Directory doc/

Total Files:
8
Deleted Files:
6
Lines of Code:
112

[root]/doc
        directory in repo BookSection (12 files, 6 lines)
        directory in repo EBSP (1 files, 0 lines)
            Folder removed from repo mystery-mammal (0 files, 0 lines)
            directory in repo mystery-run-1 (5 files, 0 lines)
            Folder removed from repo scripts (0 files, 0 lines)
        directory in repo PackageStructure (4 files, 125 lines)
        directory in repo StarBEAST (1 files, 0 lines)
            directory in repo figures (20 files, 0 lines)
        directory in repo Virus Practical Tex (0 files, 0 lines)
            directory in repo figures1 (14 files, 0 lines)
            directory in repo figures2 (7 files, 0 lines)
            directory in repo figures3 (4 files, 0 lines)
        directory in repo tutorial (0 files, 0 lines)
            directory in repo BSP (7 files, 6877 lines)
                directory in repo figures3 (10 files, 0 lines)
            directory in repo DivergenceDating (1 files, 24 lines)
                directory in repo 1.1a_Primates (2 files, 423 lines)
                    directory in repo latex (1 files, 585 lines)
                        directory in repo figures (19 files, 0 lines)
                directory in repo 1.2_Primates (4 files, 3 lines)
                    directory in repo latex (2 files, -2 lines)
                        directory in repo figures (19 files, -825 lines)
            directory in repo EBSP (0 files, 0 lines)
                directory in repo flu (2 files, 512 lines)
                    directory in repo figures (14 files, 814 lines)
            directory in repo StarBEAST (3 files, 1477 lines)
                directory in repo figures (11 files, 0 lines)
            Folder removed from repo Virus Practical Tex (0 files, 0 lines)
                Folder removed from repo figures3 (0 files, 0 lines)
            directory in repo Virus_Practical_1_6_1 (2 files, 1007 lines)
                directory in repo figures1 (17 files, 0 lines)
                directory in repo figures2 (9 files, 0 lines)
                directory in repo figures3 (9 files, 0 lines)

Lines of Code

doc/ Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 53 (100.0%) 16271 (100.0%) 307.0
alexei.drummond 40 (75.5%) 15648 (96.2%) 391.2
rambaut 9 (17.0%) 623 (3.8%) 69.2
dong.w.xie 4 (7.5%) 0 (0.0%) 0.0

Most Recent Commits

dong.w.xie 2010-11-16 14:19 Rev.: 3724

Trunk: update New Tracer doc, because key word "category" is changed into "categorical".

0 lines of code changed in 2 files:

  • doc: New Tracer.docx (changed)
dong.w.xie 2010-06-11 18:47 Rev.: 3251

TRUNK: new tracer dev: user guide.

0 lines of code changed in 1 file:

  • doc: New Tracer.docx (changed)
dong.w.xie 2010-03-17 14:11 Rev.: 3049

TRUNK: update package structure by adding tracer dependency.

0 lines of code changed in 1 file:

  • doc: PackageStructure.pdf (del)
alexei.drummond 2009-07-17 02:02 Rev.: 1864

Added a diagram outlining the *intended* top-level package structure dependencies. They are not quite realized yet -- and I don't say anything about the *intended* dependency structure within some of the large package namespaces like dr.evolution.* and dr.inference.*

0 lines of code changed in 1 file:

  • doc: PackageStructure.pdf (new)
alexei.drummond 2007-07-22 18:30 Rev.: 418

1 lines of code changed in 2 files:

  • doc: SerialSampleCoalescent.tex (new)
alexei.drummond 2007-07-12 22:51 Rev.: 396

1 lines of code changed in 3 files:

  • doc: SerialSampleCoalescent.pdf (new), SerialSampleCoalescent.tex (+1 -1)
alexei.drummond 2007-07-12 22:32 Rev.: 395

Why the coalescent likelihood we currently have is right :-) (of course!)

118 lines of code changed in 2 files:

  • doc: SerialSampleCoalescent.pdf (changed), SerialSampleCoalescent.tex (+118)
alexei.drummond 2007-07-09 17:49 Rev.: 375

Split TreeModel XML parser into separate class because TreeModel is a monolithic class. Fixed a labeling problem introduced into CoalescentLikelihood. However the CoalescentLikelihood now returns weird probabilities after jheled's last commit -- so this still needs looking into.

