permanova_test {mixtree} | R Documentation |
Perform PERMANOVA on Sets of Transmission Trees
Description
Tests for topological differences between sets of transmission trees using PERMANOVA (via vegan::adonis2
).
Usage
permanova_test(
...,
within_dist = patristic,
between_dist = euclidean,
test_args = list()
)
Arguments
... |
Two or more sets of transmission trees. Each set is a list of dataframes with columns |
within_dist |
A function to compute pairwise distances within a tree. Takes a dataframe, returns a square matrix. Default is |
between_dist |
A function to compute distance between two trees. Takes two matrices, returns a numeric value. Default is |
test_args |
A list of additional arguments to pass to |
Value
A vegan::adonis2
object containing the test results.
Examples
set.seed(1)
# No difference in the sets
setA <- replicate(10, igraph::as_long_data_frame(
make_tree(n_cases = 10, R = 2, stochastic = TRUE)
),
simplify = FALSE
)
setB <- replicate(10, igraph::as_long_data_frame(
make_tree(n_cases = 10, R = 2, stochastic = TRUE)
),
simplify = FALSE
)
permanova_test(setA, setB)
# Difference in the sets
setC <- replicate(10, igraph::as_long_data_frame(
make_tree(n_cases = 10, R = 4, stochastic = TRUE)
),
simplify = FALSE
)
permanova_test(setA, setB, setC)
[Package mixtree version 0.0.1 Index]