47 lines
No EOL
3.1 KiB
Markdown
47 lines
No EOL
3.1 KiB
Markdown
# Roadmap for next stable release
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## Minimum requirements
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For the first stable release of rBAPS, the following features should be implemented:
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- [ ] Clustering of individuals (import `greedyMix.m` from BAPS)
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- [ ] Clustering of populations (import `greedyPoPMix.m` from BAPS)
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- [ ] Spatial clustering of individuals (import `spatialMixture.m` from BAPS)
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- [ ] Spatial clustering of populations (import `spatialPoPMixture.m` from BAPS)
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- [x] Admixture analysis (import `admix1.m` from BAPS)
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Note to contributors: as tasks get finished (translated, not necessarily tested), please update this file with an `x` and keep it there. This should help us fill out a changelog for an eventual stable release.
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## Wishlist
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The list below contains non-essential but nice-to-have tasks for the next stable release.
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- [ ] Implement sparse matrix optimizations from [`fastbaps`](https://github.com/gtonkinhill/fastbaps)
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- [ ] Implement plotting functionality from [`starmie`](https://github.com/sa-lee/starmie)
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- [ ] Standardize capitalization of function names
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- [ ] Standardize capitalization of function arguments
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- [ ] Replace redundant functions (ex.: `randga`)
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# Known pitfalls
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The following behavioral differences have been detected between the Matlab functions and their R counterparts. In order to save time, these differences will not be addressed, since they could require extensive reworking of a function. However, such differences may very well cause unexpected problems in some situations, which is why compiling this list is so important. The tables below might provide a good starting point for identifying and fixing bugs.
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As general remarks, one should keep in mind that:
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- For compliance with IEC 60559, the `round` in base R rounds .5 to the nearest even integer, whereas the homonym function in Matlab rounds up (or down, if negative).
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- Some clobal variables have been added as a new (last) argument to the function they appear in.
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- When a function is defined on Matlab with multiple outputs, as in `[y1, y2] = f(x)`, it will output only `y1` if called without assignment, as in `f(3)`, or if called with a one-length assignment, as in `a = f(3)`. In order to receive the full output, one must assign two variables to the left side of the assignment operator, as in `[a, b] = f(3)`. rBAPS Functions that might be affected by this behavior include `etsiParas`.
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## Functional differences in rBAPS functions
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| Function | Argument | Value | Matlab output | R output |
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| ----------------- | ------------------ | -------------- | --------------------- | ------------------------------- |
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| `ownNum2Str` | `number` | `NaN` | `'NAN'` | error |
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| `ownNum2Str` | `number` | `<vector>` | `'<vector elements>'` | `'<vector elements>'` + warning |
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| `repmat` | `length(n)` | `> 2` | > 2D matrix | 2D matrix |
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## Functional differences in base Matlab functions
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Function | Matlab output | R output
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-------- | ------------- | --------
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`max` | Can handle complex numbers | Cannot handle complex numbers |