ses.UniFrac: Standardized effect size of unifrac

ses.UniFracR Documentation

Standardized effect size of unifrac

Description

Standardized effect size of unifrac

Usage

ses.UniFrac(
  physeq,
  method = "taxa.labels",
  fixedmar = "both",
  shuffle = "both",
  strata = NULL,
  mtype = "count",
  burnin = 0,
  thin = 1,
  weighted = TRUE,
  normalized = TRUE,
  runs = 99,
  cores = 1
)

Arguments

physeq

phyloseq-class, containing at minimum a phylogenetic tree and otu table

method

"taxa.labels" shuffles labels in phylogenetic tree (Ignores fixedmar, shuffle, strata, mtype). If NULL then no swap algorithm is applied (i.e. uses permatfull from vegan). Else the method used for the swap algorithm ("swap", "tswap", "quasiswap", "backtrack"). If mtype="count" the "quasiswap", "swap", "swsh" and "abuswap" methods are available (see details).

fixedmar

Character, stating which of the row/column sums should be preserved ("none", "rows", "columns", "both").

shuffle

Character, indicating whether individuals ("ind"), samples ("samp") or both ("both") should be shuffled.

strata

Numeric vector or factor for grouping samples within strata for restricted permutations. Unique values or levels are used.

mtype

Matrix data type, either "count" for count data, or "prab" for presence-absence type incidence data.

burnin

Number of null communities discarded before proper analysis in sequential ("swap", "tswap") methods.

thin

Number of discarded permuted matrices between two evaluations in sequential ("swap", "tswap") methods.

weighted

Should unifrac be weighted by species abundance? (default = TRUE)

normalized

(Optional). Logical. Should the output be normalized such that values range from 0 to 1 independent of branch length values? Default is TRUE. Note that (unweighted) UniFrac is always normalized by total branch-length, and so this value is ignored when weighted == FALSE.

runs

Number of randomizations

cores

Number of cores to use for UniFrac of null communities. Default is 1

Details

See permat (vegan) for detailed options on permutation

Value

A list of results:

  • unifrac.obs - Observed unifrac between communities

  • unifrac.rand.mean - Mean unifrac between null communities

  • unifrac.rand.sd - Standard deviation of unifrac between null communities

  • unifrac.obs.rank - Rank of observed unifrac vs. null unifrac

  • unifrac.obs.z - Standardized effect size of unifrac vs. null unifrac (= (unifrac.obs - unifrac.rand.mean) / unifrac.rand.sd)

  • unifrac.obs.p - P-value (quantile) of observed unifrac vs. null communities (= unifrac.obs.rank / runs + 1)


Russel88/MicEco documentation built on Nov. 24, 2022, 2:33 a.m.