Description Usage Arguments Value Examples
This function takes one or more rwty.chain ojects and returns a plot of CSF within each chain as the MCMC progresses. The solid line with points shows the Average Change in Split Frequencies (ACSF; it is average across the changes in split frequencies from all clades in the analysis) between this window and the previous window The grey ribbon shows the upper and lower 95
1 2 | makeplot.acsf.cumulative(chains, burnin = 0, window.size = 20,
facet = TRUE)
|
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) |
facet |
(TRUE/FALSE). TRUE: return a single plot with one facet per chain; FALSE: return a list of individual plots with one plot per chain |
output A plof of the CSF between sliding windows over all chains
acsf.plot A ggplot object, or list of ggplot objects
1 2 3 4 5 | ## Not run:
data(fungus)
makeplot.acsf.cumulative(fungus, burnin=20)
## End(Not run)
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