IdentifyStructure: Run the EMS analysis and identify the idealized structure

In RodolfoPelinson/AtlanticForestMetacommunity: Gives the functions and data for the Analysis of Pelinson et al. 2021 "Disentangling the multiple drivers of amphibian metacommunity structure in the Atlantic Forest at multiple spatial scales"

Run the EMS analysis and identify the idealized structure

Description

This function 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

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

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?

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