| Directory | Changes | Lines of Code | Lines per Change |
|---|---|---|---|
| Totals | 24 (100.0%) | 3643 (100.0%) | 151.7 |
| examples/unrelease/ | 1 (4.2%) | 1880 (51.6%) | 1880.0 |
| src/dr/evomodel/tree/ | 4 (16.7%) | 742 (20.4%) | 185.5 |
| src/dr/evolution/ | 3 (12.5%) | 202 (5.5%) | 67.3 |
| src/dr/evomodelxml/tree/ | 4 (16.7%) | 200 (5.5%) | 50.0 |
| src/dr/evomodel/operators/ | 2 (8.3%) | 193 (5.3%) | 96.5 |
| src/dr/evoxml/ | 3 (12.5%) | 187 (5.1%) | 62.3 |
| src/dr/evomodel/treelikelihood/ | 4 (16.7%) | 128 (3.5%) | 32.0 |
| src/dr/evomodelxml/treelikelihood/ | 1 (4.2%) | 50 (1.4%) | 50.0 |
| src/dr/evomodelxml/operators/ | 1 (4.2%) | 48 (1.3%) | 48.0 |
| src/dr/app/beast/ | 1 (4.2%) | 13 (0.4%) | 13.0 |
Adding a very hackish and trivial example XML for using the metagenome HiddenLinkageModel.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.
1880 lines of code changed in 1 file:
Allow the use of a native general likelihood core. Change handling of TipPartialsModel change events so only affected nodes with TipPartialsModels get marked dirty -- saves lots of recompute.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.
16 lines of code changed in 1 file:
Several small changes to TreeLoggerParser that structure it in a way that allows subclasses to use much of its functionality without reimplementing or copying code.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.
33 lines of code changed in 1 file:
Warn the user when the native general likelihood core could not be loaded.
1 lines of code changed in 2 files:
Making a tiny change to TreeLogger API so that the tree can be manipulated by other classes. This gets used by the HiddenLinkageTreeLogger to avoid duplicating all the code in TreeLogger.
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Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.
10 lines of code changed in 1 file:
Adding some additional stray files that are part of the metagenome linkage model.
Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.
202 lines of code changed in 3 files:
Adding parsers for metagenome models.
Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is one part of commit phase 2.
13 lines of code changed in 1 file:
Adding a new model of hidden linkage among reads in a metagenomic dataset. The model and its application to metagenomic datasets is described in a manuscript in preparation by Aaron Darling and Jonathan Eisen. This is commit phase 1: adding new files. Phase 2 comes next, committing related changes to existing files.
1488 lines of code changed in 14 files: