Mantel test utilities for species-environment distance matrix correlation
Source:R/mantel_utils.R
mantel_utils.RdThese functions compute Mantel statistics between species and environmental
distance matrices. The implementation uses vegan::mantel and
vegan::mantel.partial directly, with a workflow designed for
ggNetView's heatmap-link visualization.
For each species column and each environmental column, builds a distance
matrix and runs Mantel test. Output format matches psych::corr.test
for drop-in use in gglink_heatmaps.
Runs Mantel test between each (spec_block, env_block) pair. Each block is a subset of columns. Uses full distance matrices per block. Output format is compatible with downstream processing when blocks are treated as single "species" and "env" units.
Usage
mantel_pairwise(
spec_df,
env_df,
method = c("pearson", "spearman", "kendall"),
alternative = c("two.sided", "less", "greater"),
permutations = 999L,
na_omit = TRUE
)
mantel_between_blocks(
spec,
env,
spec_select = NULL,
env_select = NULL,
test_type = c("mantel", "mantel.partial"),
env_ctrl = NULL,
method = c("pearson", "spearman", "kendall"),
spec_dist_method = "euclidean",
env_dist_method = "euclidean",
na_omit = TRUE,
permutations = 999L,
seed = NULL
)Arguments
- spec_df
Data frame or matrix of species abundances (samples as rows).
- env_df
Data frame or matrix of environmental variables (samples as rows).
- method
Correlation method:
"pearson","spearman", or"kendall".- alternative
Alternative hypothesis for the test.
- permutations
Number of permutations.
- na_omit
If
TRUE, remove incomplete cases.- spec
Data frame of species abundances.
- env
Data frame of environmental variables.
- spec_select
Named list of column indices or names for species blocks. E.g.
list(block1 = 1:5, block2 = 6:10).- env_select
Named list of column indices or names for env blocks.
- test_type
"mantel"or"mantel.partial".- env_ctrl
For
test_type = "mantel.partial", a data frame of controlling variables (same rows as spec/env).- spec_dist_method
Distance method for species matrix when using
mantel_between_blocks. One of"euclidean","bray","manhattan", etc. (seevegan::vegdist).- env_dist_method
Distance method for environmental matrix.
- seed
Random seed for reproducibility.