June 2012 Commit Log

Number of Commits:
54
Number of Active Developers:
6
msuchard 2012-06-30 12:04 Rev.: 5059

Checking equations for Pybus et al. manuscript

70 lines of code changed in 2 files:

sibon.li 2012-06-29 12:29 Rev.: 5058

Deleted a non-essential tool that I wrote.

0 lines of code changed in 1 file:

fbielejec 2012-06-28 23:46 Rev.: 5057

working on bss UI

46 lines of code changed in 1 file:

fbielejec 2012-06-28 23:35 Rev.: 5056

working on bss UI

62 lines of code changed in 4 files:

tbcbedford@gmail.com 2012-06-28 23:10 Rev.: 5055

Moving from a gamma jump distribution to an exponential jump distribution.

With a gamma distribution of year-to-year jumps I was getting a linear trend (mean = 1, sd = 0.01), but I think this came from the initial conditions. I'm thinking this is overparameterized.

5 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-06-28 22:33 Rev.: 5054

Defaulting mergeColumns to "false".

2 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-06-28 21:36 Rev.: 5053

Fixed dropping of virus names when duplicate sera name exists.

There was a bug in which if there was a row with the same name as a column, this row name would not be added to the virusStrains list.

14 lines of code changed in 1 file:

fbielejec 2012-06-28 20:57 Rev.: 5052

ant buildfile for bss

158 lines of code changed in 1 file:

tbcbedford@gmail.com 2012-06-28 03:32 Rev.: 5051

Implementing a more flexible "jump" prior for antigenic locations.

Instead of the linear relationship of AG1 vs time, AntigenicJumpPrior gives a hierarchical prior for picking the
movement of each year from a gamma distribution. The parameters of this gamma distribution are estimated
from the data.

307 lines of code changed in 2 files:

rambaut 2012-06-27 09:32 Rev.: 5050

Fixed issue with trees with polytomies having bad branch lengths.

2 lines of code changed in 2 files:

rambaut 2012-06-27 09:21 Rev.: 5049

Fixed issue with trees with polytomies having bad branch lengths.

10 lines of code changed in 2 files:

fbielejec 2012-06-25 06:34 Rev.: 5048

working on bss UI

203 lines of code changed in 7 files:

fbielejec 2012-06-25 05:40 Rev.: 5047

test method for codon model

20 lines of code changed in 1 file:

fbielejec 2012-06-23 11:22 Rev.: 5046

working on Beagle Sequence Simulator UI

498 lines of code changed in 7 files:

fbielejec 2012-06-23 11:21 Rev.: 5045

working on bss UI

517 lines of code changed in 4 files:

fbielejec 2012-06-23 11:18 Rev.: 5044

fixed typo

1 lines of code changed in 1 file:

msuchard 2012-06-23 09:32 Rev.: 5043

Fixing inconsistency when reporting a filtered state-change history

56 lines of code changed in 3 files:

msuchard 2012-06-23 08:34 Rev.: 5042

Standardizing format for change events; these should always be an array of arrays because the number of events is variable.

105 lines of code changed in 4 files:

msuchard 2012-06-23 03:20 Rev.: 5041

Possible new string format for change events

38 lines of code changed in 1 file:

fbielejec 2012-06-21 21:27

working on bss UI

396 lines of code changed in 6 files:

fbielejec 2012-06-20 21:39 Rev.: 5038

working on bss UI

1039 lines of code changed in 11 files:

fbielejec 2012-06-16 02:36 Rev.: 5037

cleaning code

4 lines of code changed in 3 files:

fbielejec 2012-06-16 02:32 Rev.: 5036

syntax rules in parser

24 lines of code changed in 1 file:

fbielejec 2012-06-16 01:44 Rev.: 5035

print some logging messages

13 lines of code changed in 1 file:

fbielejec 2012-06-12 23:42 Rev.: 5034

cleaning code

31 lines of code changed in 2 files:

fbielejec 2012-06-12 23:40 Rev.: 5033

simulate homogenous sequences

43 lines of code changed in 4 files:

fbielejec 2012-06-11 23:39 Rev.: 5032

cleaning code

29 lines of code changed in 2 files:

fbielejec 2012-06-11 23:21 Rev.: 5031

safeguard from a null pointer exception if branch rate model is not specified

14 lines of code changed in 2 files:

fbielejec 2012-06-11 23:04 Rev.: 5030

throw meaningful xml parse exceptions

14 lines of code changed in 1 file:

fbielejec 2012-06-08 23:33 Rev.: 5029

branch rate issues

94 lines of code changed in 3 files:

baele.guy@gmail.com 2012-06-08 20:21 Rev.: 5028

Added ArithmeticMeanAnalysisParser to the list.

