| 5f267bc | Trevor Bedford | 01 August 2009, 18:31:22 UTC | Full read of parameters file completed. | 01 August 2009, 18:31:22 UTC |
| 0a3ae8b | Trevor Bedford | 01 August 2009, 17:53:18 UTC | Restricting scope of parameters. Public members of Parameters class. | 01 August 2009, 17:53:18 UTC |
| a0e158e | Trevor Bedford | 01 August 2009, 17:38:37 UTC | First attempt at Parameter class. | 01 August 2009, 17:38:37 UTC |
| fc11e8e | Trevor Bedford | 31 July 2009, 21:21:03 UTC | Minor cleanup. | 31 July 2009, 21:21:03 UTC |
| 31ff44f | Trevor Bedford | 31 July 2009, 16:03:46 UTC | Progess on IO class. | 31 July 2009, 16:03:46 UTC |
| d18b31d | Trevor Bedford | 30 July 2009, 20:36:55 UTC | Skeleton of IO class. This will handle treefile import and file output of trees and statistics. | 30 July 2009, 20:36:55 UTC |
| d3f4dc0 | Trevor Bedford | 30 July 2009, 20:07:22 UTC | Incorporating multiple trees into main. | 30 July 2009, 20:07:22 UTC |
| d8afc04 | Trevor Bedford | 30 July 2009, 18:26:14 UTC | Extending tree input file. | 30 July 2009, 18:26:14 UTC |
| 94a7e87 | Trevor Bedford | 30 July 2009, 17:29:54 UTC | Basic functions in place for Series. Removed deprecated classes Measurement and Skyline. | 30 July 2009, 17:29:54 UTC |
| d8dbbb3 | Trevor Bedford | 29 July 2009, 20:03:02 UTC | Major cleanup of includes. Purposing avoiding namespace std. Helps me identify which functions I'm using and hence which library files I need to include. | 29 July 2009, 20:03:02 UTC |
| eb3c4d7 | Trevor Bedford | 29 July 2009, 19:42:16 UTC | Getting things into more of a proper configuration. Having makefile will reduce compile times. | 29 July 2009, 19:42:16 UTC |
| cf578d3 | Trevor Bedford | 29 July 2009, 18:39:56 UTC | section now works with all statistics. | 29 July 2009, 18:39:56 UTC |
| f522f9f | Trevor Bedford | 29 July 2009, 17:04:31 UTC | Added ignore bool to Node. trimEnds now marks root nodes as ignored. Also, fixed branch lengths with trimEnds. Need to update statistics to deal with ignore. | 29 July 2009, 17:04:31 UTC |
| d056b18 | Trevor Bedford | 28 July 2009, 23:50:17 UTC | Section function mostly working. Just need to ignore migration events and coalescent events at the window starts. (This is a problem for trimEnds as well) | 28 July 2009, 23:50:17 UTC |
| 2a1fa88 | Trevor Bedford | 28 July 2009, 23:01:33 UTC | Continuing with section function. Also, root no longer needs to be 0. | 28 July 2009, 23:01:33 UTC |
| dcb5616 | Trevor Bedford | 28 July 2009, 21:16:37 UTC | Started into the section function. This should eventually make it much easier to deal with seasonality. | 28 July 2009, 21:16:37 UTC |
| b313051 | Trevor Bedford | 28 July 2009, 20:46:07 UTC | Significant trimming. Got rid of ctree and all its associated structures. | 28 July 2009, 20:46:07 UTC |
| 2f96d1b | Trevor Bedford | 28 July 2009, 20:04:25 UTC | Implemented getDiversity and getTajimaD | 28 July 2009, 20:04:25 UTC |
| b5d0a07 | Trevor Bedford | 28 July 2009, 18:01:45 UTC | Minor cleanup. | 28 July 2009, 18:01:45 UTC |
| cd47f59 | Trevor Bedford | 28 July 2009, 16:00:34 UTC | Modified padTree() + general cleanup. | 28 July 2009, 16:00:34 UTC |
| 64736dd | Trevor Bedford | 28 July 2009, 01:31:47 UTC | Basic migration statistics. | 28 July 2009, 01:31:47 UTC |
| bc05442 | Trevor Bedford | 28 July 2009, 00:24:37 UTC | Renamed coaltree to ctree | 28 July 2009, 00:24:37 UTC |
| e2702e2 | Trevor Bedford | 27 July 2009, 23:08:57 UTC | Coalescent rate estimation included. | 27 July 2009, 23:08:57 UTC |
