| 8ac38b4 | Trevor Bedford | 06 August 2015, 22:12:27 UTC | Update to print any-to-any migration rates in mig skyline. | 06 August 2015, 22:12:27 UTC |
| df1644c | Trevor Bedford | 12 May 2015, 05:25:19 UTC | Update with accumulate and other additions. | 12 May 2015, 05:25:19 UTC |
| 924a124 | Trevor Bedford | 22 April 2014, 18:37:17 UTC | Update gitignore. | 22 April 2014, 18:37:17 UTC |
| 42123ad | Trevor Bedford | 22 April 2014, 02:50:27 UTC | Fix string import. | 22 April 2014, 02:50:27 UTC |
| ab20f93 | Trevor Bedford | 22 April 2014, 01:07:13 UTC | Fix remove tips. | 22 April 2014, 01:07:13 UTC |
| 61f53a1 | Trevor Bedford | 22 April 2014, 00:26:36 UTC | Include option to remove tips. | 22 April 2014, 00:26:36 UTC |
| 6d5fc6d | Trevor Bedford | 12 February 2014, 19:06:47 UTC | Remove "peel back" when pruning to trunk. | 12 February 2014, 19:06:47 UTC |
| 7cff89b | Trevor Bedford | 16 December 2013, 19:30:11 UTC | Include link in readme. | 16 December 2013, 19:30:11 UTC |
| 49b86c0 | Trevor Bedford | 21 November 2013, 22:25:04 UTC | Include prune to tips function. @metasoarous: this should be it. Include something like: prune to tips 0EU514626 0EU856858 0EU514624 5AB281205 0EU857041 Due to a stupid bit of parsing on my part (when originally written I had imagined only numbers following the initial command string), tip names must begin with either capital letters or numbers. | 21 November 2013, 22:25:04 UTC |
| a09d33b | Trevor Bedford | 22 October 2013, 00:37:51 UTC | Include example. | 22 October 2013, 00:37:51 UTC |
| d09b9b3 | Trevor Bedford | 20 October 2013, 01:39:38 UTC | Update readme. | 20 October 2013, 01:40:57 UTC |
| 8f9650a | Trevor Bedford | 24 September 2013, 02:25:07 UTC | Merge pull request #4 from metasoarous/patch-1 Fix for compile errors (issue #3) | 24 September 2013, 02:25:07 UTC |
| 085e6da | Christopher Small | 24 September 2013, 01:52:42 UTC | Fix for compile errors (issue #3) | 24 September 2013, 01:52:42 UTC |
| 065f2e3 | Trevor Bedford | 24 April 2013, 16:34:58 UTC | Include from deme and to deme in proportion skylines. | 24 April 2013, 16:34:58 UTC |
| 5cf46ff | Trevor Bedford | 24 April 2013, 12:34:38 UTC | Include skyline for "pro history from tips". | 24 April 2013, 12:34:38 UTC |
| fc97255 | Trevor Bedford | 15 April 2013, 22:41:32 UTC | Include root proportion summary statistic. | 15 April 2013, 22:41:32 UTC |
| 99b6800 | Trevor Bedford | 26 March 2013, 14:00:10 UTC | Added function 'pad migration events' that adds extra nodes in the tree demarking migration events. | 26 March 2013, 14:00:10 UTC |
| 5e1caa1 | Trevor Bedford | 24 March 2013, 11:08:24 UTC | Include persistence summary. | 24 March 2013, 11:08:24 UTC |
| 56ea550 | Trevor Bedford | 24 March 2013, 10:35:24 UTC | Include 'latitude' in locs parsing. | 24 March 2013, 10:35:24 UTC |
| b486e87 | Trevor Bedford | 05 February 2013, 10:18:46 UTC | Implement unrooted (circular) tree printing using equal-angle algorithm. | 05 February 2013, 10:21:14 UTC |
| 2ab1c43 | Trevor Bedford | 31 January 2013, 18:22:41 UTC | Prep for unrooted tree drawing. Include xCoord and yCoord in node. | 31 January 2013, 18:22:41 UTC |
| 6f434c0 | Trevor Bedford | 31 January 2013, 17:38:18 UTC | Implement skyline for difference in X location between trunk and population mean. | 31 January 2013, 17:38:18 UTC |
| a093a4e | Trevor Bedford | 22 January 2013, 17:10:14 UTC | Refix of diffusion coefficients. Coefficient is total squared distance / total time. | 22 January 2013, 17:10:14 UTC |
| c7a9ad1 | Trevor Bedford | 22 January 2013, 16:51:17 UTC | Fix calculation of diffusion coefficient. | 22 January 2013, 16:51:17 UTC |
