permanova_test: Perform PERMANOVA on Sets of Transmission Trees

In mixtree: A Statistical Framework for Comparing Sets of Trees

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 from (infector) and to (infectee).
within_dist	A function to compute pairwise distances within a tree. Takes a dataframe, returns a square matrix. Default is patristic.
between_dist	A function to compute distance between two trees. Takes two matrices, returns a numeric value. Default is euclidean.
test_args	A list of additional arguments to pass to vegan::adonis2. Default is an empty list.

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)

mixtree documentation built on April 3, 2025, 8:01 p.m.