Description Usage Arguments Value Examples
This function takes two or more rwty.chain ojects and returns a plot of ASDSF as the run progresses. The solid line with points shows the Average Standard Deviation of Split Frequences at the current generation The grey ribbon shows the upper and lower 95
1 | makeplot.asdsf(chains, burnin = 0, window.size = 20, min.freq = 0)
|
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 between each point at which the ASDSFs is calculated (note, specified as a number of sampled trees, not a number of generations) |
min.freq |
The minimum frequency for a node to be used for calculating ASDSF. |
output A cumulative plot of ASDSF across all chains
1 2 3 4 5 6 | ## Not run:
data(fungus)
p <- makeplot.asdsf(fungus, burnin = 20)
p
## End(Not run)
|
Loading required package: ape
Loading required package: ggplot2
[1] "Creating ASDSF plot"
$asdsf.plot
Warning messages:
1: Transformation introduced infinite values in continuous y-axis
2: Transformation introduced infinite values in continuous y-axis
3: Transformation introduced infinite values in continuous y-axis
4: Transformation introduced infinite values in continuous y-axis
5: Transformation introduced infinite values in continuous y-axis
6: Transformation introduced infinite values in continuous y-axis
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.