| 13cdd69 | Eric Hare | 28 June 2016, 11:48:59 UTC | Clean nasty files | 28 June 2016, 11:48:59 UTC |
| 9c1204a | Eric Hare | 07 January 2016, 14:58:54 UTC | Rebuild with latest toolkit | 07 January 2016, 14:58:54 UTC |
| 103da15 | Eric Hare | 14 December 2015, 13:10:25 UTC | Update README.md | 14 December 2015, 13:10:25 UTC |
| caf00ff | Eric Hare | 15 September 2015, 18:21:42 UTC | Bump for cran resubmit | 15 September 2015, 18:21:42 UTC |
| 6e8d326 | Eric Hare | 23 July 2015, 10:23:34 UTC | CRAN compatibility | 23 July 2015, 10:23:34 UTC |
| e326dec | Eric Hare | 17 April 2015, 11:49:03 UTC | Rebuild and bump peptider | 17 April 2015, 11:49:03 UTC |
| dafd8ee | Eric Hare | 09 April 2015, 12:45:18 UTC | Update description file | 09 April 2015, 12:45:18 UTC |
| 87b25e8 | Eric Hare | 04 April 2015, 14:11:49 UTC | Compatible with latest discreteRV | 04 April 2015, 14:11:49 UTC |
| 0fc0333 | Eric Hare | 03 February 2015, 00:34:02 UTC | Bump date | 03 February 2015, 00:34:02 UTC |
| 87ff827 | Eric Hare | 14 January 2015, 19:49:29 UTC | Change the name of trimer to 2020 | 14 January 2015, 19:49:29 UTC |
| 822b23c | Eric Hare | 09 January 2015, 18:28:33 UTC | Rmpfr is too slow to be useable for this... | 09 January 2015, 18:28:33 UTC |
| 7b1dd7a | Eric Hare | 09 January 2015, 18:12:55 UTC | Custom defaults are different now | 09 January 2015, 18:12:55 UTC |
| 172ea73 | Heike Hofmann | 06 January 2015, 12:24:52 UTC | variances for diversity | 06 January 2015, 12:24:52 UTC |
| e42c6f3 | Eric Hare | 06 January 2015, 01:25:28 UTC | Variance stuff | 06 January 2015, 01:25:28 UTC |
| 869758e | Eric Hare | 05 January 2015, 00:15:25 UTC | Initial variance computation in diversity, but problems... | 05 January 2015, 00:15:25 UTC |
| f97c216 | Eric Hare | 01 January 2015, 15:41:58 UTC | Use Rmpfr for numerical precision | 01 January 2015, 15:41:58 UTC |
| d5de796 | Eric Hare | 03 December 2014, 13:27:14 UTC | Bump version number, new cran checks | 03 December 2014, 13:27:14 UTC |
| f2f7979 | Eric Hare | 28 July 2014, 12:47:02 UTC | Yikes, require latest discreteRV | 28 July 2014, 12:47:02 UTC |
| 963eb17 | Eric Hare | 28 July 2014, 11:54:56 UTC | Fix for require plyr call | 28 July 2014, 11:54:56 UTC |
| 278932f | Eric Hare | 02 July 2014, 16:11:02 UTC | Fix typos | 02 July 2014, 16:11:02 UTC |
| 0d421fe | Heike Hofmann | 01 July 2014, 21:39:00 UTC | added reduced version of genNeighbors | 01 July 2014, 21:39:00 UTC |
| 27bec07 | Heike Hofmann | 30 June 2014, 17:49:44 UTC | calcNeighbors renamed to genNeighbors, parameters are k and scheme | 30 June 2014, 17:49:44 UTC |
| 0761d69 | Heike Hofmann | 30 June 2014, 14:58:17 UTC | calcNeighbors added | 30 June 2014, 14:58:17 UTC |
| 55bcb6d | Heike Hofmann | 30 June 2014, 13:28:46 UTC | neighborhoods | 30 June 2014, 13:29:00 UTC |
| 371544b | Eric Hare | 29 June 2014, 17:30:44 UTC | Try filter | 29 June 2014, 17:30:45 UTC |
| 63ed1ad | Heike Hofmann | 27 June 2014, 15:21:36 UTC | number of codon neighbors is sum of codons of all neighbors | 27 June 2014, 15:21:36 UTC |
