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Author SHA1 Message Date
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
Waldir Leoncio
0f3c5708d6 Merge compress-writeMixtureInfo-output into develop 
* compress-writeMixtureInfo-output:
  Updated docs
  Improved output of writeMixtureInfo()
  Auto-recognizing format of greedyMix() data
  Fixed output of greedyMix()
 2023-09-14 12:55:51 +02:00
Waldir Leoncio
9ed39d403b Updated docs 2023-09-14 12:53:34 +02:00
Waldir Leoncio
273edafd30 Improved output of writeMixtureInfo() 
Also, incremented version number to 0.0.0.9024
 2023-09-14 12:52:30 +02:00
Waldir Leoncio
63af25a63d Auto-recognizing format of greedyMix() data 
Works as long as there's only one period in the file path
 2023-09-14 11:11:37 +02:00
Waldir Leoncio
a73752364b Fixed output of greedyMix() 2023-09-14 11:02:06 +02:00
Waldir Leoncio
bde3be6344 Merge branch 'silence-writeMixtureInfo' into develop 
* silence-writeMixtureInfo:
  Added verbose argument to writeMixtureInfo()
  Increment version number to 0.0.0.9023
 2023-09-11 14:07:04 +02:00
Waldir Leoncio
ceaf7eca4b Added verbose argument to writeMixtureInfo() 2023-09-11 14:06:45 +02:00
Waldir Leoncio
fa2381411f Increment version number to 0.0.0.9023 2023-09-11 13:54:52 +02:00
Waldir Leoncio
e3f14ee97d Fixed object name in test 2023-09-11 13:53:42 +02:00
Waldir Leoncio
59fbb0a167 Merge branch 'issue-25' into develop 
* issue-25: (38 commits)
  Adjusted unit tests for #25
  Fixed sink() usage
  Fixed docs
  Exporting importFile()
  Improved handling of supported formats for greedyMix() (#25)
  Fixed basic parsing of FASTA files (#25)
  Increment version number to 0.0.0.9022
  Fixed syntax (#25)
  Improved printing (#25)
  Partial reversion of b034158 (#25)
  Fixed to indMix (#25)
  Incorporated handleData() on greedyMix() (#25)
  Improved handleData() to handle FASTA (#25)
  Added numeric output option to load_fasta() (#25)
  Fixed test text (#25)
  Added missing documentation for arguments (#25)
  Syntax fix (#25)
  Delayed resolution of FIXMEs (#25)
  Workaround for usage of MATLAB any() (#25)
  Fixed argument passing (#25)
  ...
 2023-09-11 13:15:55 +02:00
Waldir Leoncio
ce954bf801 Adjusted unit tests for #25 2023-09-11 13:14:23 +02:00
Waldir Leoncio
2b756576ac Fixed sink() usage 2023-09-11 13:14:08 +02:00
Waldir Leoncio
70ec460106 Fixed docs 2023-09-11 13:13:55 +02:00
Waldir Leoncio
882fcd4112 Exporting importFile() 2023-09-11 12:51:41 +02:00
Waldir Leoncio
3e4044bcec Improved handling of supported formats for greedyMix() (#25) 2023-09-11 12:49:21 +02:00
Waldir Leoncio
76828387a3 Fixed basic parsing of FASTA files (#25) 2023-09-11 12:15:30 +02:00
Waldir Leoncio
a88f31b3a5 Increment version number to 0.0.0.9022 2023-08-11 16:27:23 +02:00
Waldir Leoncio
cfb71bfd6d Fixed syntax (#25) 2023-08-11 16:23:02 +02:00
Waldir Leoncio
44e418f838 Improved printing (#25) 2023-08-11 16:22:45 +02:00
Waldir Leoncio
177685b6a2 Partial reversion of b034158 (#25) 
It should be OK for Z to be NULL. This currently triggers an issue on initialCounts(), which should be fixed
 2023-08-11 16:22:29 +02:00
Waldir Leoncio
372891fbe1 Fixed to indMix (#25) 2023-08-11 14:31:08 +02:00
Waldir Leoncio
3537f18d2c Incorporated handleData() on greedyMix() (#25) 2023-08-11 11:18:03 +02:00
Waldir Leoncio
f47e13d3a9 Improved handleData() to handle FASTA (#25) 2023-08-11 11:13:24 +02:00
Waldir Leoncio
95d9d658cb Added numeric output option to load_fasta() (#25) 2023-08-11 11:01:20 +02:00
Waldir Leoncio
a51816d5c0 Fixed test text (#25) 2023-08-11 08:17:56 +02:00
Waldir Leoncio
bd932e2b6d Added missing documentation for arguments (#25) 2023-08-09 15:27:45 +02:00
Waldir Leoncio
85c8c01816 Syntax fix (#25) 2023-08-09 15:11:54 +02:00
Waldir Leoncio
2739442541 Delayed resolution of FIXMEs (#25) 2023-08-09 15:09:13 +02:00
Waldir Leoncio
bcdfc5d22d Workaround for usage of MATLAB any() (#25) 2023-08-09 15:08:00 +02:00
Waldir Leoncio
b75d38fee4 Fixed argument passing (#25) 2023-08-09 14:45:43 +02:00
Waldir Leoncio
3d3131b68c squash! Replaced 1:npops with seq_len(npops) (#25) 
Replaced 1: with seq_len() and seq_along() (#25).

Helps working around NULL and 0 values.
 2023-08-09 14:40:09 +02:00
Waldir Leoncio
7bb1a8181e Commented-out debugging print() usage (#25) 2023-08-09 14:19:06 +02:00
Waldir Leoncio
f93f7c7de9 Replaced 1:npops with seq_len(npops) (#25) 2023-08-09 14:18:43 +02:00
Waldir Leoncio
5d3acc7cb0 Improved messages (#25) 2023-08-09 14:18:20 +02:00
Waldir Leoncio
3ab0a73a02 Added iter limit to prevent infinite loop (#25) 2023-08-09 14:17:54 +02:00
Waldir Leoncio
b034158e2b Improved handling of NULL objects (#25) 2023-08-09 14:17:17 +02:00
Waldir Leoncio
843a929938 Syntax fix (#25) 2023-08-09 14:16:04 +02:00
Waldir Leoncio
15da6cdced Improved argument retrieval on greedyMix() (#25) 2023-08-09 13:13:50 +02:00
Waldir Leoncio
bfeb2796c2 Improved example (#25) 2023-08-09 13:13:16 +02:00
Waldir Leoncio
ba968e77d5 Syntax fix to indMix() (#25) 2023-08-09 13:12:18 +02:00
Waldir Leoncio
3069577ebd Removing handleData() from greedyMix() (#25) 
Apparently that function is only used if the input is Genepop or BAPS format. However, its code might be useful for reducing some of the input of greedyMix(), as it contains the calculation for them.
 2023-08-09 12:50:33 +02:00
Waldir Leoncio
cae1fe4c1e Incorporating subfunctions of greedyMix() (#25) 2023-08-09 12:06:09 +02:00
Waldir Leoncio
103dc6acd6 Added MATLAB code from original greedyMix() (#25) 2023-08-09 11:26:29 +02:00
Waldir Leoncio
bf7d05eb8d Moved file import away from greedyMix() (#25) 2023-08-09 11:11:12 +02:00
Waldir Leoncio
7888012bf6 Add NEWS.md 2023-08-09 10:56:24 +02:00
Waldir Leoncio
687a6fb671 Moved used datasets to /isnt/extdata (#25) 2023-08-09 10:54:48 +02:00