Description Usage Arguments Details Value Examples
Compute the total number of alleles in a sample.
1 | number.of.alleles(tree.with.mutations)
|
tree.with.mutations |
an object generated by the |
Once the sim.tree
and add.mutations
command lines have been executed, number.of.alleles
can be used to compute the number of alleles in the sample
Total number of alleles in the sample contained in the object ‘history’
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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)
## This is to compute the total number of alleles in the sample for that history
number.of.alleles(history)
|
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