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Author SHA1 Message Date
Waldir Leoncio
9e3ea49398 handleData defaults to BAPS format 2024-09-13 12:42:46 +02:00
Waldir Leoncio
54b0b081ea Added unit tests for greedyMix() on GenePop (#24) 2024-08-26 13:26:52 +02:00
Waldir Leoncio
12884cfcb6 Added GenePop data, txt and gen (#24) 2024-08-26 13:26:07 +02:00
Waldir Leoncio
fa7e750c69 Merge branch 'fix-ci' into develop 2024-08-26 10:15:36 +02:00
Waldir Leoncio
9ab4dfb29f Updated actions/checkout to v4 2024-08-26 06:53:55 +02:00
Waldir Leoncio
010f18dd19 Merge branch 'issue-24' into develop 
* issue-24:
  Increment version number to 0.0.0.9029
  Disabled FASTA tests on greedyMix() (#24)
  Added synthetic FASTA file (#24)
  Ensure diffInCounts returns as.matrix (#24)
  Adapted tests to FASTA on greedyMix() (#24)
  Removed baps file pointing to fasta
  Improved conversion from FASTA to BAPS (#24)
  Improved handling of FASTA data (#24)
  `process_BAPS_data()` can handle file being an R object
  Added function to convert from FASTA to BAPS (#24)
  Unwrapped `greedyMix() example (#24)
 2024-08-26 06:32:51 +02:00
Waldir Leoncio
d925545e70 Increment version number to 0.0.0.9029 2024-08-26 06:30:56 +02:00
Waldir Leoncio
9ff5f39c39 Disabled FASTA tests on greedyMix() (#24) 2024-08-26 06:30:49 +02:00
Waldir Leoncio
6f70f6f752 Added synthetic FASTA file (#24) 2024-08-26 06:10:07 +02:00
Waldir Leoncio
99e272a80f Ensure diffInCounts returns as.matrix (#24) 2024-08-26 06:09:27 +02:00
Waldir Leoncio
b7282d67df Adapted tests to FASTA on greedyMix() (#24) 2024-08-19 13:32:05 +02:00
Waldir Leoncio
43886d649f Removed baps file pointing to fasta 2024-08-19 13:29:18 +02:00
Waldir Leoncio
471c380ce3 Improved conversion from FASTA to BAPS (#24) 2024-08-09 15:33:03 +02:00
Waldir Leoncio
ca358ff0fb Improved handling of FASTA data (#24) 2024-08-09 14:57:07 +02:00
Waldir Leoncio
73b0a70138 process_BAPS_data() can handle file being an R object 2024-08-09 13:55:55 +02:00
Waldir Leoncio
7b7968f00b Added function to convert from FASTA to BAPS (#24) 2024-08-09 13:55:04 +02:00
Waldir Leoncio
6e08c35f13 Unwrapped `greedyMix() example (#24) 2024-08-07 11:42:29 +02:00
Waldir Leoncio
5cc111f0c1 Merge branch 'issue-24' into develop 
* issue-24:
  Increment version number to 0.0.0.9028
  Updated docs
  Added unit tests (#24)
  Fixed `greedyMix()` for BAPS files (#24) 🍾
  Fixed `indMix()` and subfunctions (#24)
  Fixed tests (#24)
 2024-07-02 16:54:33 +02:00
Waldir Leoncio
d861ffb551 Increment version number to 0.0.0.9028 2024-07-02 16:53:10 +02:00
Waldir Leoncio
3ce6659120 Updated docs 2024-07-02 16:53:04 +02:00
Waldir Leoncio
95ff2378b1 Added unit tests (#24) 2024-07-02 16:39:48 +02:00
Waldir Leoncio
e873075ebf Fixed greedyMix() for BAPS files (#24) 🍾 2024-07-02 16:39:38 +02:00
Waldir Leoncio
6aecf38231 Fixed indMix() and subfunctions (#24) 2024-07-02 16:31:17 +02:00
Waldir Leoncio
e4af251307 Fixed tests (#24) 2024-07-02 11:23:22 +02:00
Waldir Leoncio
dd025e48c9 Merge branch 'issue-24' into develop 
* issue-24:
  Increment version number to 0.0.0.9027
  Fixed docs
 2024-06-26 14:29:35 +02:00
Waldir Leoncio
00ecfa4fd8 Increment version number to 0.0.0.9027 2024-06-26 14:29:25 +02:00
Waldir Leoncio
320bb28a7a Fixed docs 2024-06-26 14:27:02 +02:00
Waldir Leoncio
2d5d93adbc Merge branch 'issue-24' into develop 
* issue-24:
