Directory src/dr/app/beagle/evomodel/utilities/

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msuchard 2012-12-21 11:28 Rev.: 5293

Standardizing output for markov jumps

5 lines of code changed in 2 files:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (new)

msuchard 2012-11-27 11:01 Rev.: 5258

Fix for complete history logging; this may break code elsewhere

8 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+8 -4)

rambaut 2012-11-15 14:45 Rev.: 5230

Updated copyright messages.

52 lines of code changed in 7 files:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+1 -1), DnDsLogger.java (+25), HistoryFilter.java (+1 -1), TreeTraitLogger.java (+25)

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.

92 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+92 -11)

msuchard 2012-05-15 20:51 Rev.: 4961

Starting work on a complete history filter

136 lines of code changed in 2 files:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+55 -8), HistoryFilter.java (+81)

philippe.lemey@gmail.com 2011-11-25 00:35 Rev.: 4486

adding the possibility to log syn and nonsyn conditional/unconditional counts to DnDsLogger

102 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: DnDsLogger.java (+102 -4)

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

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

3 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: DnDsLogger.java (+3 -3)

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:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+1 -1)

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

Extended complete histories for multiple sites

87 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+87 -52)

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

Improved error checking in CompleteHistoryLogger

25 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+25 -6)

msuchard 2011-05-31 06:47 Rev.: 3993

Playing with complete history logging; honeymoons are meant for bug-fixing

5 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+5 -4)

rambaut 2011-05-31 03:50 Rev.: 3992

Added a check that the CompleteHistoryLogger is not giving negative jump times (which it is currently).

4 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+4 -1)

msuchard 2011-04-27 15:50 Rev.: 3962

Added logging ability for complete substitution history under uniformization; there is a high likelihood that I broke some of the Markov jumps/reward mechanisms in this update.

90 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: CompleteHistoryLogger.java (+90)

msuchard 2011-04-09 08:55 Rev.: 3928

Fixed numerical instability in empirical Bayes smoother for a Poisson-Gamma model

4 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: DnDsLogger.java (+4 -2)

philippe.lemey@gmail.com 2011-02-20 05:06 Rev.: 3812

tiny DnDsLog tweak

11 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: DnDsLogger.java (+11 -3)

msuchard 2010-07-14 20:56 Rev.: 3312

Mighty cool positive selection tools through simple nucleotide models.

8 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: DnDsLogger.java (+8 -3)

msuchard 2010-07-14 09:00 Rev.: 3309

Cleaning up dN/dS summary statistics and adding TreeTraits for flu backbone

100 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: DnDsLogger.java (+100)

msuchard 2010-06-17 10:45 Rev.: 3273

Critical fix: branch rates now print out in tree log under new TreeTrait framework. Also starting to remove duplicated code from classes needing to output different combinations of TreeTrait summaries

68 lines of code changed in 2 files:

• src/dr/app/beagle/evomodel/utilities: StratifiedTraitLogger.java (del), TreeTraitLogger.java (+68)

msuchard 2010-05-29 08:37 Rev.: 3197

Two goals acheived. (1) RobustCounting now provides per site counts to a log file and (2) example of using a helper class to log traits from a TraitProvider, will remove substantial duplicated code from CPRC and MJBTL

152 lines of code changed in 1 file:

• src/dr/app/beagle/evomodel/utilities: StratifiedTraitLogger.java (new 152)