pctax (version 0.1.1)

myRDA: RDA

Description

RDA

Usage

myRDA(
  otutab,
  env,
  norm = TRUE,
  scale = FALSE,
  choose_var = FALSE,
  direction = "forward",
  nperm = 499,
  verbose = TRUE,
  method = "rda",
  dist = "bray"
)
myCCA(
  otutab,
  env,
  norm = TRUE,
  scale = FALSE,
  choose_var = FALSE,
  nperm = 499,
  verbose = TRUE
)
myCAP(
  otutab,
  env,
  norm = TRUE,
  scale = FALSE,
  choose_var = FALSE,
  nperm = 499,
  verbose = TRUE,
  dist = "bray"
)

Value

rda/cca

Arguments

otutab

an otutab data.frame, samples are columns, taxs are rows.

env

environmental factors

norm

should normalize? (default:TRUE)

scale

should scale species? (default:FALSE)

choose_var

should choose variables? use forward step

direction

The direction of the stepwise selection, "both", "forward" or "backward", default is "forward"

nperm

number of permutation

verbose

verbose

method

"rda", "cca", "cap", "dbrda"

dist

The name of the dissimilarity (or distance) index for "cap" or "dbrda", for vegdist

See Also

vegdist;unifrac

Examples

data(otutab, package = "pcutils")
env <- metadata[, 6:10]
# RDA
myRDA(otutab, env) -> phy.rda
RDA_plot(phy.rda, "Group", metadata)