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Lindsay Clark edited this page Nov 1, 2015
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- Export functions for diploid data, since version 1.4 can convert allotetraploid or allohexaploid data to a diploid format.
- Use the distribution of genotypes to give a probabalistic estimate of whether a locus is polysomic or disomic.
- Improve computational efficiency on inter-individual distance measures. (I tried vectorizing some of the code for Bruvo.distance and actually made it slower, but if I ever learn C maybe a compiled version would be faster.)
- Given probabilities of unambiguous genotypes (genotypeProbs function), randomly generate an unambiguous dataset. This could then be passed to software such as adegenet that allows for polyploidy but not allele copy number ambiguity.
- More population statistics (Weir and Cockerham 1984, etc.).
- Parentage analysis
- Options for handling data where allele copy number is known.
- Some relatedness coefficients for unambiguous genotypes, to be used with meandistance.matrix2.