procrutes_test: Procrutes test for dissimilarity matrices

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

Description

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

Usage

procrutes_test(
  spec,
  env,
  group = NULL,
  procrutes.fun = "protest",
  spec.select = NULL,
  env.select = NULL,
  use = "everything",
  spec.pre.fun = "identity",
  spec.pre.params = list(),
  env.pre.fun = spec.pre.fun,
  env.pre.params = spec.pre.params,
  seed = 123,
  ...
)

Arguments

...	extra params passing to procrutes.fun.
spec, env	data frame object.
group	vector for rows grouping.
procrutes.fun	string, name of procrutes test function. "protest" will use vegan::protest() (default). "procuste.randtest" will use ade4::procuste.randtest(). "procuste.rtest" will use ade4::procuste.rtest().
spec.select, env.select	NULL (default), numeric or character vector index of columns.
use	one of "everything", "complete" or "pairwise".
spec.pre.fun, env.pre.fun	string, function name of transform the input data.
spec.pre.params, env.pre.params	list, extra parameters for spec/env.pre.fun.
seed	a integer value.

Value

a data frame.

Author(s)

Houyun Huang, Lei Zhou, Jian Chen, Taiyun Wei

Examples

## Not run: 
library(vegan)
data("varespec")
data("varechem")
procrutes_test(varespec, varechem)
procrutes_test(varespec, varechem, procrutes.fun = "procuste.randtest")
procrutes_test(varespec, varechem,
            spec.select = list(spec01 = 1:6, spec02 = 7:12))
procrutes_test(varespec, varechem, spec.pre.fun = "mono_mds",
            spec.select = list(spec01 = 1:6, spec02 = 7:12),
            env.select = list(env01 = 1:4, env02 = 5:14))
set.seed(20191224)
sam_grp <- sample(paste0("sample", 1:3), 24, replace = TRUE)
procrutes_test(varespec, varechem, group = sam_grp)

## End(Not run)

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