mantel_test: Mantel test

In houyunhuang/ggcor: Extended tools for correlation analysis and visualization

Description

Mantel and partial mantel test for dissimilarity matrices

Usage

mantel_test(
  spec,
  env,
  group = NULL,
  env.ctrl = NULL,
  mantel.fun = "mantel",
  spec.select = NULL,
  env.select = NULL,
  use = "everything",
  spec.dist.method = "bray",
  env.dist.method = "euclidean",
  seed = 123,
  ...
)

Arguments

...	extra params passing to mantel.fun.
spec, env	data frame object.
group	vector for grouping the rows.
env.ctrl	NULL (default), data frame.
mantel.fun	string, function of mantel test. "mantel" will use vegan::mantel() (default). "mantel.randtest" will use ade4::mantel.randtest(). "mantel.rtest" will use ade4::mantel.rtest(). "mantel.partial" will use vegan::mantel.partial() (default).
spec.select, env.select	NULL (default), numeric or character vector index of columns.
use	one of "everything", "complete" or "pairwise".
spec.dist.method	dissimilarity index (default is 'bray'), passing to method params of vegan::vegdist.
env.dist.method	dissimilarity index (default is euclidean'), passing to method params of vegan::vegdist().
seed	a integer value.

Value

a data.frame.

Author(s)

Houyun Huang, Lei Zhou, Jian Chen, Taiyun Wei

See Also

mantel_test.

Examples

## Not run: 
library(vegan)
data("varespec")
data("varechem")
mantel_test(varespec, varechem,
  spec.select = list(spec01 = 1:5, spec02 = 6:12))
mantel_test(varespec, varechem,
  spec.select = list(spec01 = 1:5, spec02 = 6:12),
  env.select = list(env01 = 1:5, env02 = 6:10, env03 = 11:14))
set.seed(20191224)
sam_grp <- sample(paste0("sample", 1:3), 24, replace = TRUE)
mantel_test(varespec, varechem, group = sam_grp)

## End(Not run)

houyunhuang/ggcor documentation built on July 22, 2020, 8:31 p.m.