landscape.coalinput: Add loci and individuals based upon output from SimCoal 2.0
In rmetasim: An Individual-Based Population Genetic Simulation Environment

Description Usage Arguments Details Value Author(s) Examples

Take rmetasim object and replaces the locus and individual data based on the results of a SimCoal run stored in Arlequin format files

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  ## must be called AFTER integer, switch, and float params have been created
   landscape.coalinput(rland, npp=200, arlseq = NULL, arlms = NULL, seqsitemut=1e-7,
                               msmut = 5e-4, mut.rates = NULL)

`rland`	partially created landscape object, required
`npp`	number per population. Scalar or vector of length equal to number of populations. If scalar, value replicated
`arlseq`	name of the Arlequin format file containing a single locus of haploid sequence data for any number of populations
`arlms`	name of the Arlequin format file containing a single locus of diploid microsatellite data for any number of populations
`seqsitemut`	mutation rate for sequence data
`msmut`	mutation rate for diploid genotypic data
`mut.rates`	alternative means to specify mutation rates. Legal values are either NULL or a vector of rates equal to the number of loci to simulate. If NULL, SSR loci are assigned msmut as a mutation rate and sequence-based loci, seqsitemut. If a vector, ovrrides msmut and seqsitemut

This function provides part of an interface between R and SimCoal, an environment for simulating sequences and microsatellite genotypes from coalescent trees. SimCoal can be used to simulate a standing crop of alleles and their relationships under a wide range of demographies. It returns haplotypes and genotypes of individuals in Arlequin format files.

If either 'arlseq' or 'arlms' are set to NULL, their corresponding data will not be included in the landscape (for example if arlseq=NULL, only diploid genotypes will be imported

The genotypes in the Arlequin files are used to create rland\$loci objects based upon their frequencies and states. These rland\$loci sub-objects are then used to populate the rland\$individuals sub-object.

The number of populations in the Arlequin files should be the same among genetic locus types (sequence versus microsatellite) and the rland\$intparam\$habitats parameter. The per-population frequency data will be used in creating individuals

an rmetasim object with new loci and individuals

Mark Bravington and Allan Strand

  exampleland <- landscape.new.empty()
  exampleland <- landscape.new.intparam(exampleland, s=2, h=2)
  exampleland <- landscape.new.floatparam(exampleland)
  exampleland <- landscape.new.switchparam(exampleland)

#  exampleland <- landscape.coalinput(exampleland)
#  exampleland$loci