| 896303b | Heike Hofmann | 27 June 2014, 14:07:00 UTC | neighbors are additive after all | 27 June 2014, 14:07:00 UTC |
| a48da40 | Heike Hofmann | 25 June 2014, 23:55:01 UTC | bug in neighborhood calculation | 25 June 2014, 23:55:27 UTC |
| 23b2830 | Eric Hare | 25 June 2014, 16:22:33 UTC | Fix scale bug | 25 June 2014, 16:22:33 UTC |
| 1ac40ca | Eric Hare | 21 June 2014, 19:02:02 UTC | Try again | 21 June 2014, 19:02:02 UTC |
| e07d536 | Eric Hare | 21 June 2014, 00:22:59 UTC | Scale factor | 21 June 2014, 00:22:59 UTC |
| 3b3d8ea | Heike Hofmann | 20 June 2014, 20:51:12 UTC | bug fix for neighborhood of stop codon | 20 June 2014, 20:51:12 UTC |
| 4c1153e | Eric Hare | 10 June 2014, 14:43:00 UTC | Covariance matrix between peptide classes | 10 June 2014, 14:43:00 UTC |
| 67d54cd | Eric Hare | 05 June 2014, 14:22:57 UTC | Peptider with simplified variance and encoding | 05 June 2014, 14:22:57 UTC |
| 239743d | Eric Hare | 03 June 2014, 15:21:25 UTC | Variance | 03 June 2014, 15:21:25 UTC |
| 2fbaed6 | Eric Hare | 19 May 2014, 01:09:38 UTC | Weird roxygen changes | 19 May 2014, 01:09:38 UTC |
| af647a7 | Eric Hare | 18 May 2014, 16:20:48 UTC | Try one slight tweak | 18 May 2014, 16:20:48 UTC |
| c2bf140 | Eric Hare | 18 May 2014, 16:08:50 UTC | Only a single custom file... finally | 18 May 2014, 16:08:50 UTC |
| 0df5188 | Eric Hare | 06 May 2014, 20:52:55 UTC | Bump date, get ready for new CRAN version | 06 May 2014, 20:52:55 UTC |
| 68ed79d | Eric Hare | 04 May 2014, 23:05:53 UTC | Squash a little bug | 04 May 2014, 23:05:53 UTC |
| 6615414 | Eric Hare | 04 May 2014, 22:44:23 UTC | Custom neighborhood calculation | 04 May 2014, 22:44:23 UTC |
| 807f04b | Eric Hare | 01 May 2014, 21:13:37 UTC | Ugh, actually output the correct file | 01 May 2014, 21:13:37 UTC |
| 12ff064 | Eric Hare | 01 May 2014, 21:05:19 UTC | Small changes for compatibility with new pelica | 01 May 2014, 21:05:19 UTC |
| be04e82 | Eric Hare | 01 May 2014, 20:55:09 UTC | generate custom updated | 01 May 2014, 20:55:09 UTC |
| 76a6c93 | Eric Hare | 01 May 2014, 20:25:12 UTC | Support loading scheme from file | 01 May 2014, 20:25:12 UTC |
| 6797a5c | Eric Hare | 29 April 2014, 21:33:01 UTC | Fix bug with partial name matching in DFs | 29 April 2014, 21:33:01 UTC |
| 9b773db | Eric Hare | 02 April 2014, 14:00:48 UTC | Slight update to description | 02 April 2014, 14:00:48 UTC |
| 73e76d9 | Eric Hare | 02 April 2014, 13:56:05 UTC | Explicitly require latest version | 02 April 2014, 13:56:05 UTC |
| be88b98 | Eric Hare | 02 April 2014, 13:53:17 UTC | Update to support new discreteRV interface | 02 April 2014, 13:53:17 UTC |
| ee695b1 | Eric Hare | 03 February 2014, 21:50:57 UTC | Try one more time | 03 February 2014, 21:50:57 UTC |
| 7f05321 | Eric Hare | 03 February 2014, 21:45:58 UTC | Just a rebuild of the documentation | 03 February 2014, 21:45:58 UTC |
| 697435e | Eric Hare | 03 February 2014, 21:44:31 UTC | Function for diversity according to our paper, not just makowski | 03 February 2014, 21:44:31 UTC |
| ac9f1ea | Eric Hare | 19 November 2013, 17:37:30 UTC | One small bug fix | 19 November 2013, 17:37:30 UTC |
