myRDA: RDA

In pctax: Professional Comprehensive Omics Data Analysis

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"
)

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

Value

rda/cca

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)

pctax documentation built on May 29, 2024, 10:03 a.m.