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Data
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Data is from
Roewer, 2009, A Y-STR database of Iranian and Azerbaijanian minority populations.
available at http://www.sciencedirect.com/science/article/pii/S1872497309000829 .

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Important note
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Haplotypes can only have integer alleles (no null and intermediate as e.g. 10.2).
This is a limitation of the mathematical model. 
We want to remove this limitation, but it is not clear how this is done best.

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Directories
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data: Contains data from source mentioned above (just for example)
R: Contains R-code to analyse the data

Working directory must be R.

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Details
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data/data-haplotypes.csv
  The actual haplotype database.
  
data/data-coords.csv
  Coordinates (long/lat) of the locations, for plotting on maps.

data/data-fst.csv
  Fst values of the data (found using Arlequin), for comparing with 
  results from the discrete Laplace method.

R/include-load-data.R
  Load the data. Remove haplotypes with intermediate and null alleles.

R/include-fit-model.R
  Fit a discrete Laplace model. Note, that caching (to fits directory) is used.

R/include-misc.R
  Misc helping function(s).

R/analyse-hapfreq.R
  Shows how to estimate haplotype frequencies.

R/analyse-mixtures.R
  Shows how to separate mixtures.

R/analyse-phist.R
  Compare Fst values (from Arlequin) with similar quantaties from the 
  discrete Laplace method.

R/analyse-cluster.R
  Cluster analysis.

R/export-arlequin.R
  Export data to Arlequin s.t. Fst values can be calculated. Creates file
  "out-iran-db.arp".