1 lines of code changed in 2 files:

  • doc: BEAST14.tex (new)
rambaut 2007-07-07 01:47 Rev.: 362

Moved BookSection into a folder with all its figures

0 lines of code changed in 5 files:

  • doc: BookSection.tex (del), Figure_Beauti1.png (del), Figure_GuessDates.png (del), Figure_Model.png (del), fig01.pdf (del)
rambaut 2007-07-07 01:43 Rev.: 361

Updated BookSection again

244 lines of code changed in 1 file:

  • doc: BookSection.tex (new 244)
rambaut 2007-07-06 19:57 Rev.: 359

Updated book chapter

88 lines of code changed in 1 file:

  • doc: BookSection.tex (+88 -244)
alexei.drummond 2007-07-03 00:09 Rev.: 351

fixed url for Tracer, title and acknowledgements

5 lines of code changed in 3 files:

  • doc: BEAST.bib (new), BEAST14.tex (+4 -7)
alexei.drummond 2007-07-02 18:26 Rev.: 350

and bib file...

9751 lines of code changed in 1 file:

  • doc: BEAST.bib (+9751)
alexei.drummond 2007-07-02 18:25 Rev.: 349

final draft of manuscript?

30 lines of code changed in 1 file:

  • doc: BEAST14.tex (+30 -158)
alexei.drummond 2007-07-02 11:58 Rev.: 346

Updated manuscript and manual and cleaned up a bit of lint...

1910 lines of code changed in 4 files:

  • doc: BEAST14.tex (+135 -142), BEAST14_Manual.tex (+13 -3), fig01.pdf (new 1762)
alexei.drummond 2007-06-28 11:31 Rev.: 332

adding example analysis and figure

26 lines of code changed in 1 file:

  • doc: BEAST14.tex (+26 -1)
alexei.drummond 2007-06-24 21:54 Rev.: 302

Okay, I have read through the text and the BEAST paper is definitely ready! Just needs a figure which I will work on right now!

92 lines of code changed in 1 file:

  • doc: BEAST14.tex (+92 -18)
alexei.drummond 2007-06-24 19:21 Rev.: 300

Integration of Random Local Clock model into BEAUTi, plus a few improvements to TreeModel, SpeciationLikelihood and related classes

1 lines of code changed in 1 file:

  • doc: BookSection.tex (+1 -1)
rambaut 2007-06-21 21:11 Rev.: 298

Made a start on using tracer.

61 lines of code changed in 1 file:

  • doc: BookSection.tex (+61 -3)
alexei.drummond 2007-05-22 21:43 Rev.: 275

Added a little document describing why I think equation (3) in Nee is the right one...

104 lines of code changed in 2 files:

  • doc: Yule.pdf (new), Yule.tex (new 104)
alexei.drummond 2007-04-24 12:32 Rev.: 240

Added section on running BEAST from the command line

39 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+39)
alexei.drummond 2007-04-23 12:39 Rev.: 238

Removed references to example XMLs until we actually have them!

13 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+13 -11)
alexei.drummond 2007-04-19 12:21 Rev.: 237

Increased the depth of the table of contents to engineer 42 pages. The manual is now in its first final draft.

1 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+1 -1)
alexei.drummond 2007-04-19 12:08 Rev.: 236

Added a table of comments, dealt with Simon's other comments. Fixed up the TreeAnnotator section. General edits.

133 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+133 -97)
alexei.drummond 2007-04-19 10:46 Rev.: 235

Simon's edits

142 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+142 -127)
alexei.drummond 2007-04-18 18:34 Rev.: 229

Nic's edits debugged...

1 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+1 -1)
alexei.drummond 2007-04-18 18:32 Rev.: 228

Nic's edits

123 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+123 -96)
alexei.drummond 2007-04-14 14:00 Rev.: 224

Reformatted BEAST14_Manual.tex to have hard wraps. This will allow edits to be smaller, since SVN manages edits on a line-by-line basis.

733 lines of code changed in 2 files:

  • doc: BEAST14.tex (+2 -2), BEAST14_Manual.tex (+731 -155)
alexei.drummond 2007-04-13 13:15 Rev.: 223

Answered some of Andrew's questions and fixed on error (should use \textit{} instead of \mathit{} when not in math mode ($ $)

10 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+10 -15)
rambaut 2007-04-13 12:57 Rev.: 222

added link to jebl library in ant build file

230 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+230 -215)
alexei.drummond 2007-04-12 23:08 Rev.: 221

The first draft of a manual for BEAST -- please take a moment to read it and tell me what you think. On Mac OS X a good LaTeX editor is TeXShop 2.1

1070 lines of code changed in 1 file:

  • doc: BEAST14_Manual.tex (+1070)
alexei.drummond 2007-02-07 16:30 Rev.: 202

A work in progress -- this book section is for the new edition of "The Phylogenetic Handbook". It should make for the start of a very nice manual when it is finished as well.

707 lines of code changed in 4 files:

  • doc: BookSection.tex (+707), Figure_Beauti1.png (new), Figure_GuessDates.png (new), Figure_Model.png (new)
alexei.drummond 2007-01-30 13:17 Rev.: 182

added BEAST paper in LaTeX format...

636 lines of code changed in 1 file:

  • doc: BEAST14.tex (+636)
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