| b1f8000 | Trevor Bedford | 22 January 2013, 15:58:50 UTC | Revisions to calculation of 1D drift rate and 2D diffusion coefficient. | 22 January 2013, 15:58:50 UTC |
| 05036d8 | Trevor Bedford | 19 December 2012, 18:19:03 UTC | Include xdrift skyline. | 19 December 2012, 18:19:03 UTC |
| 12d4143 | Trevor Bedford | 19 December 2012, 18:09:30 UTC | Include skyline drift rate from tips. | 19 December 2012, 18:09:30 UTC |
| 3b49f31 | Trevor Bedford | 30 October 2012, 17:38:19 UTC | Update copyright info. | 30 October 2012, 17:38:19 UTC |
| 30e0e68 | Trevor Bedford | 30 October 2012, 17:35:24 UTC | Include .gitignore. | 30 October 2012, 17:35:24 UTC |
| bc6fc03 | Trevor Bedford | 16 October 2012, 15:40:04 UTC | Implement diffusion coefficient and drift rate calculcations. Also, output pairwise diversity to out.pairs. | 16 October 2012, 15:40:04 UTC |
| 95ce786 | Trevor Bedford | 11 October 2012, 13:28:23 UTC | Minor changes. | 11 October 2012, 13:28:23 UTC |
| c142ae8 | Trevor Bedford | 23 November 2011, 15:55:22 UTC | Fixed typo. | 23 November 2011, 15:55:22 UTC |
| bead5a4 | Trevor Bedford | 23 November 2011, 15:42:16 UTC | For real this time. | 23 November 2011, 15:42:16 UTC |
| 0ee5cfd | Trevor Bedford | 23 November 2011, 15:41:13 UTC | Moving README into MarkDown format. | 23 November 2011, 15:41:13 UTC |
| 9e1ecd2 | Trevor Bedford | 22 November 2011, 18:15:05 UTC | Update to README. | 22 November 2011, 18:15:05 UTC |
| 6e9349b | Trevor Bedford | 22 November 2011, 17:12:54 UTC | Adding README and other extraneous files to Git repository. Also, fixed a bug with the sorting of nodes for tree drawing. I was surprised to discover that PACT can handle polytomies in the NEWICK trees without a problem. | 22 November 2011, 17:12:54 UTC |
| befb419 | Trevor Bedford | 10 January 2011, 19:07:09 UTC | Moved "x loc history" parameters to param file. | 10 January 2011, 19:07:09 UTC |
| 9a09eea | Trevor Bedford | 10 January 2011, 18:52:33 UTC | Implemented "add tail", which adds an additional node at the root of the tree. Useful for diffusion visualization. | 10 January 2011, 18:52:33 UTC |
| cf56f00 | Trevor Bedford | 09 January 2011, 18:36:42 UTC | Implemented "print all trees", requires trees/ directory. Added parsing for "layout". | 09 January 2011, 18:36:42 UTC |
| 91c34ea | Trevor Bedford | 08 January 2011, 23:08:38 UTC | Implemented code for ordering tips. Parameters can now take a "ordering" option that lists tip names. If this is supplied then print rule tree will print tips in this order rather than sorting the tree. | 08 January 2011, 23:08:38 UTC |
| 9abe581 | Trevor Bedford | 06 December 2010, 21:46:36 UTC | Assigning a location based on geographic state to the trait y-axis. | 06 December 2010, 21:46:36 UTC |
| 8a19c01 | Trevor Bedford | 28 October 2010, 19:04:13 UTC | Tracing x loc history for tips implemented. Need to add options. | 28 October 2010, 19:04:13 UTC |
| 7d61832 | Trevor Bedford | 20 October 2010, 20:45:04 UTC | Minor change in time reporting for locgrid skyline. | 20 October 2010, 20:45:04 UTC |
| 22a9d66 | Trevor Bedford | 20 October 2010, 20:26:09 UTC | Implemented locgrid skyline. | 20 October 2010, 20:26:09 UTC |
| 2a1f627 | Trevor Bedford | 20 October 2010, 19:22:18 UTC | Implemented locsample skyline. | 20 October 2010, 19:22:18 UTC |
| 9c778cb | Trevor Bedford | 20 October 2010, 15:35:12 UTC | Added option to export skyline of mean rate of time slices. Rate comes from [rate=XXX] notation in .trees file. | 20 October 2010, 15:35:12 UTC |
| 42ef4fa | Trevor Bedford | 02 October 2010, 21:08:10 UTC | Import of rates from trees file. | 02 October 2010, 21:08:10 UTC |
