ggcor (version 0.9.6)

mantel_test: Mantel and partial mantel test for dissimilarity matrices

Description

Perform mantel test quickly and tidy up the data to data frame.

Usage

mantel_test(
  spec,
  env,
  env.ctrl = NULL,
  mantel.fun = "mantel",
  spec.select = NULL,
  env.select = NULL,
  spec.dist.method = "bray",
  env.dist.method = "euclidean",
  ...
)

Arguments

spec, env

data frame object.

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.

spec.dist.method

dissimilarity index (default is 'bray'), pass to method params of vegdist.

env.dist.method

dissimilarity index (default is euclidean'), pass to method params of vegdist.

...

extra params for mantel.fun.

See Also

vegdist, mantel, mantel.rtest, mantel.randtest.

Examples

# NOT RUN {
library(vegan)
data("varespec")
data("varechem")
mantel_test(varespec, varechem)
mantel_test(varespec, varechem, mantel.fun = "mantel.randtest")
mantel_test(varespec, varechem, mantel.fun = "mantel.randtest",
  spec.select = list(spec01 = 1:6, spec02 = 7:12))
mantel_test(varespec, varechem, mantel.fun = "mantel.randtest",
  spec.select = list(spec01 = 1:6, spec02 = 7:12),
  env.select = list(env01 = 1:4, env02 = 5:14))
nm <- names(varechem[1:9])
mantel_test(varespec, varechem, env.ctrl = varechem[10:14],
  mantel.fun = "mantel.partial",
  env.select = as.list(setNames(nm, nm)))
# }