| b8f1e02 | Eric Hare | 19 November 2013, 17:17:06 UTC | Finish up the _new functions for tabulation | 19 November 2013, 17:17:06 UTC |
| 60c60b9 | Eric Hare | 19 November 2013, 17:13:37 UTC | More updates | 19 November 2013, 17:13:37 UTC |
| c0b7696 | Eric Hare | 19 November 2013, 16:54:56 UTC | Custom Probs for new schemes | 19 November 2013, 16:54:56 UTC |
| 33dca8d | Eric Hare | 28 October 2013, 22:31:15 UTC | Detection probabilities with reduced encoding. Fast! | 28 October 2013, 22:31:15 UTC |
| 3bde20c | Eric Hare | 28 October 2013, 22:15:37 UTC | Clean up reduced encoding scheme | 28 October 2013, 22:15:37 UTC |
| 3d54e2c | Eric Hare | 26 October 2013, 18:26:40 UTC | Makowski in new scheme | 26 October 2013, 18:26:40 UTC |
| aaef46e | Eric Hare | 26 October 2013, 15:17:34 UTC | Implement effieciency in new encoding scheme | 26 October 2013, 15:17:34 UTC |
| e5d4293 | Eric Hare | 26 October 2013, 15:11:00 UTC | Fix coverage calculation | 26 October 2013, 15:11:00 UTC |
| 47b9b68 | Eric Hare | 26 October 2013, 14:47:24 UTC | Beginnings of reduced encoding for faster computation | 26 October 2013, 14:47:24 UTC |
| 22bf557 | Eric Hare | 24 October 2013, 13:57:22 UTC | Small change to make regenerating all this info faster... | 24 October 2013, 13:57:22 UTC |
| 4131ab3 | Eric Hare | 24 October 2013, 13:19:35 UTC | Oops, fix duplicate line | 24 October 2013, 13:19:35 UTC |
| 5011f4e | Eric Hare | 24 October 2013, 12:29:23 UTC | parametize | 24 October 2013, 12:29:23 UTC |
| 7e7d88d | Eric Hare | 17 October 2013, 13:21:48 UTC | One more doc update | 17 October 2013, 13:21:48 UTC |
| bd46947 | Eric Hare | 17 October 2013, 13:20:44 UTC | Blah, fix silly typo | 17 October 2013, 13:20:44 UTC |
| 5f5bd86 | Eric Hare | 17 October 2013, 13:19:08 UTC | Update peptider to 0.1.1 (update docs, fix scheme defs) | 17 October 2013, 13:19:08 UTC |
| f7bb38c | Eric Hare | 16 October 2013, 21:23:34 UTC | Prepare for CRAN submission | 16 October 2013, 21:23:34 UTC |
| 0b3cfed | Eric Hare | 10 October 2013, 16:44:43 UTC | Bring tabulate into sync with the new formate | 10 October 2013, 16:44:43 UTC |
| 9eeda31 | Eric Hare | 10 October 2013, 14:56:48 UTC | A few more compatibility updates | 10 October 2013, 14:56:48 UTC |
| 3573ee4 | Eric Hare | 10 October 2013, 14:12:59 UTC | Small update to order of arguments | 10 October 2013, 14:12:59 UTC |
| 3ca049e | Eric Hare | 10 October 2013, 13:53:29 UTC | Restructure peptide so that we don't have to build functions for each internal scheme | 10 October 2013, 13:53:29 UTC |
| 0a0f0cc | Eric Hare | 09 October 2013, 13:01:40 UTC | Redo devtools:::check() | 09 October 2013, 13:01:40 UTC |
| 9c42279 | Eric Hare | 09 October 2013, 13:00:33 UTC | As per Timo's request, add TrimerC scheme | 09 October 2013, 13:00:33 UTC |
| fa2e1f3 | Eric Hare | 08 October 2013, 12:14:43 UTC | Slight update of DESCRIPTION file to meet Hadley's versioning requirements | 08 October 2013, 12:14:43 UTC |
| 7c91753 | Eric Hare | 08 October 2013, 01:28:41 UTC | Some cat messages for tabulate | 08 October 2013, 01:28:41 UTC |