| 4aed940 | Trevor Bedford | 02 October 2010, 20:56:22 UTC | Added xmean and ymean skylines. | 02 October 2010, 20:56:22 UTC |
| 789c838 | Trevor Bedford | 01 October 2010, 21:33:05 UTC | IO support for rotate() | 01 October 2010, 21:33:05 UTC |
| afa00b7 | Trevor Bedford | 01 October 2010, 21:21:17 UTC | Added rotation to antigenic data. | 01 October 2010, 21:21:17 UTC |
| 3fe75d5 | Trevor Bedford | 01 October 2010, 20:15:25 UTC | Streamlined renewTrunk() | 01 October 2010, 20:15:25 UTC |
| 599c205 | Trevor Bedford | 30 September 2010, 21:51:56 UTC | Importing X and Y antigenic locations. | 30 September 2010, 21:51:56 UTC |
| d322c39 | Trevor Bedford | 30 September 2010, 21:05:40 UTC | Updated Node class with xloc and yloc. | 30 September 2010, 21:05:40 UTC |
| 5d0541f | Trevor Bedford | 30 September 2010, 20:59:33 UTC | Fixed bug with prune to time. | 30 September 2010, 20:59:33 UTC |
| 1633a95 | Trevor Bedford | 27 September 2010, 21:11:44 UTC | Added function pruneToTime() and fixed bug with pruneToLabel() label import. | 27 September 2010, 21:11:44 UTC |
| 7e33d5a | Trevor Bedford | 29 June 2010, 16:07:52 UTC | Updating copyright info. | 29 June 2010, 16:07:52 UTC |
| 7ff36ae | Trevor Bedford | 29 June 2010, 15:58:11 UTC | Adding RNG files. These are only used with reduceTips(). | 29 June 2010, 15:58:11 UTC |
| da4cdc5 | Trevor Bedford | 29 June 2010, 14:50:56 UTC | More naming options. | 29 June 2010, 14:50:56 UTC |
| 63de390 | Trevor Bedford | 28 June 2010, 21:20:17 UTC | Minor bug fix. Properly adding location to labelset. | 28 June 2010, 21:20:17 UTC |
| f3e10e0 | Trevor Bedford | 28 June 2010, 21:13:42 UTC | Implemented import of BEAST tagged nodes. Watching for [&state=XXXXX]. | 28 June 2010, 21:13:42 UTC |
| f6d6b86 | Trevor Bedford | 27 June 2010, 22:20:45 UTC | Moved labels to strings from ints. This change should be completely transparent when using Migrate. Will allow direct import of BEAST geotagged trees. | 27 June 2010, 22:20:45 UTC |
| 1c06c82 | Trevor Bedford | 26 June 2010, 18:02:19 UTC | Code to insert migration events in place. Should clean this up some. Also, need to confirm with Peter about from tip vs. from split. | 26 June 2010, 18:02:19 UTC |
| e05cc7b | Trevor Bedford | 25 June 2010, 01:16:51 UTC | Labelling based on initial digits. | 25 June 2010, 01:16:51 UTC |
| b6c8613 | Trevor Bedford | 25 June 2010, 00:44:46 UTC | Basics of new importer in place. Handles NEWICK with branch lengths. Nothing else at this point. | 25 June 2010, 00:44:46 UTC |
| 5966ec6 | Trevor Bedford | 24 June 2010, 17:54:51 UTC | Minor changes. | 24 June 2010, 17:54:51 UTC |
| 791caa2 | Trevor Bedford | 28 January 2010, 19:39:43 UTC | getTMRCA() now fires NAN when run on less than two tips. | 28 January 2010, 19:39:43 UTC |
| 65430b1 | Trevor Bedford | 28 January 2010, 19:32:55 UTC | Series now does a better job dealing with NAN and INF inputs. | 28 January 2010, 19:32:55 UTC |
| 53a41f8 | Trevor Bedford | 28 January 2010, 19:02:43 UTC | Added function reduceTips() that randomly prunes down tree. | 28 January 2010, 19:02:43 UTC |
| 434c5b0 | Trevor Bedford | 15 January 2010, 20:09:06 UTC | Labels can now be multiple characters in length | 15 January 2010, 20:09:06 UTC |
| cffb842 | Trevor Bedford | 15 January 2010, 16:55:44 UTC | Added functino leafSlice(). This functions in a very similar fashion to the other slices. Prunes back from leaves in a particular time window. Not all that useful so far. | 15 January 2010, 16:55:44 UTC |
| f1aa474 | Trevor Bedford | 08 January 2010, 16:02:33 UTC | Function trunkSlice() added. This removes all descendents of the trunk from a particular time forward. | 08 January 2010, 16:02:33 UTC |