2 lines of code changed in 1 file:

baele.guy@gmail.com 2012-06-08 20:19 Rev.: 5027

Parser for the arithmetic mean estimator (AME).

133 lines of code changed in 1 file:

baele.guy@gmail.com 2012-06-08 20:19 Rev.: 5026

Added calculation of the arithmetic mean estimator (AME).

27 lines of code changed in 1 file:

baele.guy@gmail.com 2012-06-08 20:18 Rev.: 5025

Added the possibility to run a power posterior for a single fixed power.

34 lines of code changed in 1 file:

rambaut 2012-06-08 04:11 Rev.: 5023

Fixed an issue with *BEAST 'species' attributes being left outside the taxon elements.

5 lines of code changed in 1 file:

fbielejec 2012-06-08 00:53 Rev.: 5022

print warning from the parser

13 lines of code changed in 2 files:

fbielejec 2012-06-07 04:57 Rev.: 5021

code cleanup

48 lines of code changed in 2 files:

fbielejec 2012-06-07 03:38 Rev.: 5020

make debugging easier

175 lines of code changed in 3 files:

fbielejec 2012-06-07 02:35 Rev.: 5019

warn user he needs to supresses count statistics in case of codon models

6 lines of code changed in 1 file:

rambaut 2012-06-07 00:48 Rev.: 5018

Logging of complete histories to trees has a more consistent format (a set of nested arrays).


17 lines of code changed in 2 files:

fbielejec 2012-06-06 23:58 Rev.: 5017

working on bias introduced when including clock rates

23 lines of code changed in 1 file:

fbielejec 2012-06-06 21:57 Rev.: 5016

set this method to return alignment only works well with all the conversion tools

46 lines of code changed in 2 files:

rambaut 2012-06-06 21:39 Rev.: 5015

Improving complete history loggin format.

21 lines of code changed in 1 file:

rambaut 2012-06-06 21:07 Rev.: 5014

Changing the 'traitFilter' behaviour of TreeLoggerParser so it only matches prefixes (previously it used contains() so this made it difficult to filter).

1 lines of code changed in 1 file:

msuchard 2012-06-05 09:39 Rev.: 5013

ProductChainSubstitutionModel now propogates submodel changes

20 lines of code changed in 2 files:

msuchard 2012-06-05 09:09 Rev.: 5012

Fixing reporting of site- and branch-specific S and N counts

42 lines of code changed in 4 files:

fbielejec 2012-06-05 00:06 Rev.: 5011

clock rate was being set but not used

7 lines of code changed in 1 file:

fbielejec 2012-06-05 00:06 Rev.: 5010

Codon models give exception when put inside report and when count statistics are done on them, this quick fix supresses count statistics in case of codon models

4 lines of code changed in 1 file:

fbielejec 2012-06-04 22:08 Rev.: 5009

He who steps on others to reach the top has good balance

15 lines of code changed in 1 file:

fbielejec 2012-06-02 23:34 Rev.: 5008

codons need ancestral sequences too

18 lines of code changed in 1 file:

fbielejec 2012-06-02 22:35 Rev.: 5007

sanity check in parser

23 lines of code changed in 1 file:

fbielejec 2012-06-02 02:45 Rev.: 5006

main method to test codon seq simulation

85 lines of code changed in 1 file:

fbielejec 2012-06-01 22:29 Rev.: 5005

simulate under codon models

33 lines of code changed in 1 file:

msuchard 2012-06-01 03:47 Rev.: 5004

Reducing over-logging on underflows

1 lines of code changed in 1 file:

May 2012 »

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