Description Usage Arguments Details Value Examples
Add mutations on a coalescent tree.
1 | add.mutations(tree,mu,graphics = TRUE, labels = TRUE)
|
tree |
an object generated by the |
mu |
mutation rate |
graphics |
a logical variable, which is TRUE if the user wants to plot the history, and FALSE otherwise |
labels |
a logical variable, which is TRUE if the user wants labels to be plotted on the tree, and FALSE otherwise |
Adds mutation on a coalescent tree generated by the sim.tree
command, using the mutation rate ‘mu’. The mutation model is an Infinite Allele Model. If ‘graphics = TRUE’, then a coalescent tree is drawn, with mutations sketched on the tree. Allelic states of the leafs are represented with different colors. If ‘labels = TRUE’, then the labels are drawn on the graph.
an object of class ‘history’ which is a list with components:
state |
the allelic state of each leaf |
node |
the list of nodes (internal and leafs) in the tree |
ancestor |
the ancestor of each node |
label |
the label of each leaf |
branch.length |
the length of the branch above each node |
1 2 3 4 5 6 7 8 9 10 | ## This is to simulate a coalescent tree using the Hudson's algorithm,
## with 20 sampled lineages. In this example, the current population size
## is 100. It was 1000 before a bottleneck that occurred 50 generations ago
tree <- sim.tree(method = "hudson",sample = 20,current = 100,ancestral = 1000,time = 50)
## This is to generate a history, with a graphical outputs with labels,
## using a mutation rate of 0.001
history <- add.mutations(tree,mu = 0.001,graphics = TRUE, labels = TRUE)
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