| 700ff5d | Trevor Bedford | 06 January 2010, 20:38:22 UTC | Slight UI changes. | 06 January 2010, 20:38:22 UTC |
| 9c04acf | Trevor Bedford | 06 January 2010, 20:29:26 UTC | Error checking for 0 trees. | 06 January 2010, 20:29:26 UTC |
| b9a272f | Trevor Bedford | 06 January 2010, 20:23:02 UTC | Added burnin. | 06 January 2010, 20:23:02 UTC |
| a3fd6bb | Trevor Bedford | 06 January 2010, 19:55:55 UTC | Added collapseLabels() function. | 06 January 2010, 19:55:55 UTC |
| ac4f4a7 | Trevor Bedford | 06 January 2010, 19:17:15 UTC | Modified the way the trunk is determined. Now take single random lineage at "present" and trace its ancestry backward. Each time the trunk will be slightly different near the present, but should be the same further into the past. | 06 January 2010, 19:17:15 UTC |
| 9092f7a | Trevor Bedford | 21 October 2009, 02:03:01 UTC | Swapped postfix for prefix iterators. Doesn't make a copy. 10% speed improvement. | 21 October 2009, 02:03:01 UTC |
| e785111 | Trevor Bedford | 15 October 2009, 14:25:18 UTC | Optimizing NEWICK readin. | 15 October 2009, 14:25:18 UTC |
| ecd6e06 | Trevor Bedford | 15 October 2009, 02:53:14 UTC | Improved compatibility with LAMARC trees (needed to ignore final enclosing parenthesis) | 15 October 2009, 02:53:14 UTC |
| 98709f7 | Trevor Bedford | 14 October 2009, 18:56:05 UTC | Version 0.9.1 | 14 October 2009, 18:56:05 UTC |
| 9c2d7c7 | Trevor Bedford | 14 October 2009, 18:16:27 UTC | Better exception handling. | 14 October 2009, 18:16:27 UTC |
| 90420bf | Trevor Bedford | 14 October 2009, 15:18:27 UTC | Cleanup. Added GPL information. Makefile is now mingw compatible. | 14 October 2009, 15:18:27 UTC |
| ce13d5e | Trevor Bedford | 12 October 2009, 20:25:37 UTC | print hp tree to print rule tree. | 12 October 2009, 20:25:37 UTC |
| d3a9fad | Trevor Bedford | 12 October 2009, 19:38:11 UTC | Finished skyline and tips UI. Split pruneToTrunk to renewTrunk and pruneToTrunk. | 12 October 2009, 19:38:11 UTC |
| 19b0ca3 | Trevor Bedford | 12 October 2009, 18:51:53 UTC | Filling out skyline UI. | 12 October 2009, 18:51:53 UTC |
| fbd0e54 | Trevor Bedford | 09 October 2009, 02:25:44 UTC | Bug fix for reduce(). Significant improvements to tree drawing. | 09 October 2009, 02:25:44 UTC |
| 4895bfb | Trevor Bedford | 08 October 2009, 18:12:58 UTC | Skeleton of PDF class. Used to render trees without the help of Mathematica. | 08 October 2009, 18:12:58 UTC |
| ae3a9d9 | Trevor Bedford | 11 August 2009, 14:25:51 UTC | Fixed a bug in sectionTree that had resulted from changes to trimEnds | 11 August 2009, 14:25:51 UTC |
| c8e0aac | Trevor Bedford | 10 August 2009, 16:24:09 UTC | Bug fix for trimEnds() | 10 August 2009, 16:24:09 UTC |
| 9d54076 | Trevor Bedford | 09 August 2009, 18:54:37 UTC | Skyline proportions is working correctly. Required a change in trimEnds, which now has multiple subtrees. | 09 August 2009, 18:54:37 UTC |
| b78b8b6 | Trevor Bedford | 08 August 2009, 00:31:16 UTC | New output type: out.tips Summarizes a statistic for each tip of tree. Have time to trunk implemented here. | 08 August 2009, 00:31:16 UTC |
| 9e0d229 | Trevor Bedford | 06 August 2009, 14:17:56 UTC | Further work on Parameters. | 06 August 2009, 14:17:56 UTC |
| 5a99dd4 | Trevor Bedford | 03 August 2009, 17:38:06 UTC | Param cleanup. | 03 August 2009, 17:38:06 UTC |
| 146d8e2 | Trevor Bedford | 02 August 2009, 15:59:29 UTC | Finished with first version of Parameter class. | 02 August 2009, 15:59:29 UTC |
| ee66c19 | Trevor Bedford | 01 August 2009, 19:22:41 UTC | Replace parameter double with vector<double>. This will make determining if user values are present easier. | 01 August 2009, 19:22:41 UTC |
| 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 |
