IdentifyStructure2: Run the EMS analysis and identify the idealized structure

View source: R/IdentifyStructure2_function.R

IdentifyStructure2R Documentation

Run the EMS analysis and identify the idealized structure

Description

This function is the same as IdentifyStructure but uses apply functions intead of for loops. It enables multicore processing, which may be useful if you have too many metacommunties (> 100). It simply runs the functions Coherence(), Turnover() and BoundaryClump() from package metacom and automaticaly identify the idealizes structure according to Presley et al. 2010 "A comprehensive framework for the evaluation of metacommunity structure". Oikos 119 (6).

Usage

IdentifyStructure2(
  comm,
  names = NULL,
  scores = 1,
  CoherenceMethod = "curveball",
  turnoverMethod = "EMS",
  sims = 1000,
  order = T,
  orderNulls = F,
  seed = NULL,
  fill = T,
  round = NULL,
  elapsed_time = TRUE,
  multicore = TRUE,
  n_cores = NULL
)

Arguments

comm

A list of incidence matrices (i.e. metacommunities).

names

The names of the metacommunities. A vector with the same length as the list of metacommunities.

scores

Numeric. What axis of the CA should be used for ordination? (Defaut is 1)

CoherenceMethod

null model randomization method used by 'nullmaker' to compute Coherence. See the Coherence function from package metacom. (default is "curveball")

turnoverMethod

null model randomization method used by 'nullmaker' or 'EMS' to use the approach outlined in Leibold and Mikkelson 2002. See the Turnover function from package metacom. (default is "EMS")

sims

Number of randomizations (default is 1000)

order

Should the original matrix be ordered by reciprocal averaging?

orderNulls

Should the null communities be ordered? (default is TRUE)

seed

seed for simulating the null model. Null matrices should be repeatable.

fill

should embedded absences be filled before the statistics are calculated? (default is TRUE)

round

Numeric. Should numeric results be rounded? If so, how many digits? Defaut is set to NULL.

elapsed_time

Logical. Should a message with the elapsed time be returned?

multicore

Logical. Should multicore processing be enabled? The default number of cores is the total number of cores minus 1. Alternative number of cores can be set by the n_cores argument.

n_cores

Number of cores to be used with multicore processing. It will be ignored if multicore is set to FALSE.


RodolfoPelinson/AtlanticForestMetacommunity documentation built on Aug. 5, 2023, 3:53 p.m.