An R function implementing the "All Marker Alleles" (AMA) algorithm

The "AMA" R function implements the "All Marker Alleles" algorithm as described in (Hayano-Kanashiro et al. 2017). 
For details of the algorithm please see the supplementary file "ece32754-sup-0001-DataS1.pdf" of that paper that you can download from the URL:

https://onlinelibrary.wiley.com/doi/10.1002/ece3.2754

Download directly from ece32754-sup-0001-DataS1.pdf

In summary, given a matrix of accessions (rows) and frequencies of different genetic markers (columns), the algorithm selects the minimum collection of accessions that contains all genetic markers.

In many cases this algorithm dramatically reduces the collection of accessions to a "core" collection which represents all genetic diversity present in the larger original collection. This is useful to prioritize germplasm for conservation proposes.

Additionally, the function produces a rareness coefficient for each one of the accessions. This could be also useful to prioritize conservation of germplasm.

The algorithm is exemplified with a collection of 1338 Mexican maize accessions which are genotyped for a total of 333 combination of SSR marker/allele combinations; see 

Martínez O., Ceniceros-Ojeda A., Hayano-Kanashiro C., Reyes-Valdés H., Pons-Hernández J.L. and Simpson J. "Criteria for prioritizing selection of Mexican maize landrace accessions for conservation in situ or ex situ based on phylogenetic analysis". 2023 (In preparation).