ourMELONS/TODO.md

Roadmap for next stable release

Minimum requirements

For the first stable release of rBAPS, the following features should be implemented:

• Clustering of populations (import greedyPoPMix.m from BAPS)
• Clustering of individuals (import greedyMix.m from BAPS)
• Spatial clustering of populations (import spatialPoPMixture.m from BAPS)
• Spatial clustering of individuals (import spatialMixture.m from BAPS)
• Admixture analysis (import admix1.m from BAPS)

Note to contributors: as tasks get finished, please update this file with an x and keep it there. This should help us fill out a changelog for an eventual stable release.

Wishlist

The list below contains non-essential but nice-to-have tasks for the next stable release.

• Implement sparse matrix optimizations from fastbaps
• Standardize capitalization of function names
• Standardize capitalization of function arguments
• Replace redundant functions (ex.: randga)

Known pitfalls

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.

As general remarks, one should keep in mind that:

• 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).
• Some clobal variables have been added as a new (last) argument to the function they appear in.
• 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.

Functional differences in rBAPS functions

Function	Argument	Value	Matlab output	R output
ownNum2Str	number	NaN	'NAN'	error
ownNum2Str	number	<vector>	'<vector elements>'	'<vector elements>' + warning
repmat	length(n)	> 2	> 2D matrix	2D matrix

Functional differences in base Matlab functions

Function	Matlab output	R output
max	Can handle complex numbers	Cannot handle complex numbers