| f14ea6e | Eric Hare | 08 October 2013, 00:50:11 UTC | Merge branch 'master' of https://github.com/heike/peptider | 08 October 2013, 00:50:11 UTC |
| 2707af7 | Eric Hare | 08 October 2013, 00:49:34 UTC | Update coverage() and efficiency() to not assume 19 valid AAs but rather calculate it from the given scheme | 08 October 2013, 00:49:34 UTC |
| 523895d | Eric Hare | 07 October 2013, 17:41:23 UTC | Create README.md | 07 October 2013, 17:41:23 UTC |
| f2e37a5 | Eric Hare | 07 October 2013, 17:40:47 UTC | Update the package to include tabulate (generateCustom) and pass CRAN check | 07 October 2013, 17:40:47 UTC |
| 1dcc6d0 | Eric Hare | 05 October 2013, 18:22:53 UTC | Rebuild the documentation | 05 October 2013, 18:22:53 UTC |
| f210431 | Eric Hare | 05 October 2013, 18:03:49 UTC | New peptider functions for encodings with C not ignored | 05 October 2013, 18:03:49 UTC |
| b15cf5c | Eric Hare | 30 September 2013, 16:18:41 UTC | Fix bug in calculating the number of valid amino acids in a particular encoding | 30 September 2013, 16:18:41 UTC |
| 54ef44a | Heike Hofmann | 25 September 2013, 18:41:32 UTC | example for user defined library | 25 September 2013, 18:41:32 UTC |
| 0f36228 | Heike Hofmann | 02 September 2013, 16:22:14 UTC | not sure what was changed | 02 September 2013, 16:22:14 UTC |
| 6f67280 | Heike Hofmann | 23 June 2013, 19:17:55 UTC | changes to documentation | 23 June 2013, 19:17:55 UTC |
| ab792c2 | Heike Hofmann | 18 June 2013, 11:45:11 UTC | clean up | 18 June 2013, 11:45:11 UTC |
| 083a543 | Heike Hofmann | 17 June 2013, 00:51:59 UTC | added documentation for nns_scheme | 17 June 2013, 00:51:59 UTC |
| 376c294 | Heike Hofmann | 17 June 2013, 00:51:27 UTC | library fixed - should install now and pass check | 17 June 2013, 00:51:27 UTC |
| 5149b46 | Heike Hofmann | 17 June 2013, 00:05:35 UTC | adding documentation to the package | 17 June 2013, 00:05:35 UTC |
| c91687a | Heike Hofmann | 16 June 2013, 23:05:10 UTC | comments for some of the new functions | 16 June 2013, 23:05:10 UTC |
| 55271e6 | Heike Hofmann | 16 June 2013, 23:02:57 UTC | ... and another silly bug. Now the detection probabilities match ... | 16 June 2013, 23:02:57 UTC |
| 8d9bdad | Heike Hofmann | 16 June 2013, 20:01:55 UTC | probability for neighborhoods needs to be combined into one number | 16 June 2013, 20:01:55 UTC |
| bd7da29 | Heike Hofmann | 16 June 2013, 16:27:50 UTC | stupid bug in codonsOne fixed | 16 June 2013, 16:27:50 UTC |
| 5920b1a | Heike Hofmann | 14 June 2013, 21:45:11 UTC | BLOSUM80 data was messed up - is it fixed now? | 14 June 2013, 21:45:11 UTC |
| 7106fc6 | Heike Hofmann | 14 June 2013, 19:00:06 UTC | detection probabilities | 14 June 2013, 19:00:06 UTC |
| b7733e6 | Heike Hofmann | 14 June 2013, 01:35:53 UTC | neighbor calculations | 14 June 2013, 01:35:53 UTC |
| 951c3ff | Heike Hofmann | 10 June 2013, 00:47:11 UTC | typos fixed | 10 June 2013, 00:47:11 UTC |
| 8453165 | Heike Hofmann | 09 June 2013, 22:13:54 UTC | first commit | 09 June 2013, 22:13:54 UTC |
