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Prepare CRAN release #25

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6 of 10 tasks
wleoncio opened this issue Feb 28, 2023 · 1 comment
Open
6 of 10 tasks

Prepare CRAN release #25

wleoncio opened this issue Feb 28, 2023 · 1 comment
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wleoncio commented Feb 28, 2023 •
edited

  • Internalize functions other than greedyMix()
  • Stop to-be-implemented functions on greedyMix()
  • Add examples to greedyMix()
  • Incorporate functions that performs clustering on greedyMix()
  • Achieve minimal input of greedyMix()
  • Achieve minimal input of greedyMix() with indMix() parsing
  • Make sure output of greedyMix() for FASTA files is correct (minimum quality for CRAN release)
  • Decide package function (rBAPS or BAPS?)
  • Create GH issue form for easy reporting
  • Add welcome message on load with URL to issues
@wleoncio wleoncio self-assigned this Feb 28, 2023
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Internalized all functions except greedyMix() and load_fasta() (#25)
7aff7bb
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Moved used datasets to /isnt/extdata (#25)
687a6fb
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Moved file import away from greedyMix() (#25)
bf7d05e
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Added MATLAB code from original greedyMix() (#25)
103dc6a
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Incorporating subfunctions of greedyMix() (#25)
cae1fe4
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Removing handleData() from greedyMix() (#25)
3069577 
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.
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Syntax fix to indMix() (#25)
ba968e7
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Improved example (#25)
bfeb279
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Improved argument retrieval on greedyMix() (#25)
15da6cd
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Syntax fix (#25)
843a929
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Improved handling of NULL objects (#25)
b034158
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Added iter limit to prevent infinite loop (#25)
3ab0a73
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Improved messages (#25)
5d3acc7
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Replaced 1:npops with seq_len(npops) (#25)
f93f7c7
wleoncio added a commit that referenced this issue Aug 11, 2023
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Commented-out debugging print() usage (#25)
7bb1a81
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
squash! Replaced 1:npops with seq_len(npops) (#25)
3d3131b 
Replaced 1: with seq_len() and seq_along() (#25).

Helps working around NULL and 0 values.
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Fixed argument passing (#25)
b75d38f
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Workaround for usage of MATLAB any() (#25)
bcdfc5d
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Delayed resolution of FIXMEs (#25)
2739442
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Syntax fix (#25)
85c8c01
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Added missing documentation for arguments (#25)
bd932e2
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Fixed test text (#25)
a51816d
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Added numeric output option to load_fasta() (#25)
95d9d65
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Improved handleData() to handle FASTA (#25)
f47e13d
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Incorporated handleData() on greedyMix() (#25)
3537f18
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Fixed to indMix (#25)
372891f
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Partial reversion of b034158 (#25)
177685b 
It should be OK for Z to be NULL. This currently triggers an issue on initialCounts(), which should be fixed
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Improved printing (#25)
44e418f
wleoncio added a commit that referenced this issue Aug 11, 2023
@wleoncio
Fixed syntax (#25)
cfb71bf
wleoncio added a commit that referenced this issue Sep 11, 2023
@wleoncio
Fixed basic parsing of FASTA files (#25)
7682838
wleoncio added a commit that referenced this issue Sep 11, 2023
@wleoncio
Improved handling of supported formats for greedyMix() (#25)
3e4044b
wleoncio added a commit that referenced this issue Sep 11, 2023
@wleoncio
Adjusted unit tests for #25
ce954bf
wleoncio added a commit that referenced this issue Sep 11, 2023
@wleoncio
Merge branch 'issue-25' into develop
59fbb0a 
* 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)
  ...
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wleoncio commented Sep 18, 2023 •
edited

Some ideas/insights after a meeting with Jukka:

  • Fasta dataset: generate more data
    • Replicate the dataset 10-20x for each individual (row)
    • Generate more columns (ACGT alphabet)
  • Set cluster default to 5 (all dimensions of all generic objects?)
    • Alternatively, re-dim used generics before handling them
  • Investigate df_fasta$data
    • It has 6 rows when it should have 5 (looks like MATLAB also does that)
    • The first row is just zeros: may be an error (handleData() adds a row of zeros, even on MATLAB)
    • Why 99 columns when each individual has 100 letters? (handleData() drops column with 1 unique letter)
  • Investigate ninds calculation
    • Perhaps indMix() gets stuck because ninds is at 2 (when there are 5 individuals)
    • A higher ninds, say 5, should help
  • Create new haploid data from BAPS_format_clustering_diploid.txt (are BAPS files going to be supported? No pre-processing available (importFile(), handleData())
    • Each individual (integer in last column) has two rows assigned to them (ergo, "diploid")
    • Some creatures have 4 rows (tetraploid)
    • Erase every other row to create a sinthetic haploid example

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