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351 commits

Author SHA1 Message Date
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
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
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
ceaf7eca4b Added verbose argument to writeMixtureInfo() 2023-09-11 14:06:45 +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
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
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
687a6fb671 Moved used datasets to /isnt/extdata (#25) 2023-08-09 10:54:48 +02:00
Waldir Leoncio
7aff7bbb82 Internalized all functions except greedyMix() and load_fasta() (#25) 2023-08-09 09:36:15 +02:00
Waldir Leoncio
8bddd70781 Syntax fixes (#3) 2023-02-16 15:30:15 +01:00
Waldir Leoncio
a8cae95c82 Added tests, fixed subfunctions (#3) 2023-02-10 15:11:54 +01:00