Directory src/dr/stats/

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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.

3 lines of code changed in 4 files:

• src/dr/stats: Regression.java (new), Variate.java (new)

dong.w.xie 2011-02-17 15:31 Rev.: 3805

Trunk new Trace: 1) Try to replace Double[] as List<Double>, which save some memory, but it still crashes after loading a big log; 2) use traceType to detemine type, instead of prime type (T) of List<T> in Trace, and integer is stored as List<Double> currently for simlple solution of plotting.

7 lines of code changed in 1 file:

• src/dr/stats: Variate.java (+7)

dong.w.xie 2011-02-15 09:08 Rev.: 3796

Trunk: big change of new Tracer, and this check-in starts using List instead array in Variate.

103 lines of code changed in 2 files:

• src/dr/stats: Regression.java (+7 -7), Variate.java (+96 -211)

rambaut 2010-10-10 20:55 Rev.: 3623

Experimenting with Path-O-Gen

10 lines of code changed in 1 file:

• src/dr/stats: Regression.java (+10)

rambaut 2010-05-11 01:49 Rev.: 3165

Fixed an issue with root optimization for some trees in PathOGen.

6 lines of code changed in 1 file:

• src/dr/stats: Regression.java (+6 -1)

msuchard 2010-03-08 08:16 Rev.: 3031

Added mean square error estimator to traceAnalysis; could build this feature into Tracer for users doing simulations

22 lines of code changed in 2 files:

• src/dr/stats: DiscreteStatistics.java (+22)

rambaut 2009-11-29 08:53 Rev.: 2625

New version of Path-O-Gen v1.2 released.

10 lines of code changed in 1 file:

• src/dr/stats: Regression.java (+10)

jheled 2009-10-09 08:28 Rev.: 2369

code police and spelling

1 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+1 -1)

jheled 2009-09-07 08:15 Rev.: 2205

code police

8 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+8 -13)

alexei.drummond 2009-07-13 23:44 Rev.: 1848

Refactoring tidy up. Reducing interdependencies between top-level packages. Will upload dependency guidelines to wiki soon.

438 lines of code changed in 2 files:

• src/dr/stats: Regression.java (+19 -21), Variate.java (+419)

rambaut 2009-02-14 07:26 Rev.: 1434

Pathogen improvements

1 lines of code changed in 1 file:

• src/dr/stats: Regression.java (+1 -1)

rambaut 2009-02-14 04:37 Rev.: 1433

Pathogen work.

4 lines of code changed in 1 file:

• src/dr/stats: Regression.java (+4 -1)

rambaut 2008-08-15 11:08 Rev.: 1133

Started work on a TreesPanel. Moved tree prior stuff here. Allow selection of user tree (from those loaded). Other features to be added soon is the ability to do a root to tip plot to check temporal signal. Other tweaks and fixes.

174 lines of code changed in 1 file:

• src/dr/stats: Regression.java (+174 -166)

rambaut 2008-08-08 04:14 Rev.: 1097

Some fixes to Tracer: checked reading scientific format. Cleaned up the formating of numbers in the tables and in the plots. Added a yellow colour for 100<ESS<200. Fixed an issue about NaN in trace files - possibly not required.

27 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+27 -15)

alexei.drummond 2008-04-10 21:14 Rev.: 809

added geometric mean summary statistic to tracer for traces with all values positive. Should be better point estimate for scale parameters.

205 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+205 -226)

jheled 2008-01-15 10:30 Rev.: 661

comment addition

1 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+1)

rambaut 2008-01-05 03:18 Rev.: 651

Tracer tweaks

1 lines of code changed in 1 file:

• src/dr/stats: DiscreteStatistics.java (+1 -1)

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:

• src/dr/stats: DiscreteStatistics.java (+58 -19)