the discrete CTMC diffusion models.

344 lines of code changed in 7 files:

jheled 2007-11-08 09:06 Rev.: 582

HKY matrix exp test

129 lines of code changed in 1 file:

October 2007 »

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