| 303898e | Trevor Bedford | 27 July 2009, 06:13:49 UTC | Streamlined constructor. printRuleList, pruneToTrunk and pruneToLabel working. | 27 July 2009, 06:13:49 UTC |
| 20fc488 | Trevor Bedford | 27 July 2009, 02:32:58 UTC | Migration events. | 27 July 2009, 02:32:58 UTC |
| f1cac0d | Trevor Bedford | 27 July 2009, 00:58:01 UTC | Transitioning constructor to use nodetree. Almost finished. Just need to do migration events. Removed ctree functionality. | 27 July 2009, 00:58:01 UTC |
| 4888807 | Trevor Bedford | 26 July 2009, 19:17:53 UTC | Minor cleanup | 26 July 2009, 19:17:53 UTC |
| 8bd9e48 | Trevor Bedford | 25 July 2009, 18:28:58 UTC | More cleanup to the gather tips section of coal tree constructor | 25 July 2009, 18:28:58 UTC |
| 263eaca | Trevor Bedford | 24 July 2009, 22:26:40 UTC | Pushed coal_tree function to convert names to digits in the initial paren string. | 24 July 2009, 22:26:40 UTC |
| 124f64e | Trevor Bedford | 24 July 2009, 21:08:43 UTC | Stripped out checks, one set of code for migration events and no migration events | 24 July 2009, 21:08:43 UTC |
| a3a4eaf | Trevor Bedford | 24 July 2009, 20:10:43 UTC | Set functions for Node. | 24 July 2009, 20:10:43 UTC |
| a27f0cf | Trevor Bedford | 24 July 2009, 19:35:51 UTC | Data structures and get functions for Node class. | 24 July 2009, 19:35:51 UTC |
| 8f97889 | Trevor Bedford | 24 July 2009, 19:11:27 UTC | Trying something new. Making new node class that stores relevant node-specific parameters. Should be easier than dealing with the plethora of maps (eventually) | 24 July 2009, 19:11:27 UTC |
| 950758d | Trevor Bedford | 24 July 2009, 19:05:45 UTC | Minor changes. | 24 July 2009, 19:05:45 UTC |
| 3249c2d | Trevor Bedford | 24 July 2009, 16:57:17 UTC | Changed Statistic object to be called Measurement. Also, added the skeleton of Series object. | 24 July 2009, 16:57:17 UTC |
| 13ff4e9 | Trevor Bedford | 24 July 2009, 07:57:17 UTC | Further cleanup. | 24 July 2009, 07:57:17 UTC |
| 7d235e9 | Trevor Bedford | 24 July 2009, 07:16:46 UTC | Added cleanup function to CoalTree | 24 July 2009, 07:16:46 UTC |
| cc1947b | Trevor Bedford | 24 July 2009, 05:54:48 UTC | Improvements to stat and to labelPro | 24 July 2009, 05:54:48 UTC |
| 070f890 | Trevor Bedford | 24 July 2009, 02:38:49 UTC | Basic functions for Statistics class established. | 24 July 2009, 02:38:49 UTC |
| 65fcab1 | Trevor Bedford | 24 July 2009, 01:43:22 UTC | Skeleton of Statistic class. | 24 July 2009, 01:43:22 UTC |
| b597f91 | Trevor Bedford | 24 July 2009, 01:39:36 UTC | More cleanup. | 24 July 2009, 01:39:36 UTC |
| 631be5b | Trevor Bedford | 23 July 2009, 20:30:32 UTC | Modifying functions to deal with forward time. Fixed pruneTrunk, pruneLabel and trimEnds. | 23 July 2009, 20:30:32 UTC |
| f261da4 | Trevor Bedford | 22 July 2009, 19:37:12 UTC | Stripped out paddedTree. May have missed some necessary changes. | 22 July 2009, 19:37:12 UTC |
| 34b7af1 | Trevor Bedford | 22 July 2009, 19:24:09 UTC | Time runs forward. Hasn't been checked against all functions. | 22 July 2009, 19:24:09 UTC |
| 0589367 | Trevor Bedford | 16 July 2009, 18:36:57 UTC | Added the function printTrunkRate() | 16 July 2009, 18:36:57 UTC |
| 45fd523 | Trevor Bedford | 10 July 2009, 22:11:59 UTC | Added pushTimesBack to adjust all coalescent dates | 10 July 2009, 22:11:59 UTC |
| da4eda4 | Trevor Bedford | 10 July 2009, 21:24:05 UTC | Delete. | 10 July 2009, 21:24:05 UTC |
| 3eb909e | Trevor Bedford | 10 July 2009, 21:20:19 UTC | Initial commit. | 10 July 2009, 21:20:19 UTC |