  Increment version number to 0.0.0.9026
  Added (commented) test for BAPS data (#24)
  Renamed global environment, fixed assignments (#24)
  Fixes to `laskeMuutokset()` (#24)
  Syntax fix to `indMix()` (#24)
  Retranslated `computeDiffInCounts()` (#24)
  Changed default `npops` to 3 (#24)
  `laskeMuutokset()` reads `npop` from parent functions (#24)
  Using a dedicated environment for globals (#24)
  Retranslated `computePopulationLogml()` (#24)
  Added/renamed BAPS example data (#24)
 2024-04-11 09:49:00 +02:00
Waldir Leoncio
e615bb8b50 Increment version number to 0.0.0.9026 2024-04-11 09:47:49 +02:00
Waldir Leoncio
2a815f15cd Added (commented) test for BAPS data (#24) 2024-04-11 09:47:30 +02:00
Waldir Leoncio
99f28ba215 Renamed global environment, fixed assignments (#24) 2024-04-11 09:47:29 +02:00
Waldir Leoncio
ec959fcfb2 Fixes to laskeMuutokset() (#24) 2024-04-10 16:07:00 +02:00
Waldir Leoncio
d1e567c326 Syntax fix to indMix() (#24) 2024-04-10 16:07:00 +02:00
Waldir Leoncio
55a36e81ae Retranslated computeDiffInCounts() (#24) 2024-04-10 16:07:00 +02:00
Waldir Leoncio
c3b8da0012 Changed default npops to 3 (#24) 2024-04-10 16:06:59 +02:00
Waldir Leoncio
58a5e5a2fd laskeMuutokset() reads npop from parent functions (#24) 2024-04-10 16:06:58 +02:00
Waldir Leoncio
5deadcf3ee Using a dedicated environment for globals (#24) 
Based on suggestion from <https://stackoverflow.com/a/12605694/1169233>.
 2024-04-10 16:06:58 +02:00
Waldir Leoncio
55d302ab67 Retranslated computePopulationLogml() (#24) 2024-04-10 16:06:58 +02:00
Waldir Leoncio
98b5e7a154 Added/renamed BAPS example data (#24) 2024-04-10 16:06:56 +02:00
Waldir Leoncio
9b8da3ab4d Merge branch 'baps-format' into develop 
* baps-format:
  Increment version number to 0.0.0.9025
  Skips `greedyMix()` example until #24 is fixed
  Updated documentation (#24)
  Fails for FAST input to `greedyMix()` (#24)
  Fixed calculation og `ninds` (#24)
  Bugfixes to `indMix()` and subfunctions (#24)
  Improved handling of BAPS format (#24)
  Fixed calculation of `ninds` `ekat` (#24)
  Added processing of BAPS format
 2024-04-08 13:35:51 +02:00
Waldir Leoncio
6d875dfd8d Increment version number to 0.0.0.9025 2024-04-08 13:34:21 +02:00
Waldir Leoncio
f5c09094b0 Skips greedyMix() example until #24 is fixed 2024-04-08 13:34:14 +02:00
Waldir Leoncio
f676042a17 Updated documentation (#24) 2024-04-08 13:29:03 +02:00
Waldir Leoncio
6209bb33fa Fails for FAST input to greedyMix() (#24) 
This is a desirable feature, but was not implemented in the original BAPS, so better leave it out until the original planned features is working.
 2024-04-08 13:14:54 +02:00
Waldir Leoncio
6c3e2aff04 Fixed calculation og ninds (#24) 2024-04-08 10:11:25 +02:00
Waldir Leoncio
5c35b9ad1e Bugfixes to indMix() and subfunctions (#24) 2024-03-25 16:10:44 +01:00
Waldir Leoncio
26ab0107a8 Improved handling of BAPS format (#24) 2024-03-25 16:10:43 +01:00
Waldir Leoncio
f361975254 Fixed calculation of ninds ekat (#24) 2024-03-25 16:10:43 +01:00
Waldir Leoncio
530442487f Added processing of BAPS format 
To be eventually dropped, but useful for comparing output with MATLAB code.
 2024-03-25 16:10:41 +01:00
Waldir Leoncio
d2ec5894b3 Removed MATLAB files 
Those are now present on https://github.com/ocbe-uio/rBAPS/ and may be reconnected to this repository as a submodule
 2024-01-19 09:49:10 +01:00