ses.comdistnt2: Standardized effect size of inter-community MNTD (betaMNTD,...

Description Usage Arguments Details Value

View source: R/ses.comdistnt2.R

Description

Standardized effect size of MNTD (mean nearest taxon distance) separating taxa in two communities, a measure of phylogenetic beta diversity

Usage

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ses.comdistnt2(samp, dis, method = "quasiswap", fixedmar = "both",
  shuffle = "both", strata = NULL, mtype = "count", burnin = 0,
  thin = 1, abundance.weighted = FALSE, exclude.conspecifics = FALSE,
  runs = 999, cores = 1)

Arguments

samp

Community data matrix with samples as rows

dis

Distance matrix (generally a phylogenetic distance matrix)

method

Character for method used for the swap algorithm ("swap", "tswap", "quasiswap", "backtrack"). If NULL no swap algorithm is applied (uses permatfull from vegan). 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, see details.

strata

Numeric vector or factor with length same as nrow(m) for grouping rows 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.

abundance.weighted

Should mean nearest taxon distances for each species be weighted by species abundance? (default = FALSE)

runs

Number of randomizations

cores

Number of cores to use for parallel computing

Details

See permat (vegan) for detailed options

Value

A list of results:


Russel88/MicEco documentation built on Oct. 24, 2018, 3:07 p.m.