LDhat

Also, see myLD for a description of how I ended up bootstrapping for the linkage decay plot.

LDhat (manual) is what many have recommended to use to estimate rho (population-scaled recombination rate). r is the per-generation recombination rate. Good review here. However, it seems that LDhat won't draw those decay graphs - is this true?

I would like to use recombination to do two things:

1. Make a P. vivax recombination paper
2. Do a formal test of whether the P. falciparum subpopulations are clonal outbreaks. Planning to do this by measuring recombination / decay in the subpopulations and comparing that to similar sized random draws from the entire population.

To do #2 above, I could probably still use LDhat + bootstrapping, but I maybe won't get a figure out of it? Just a range of rhos?