Merge pull request #3 from jianan/master

use list instead of data.frame
sim_meiosis.cpp: use std::copy instead of loop-based copying
Fix bug in simulation for Stahl model

 - for simulation of no. chiasmata from process with no interference,
   had the wrong mean; was L/100*p but should be L/50*p

 - also added a couple of R:: for calls to runif()
Avoid repeated calls to RNGScope

 - really need it in sim_meiosis
 - not needed in sim_crossovers unless called from R
Oops! some of those R:: should've been Rcpp::
Back to avoiding repeated calls to RNGScope

 - also ensure call to RNGScope within sim_meiosis

 - doesn't pass tests, but that's because of the bug fix for Stahl model
   (don't commit until you've run the tests!)
Fix tests of sim_meiosis

  - bug fix re stahl model results in different simulation results in
    tests/testthat/test-sim_meiosis.R
Update version + date

[skip ci]
Line break in ReadMe

[skip ci]
ReadMe: change url biostat.wisc.edu/~kbroman -> kbroman.org
[skip ci]
convert2geno: force output to be matrix of _integers_
Add tests of convert2geno
convert2geno: change coding for multi-allele case

  - instead of 2^g1 + 2^g2, use 2^(g1-1) + 2^(g2-1)
Move convert2geno from R to c++
convert2geno: work with matrix not vector

 - Was working with IntegerVector and then copying to IntegerMatrix,
   'cause I'd not figured out how to deal with a matrix as if it's a
   vector.

 - IntegerMatrix has no .size(), but you can get
      int n = mat.nrow() * mat.ncol()
   then do like for(int i=0; i<n; i++) mat[i] = ...
Move get_geno from R to c++
Fix doc'n re sim_meiosis: data frame -> list
[skip ci]
convert2geno: founder_geno as optional arg, to give SNP genotypes

 - founder_geno must be matrix of 1's and 2's, taken to be the two
   alleles at a set of SNPs
 - output then is matrix of 1's, 2's, and 3's
convert2geno.cpp: Add a bunch of const declarations
Add a bunch more const declarations in c++ code