Description Usage Arguments Value Examples
This function takes sliding windows of a specified length over an MCMC chain and calculates the split frequency of clades within that window. It allows users to see whether the chain is visiting different areas of treespace.
1 | slide.freq(chains, burnin = 0, window.size = 20)
|
chains |
A list of rwty.chain objects. |
burnin |
The number of trees to eliminate as burnin. Defaults to zero. |
window.size |
The number of trees to include in each window (note, specified as a number of sampled trees, not a number of generations) |
A list of rwty.slide objects, one per chain in the input list of chains. Each rwty.slide object contains the frequencies of clades in the sliding windows, and a translation table that converts clade groupings to factors.
1 2 3 4 5 | ## Not run:
data(fungus)
slide.data <- slide.freq(fungus, burnin=20)\
## End(Not run)
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