standefsize: standefsize This function generates nb null assemblages of...

In JulietteLgls/aesthcorareef: Supplementary materail to the article "An integrated approach to measure aesthetic and ecological values of coralligenous reefs"

Description

standefsize This function generates nb null assemblages of each possible number of species in the data table computes the mean and sd of the div index on these assemblages computes the deviation between the observed div and the SES_div

Usage

standefsize(
  div,
  data,
  tree = NULL,
  dij = NULL,
  tau = NULL,
  q,
  hilldiv,
  log_trans = FALSE,
  nb = 10,
  mcores = 20
)

Arguments

div	the diversity worked with : c(PD,FD) if div = PD, hillfun = relab_hill_phylo if div = FD, hillfun = FD_MLE
data	matrix of relative abundance. Quadrat_code must be rownames and Species_name must be colnames
tree	phylotree generated by ape::read_tree. Default is NULL. Only needed if div = PD
dij	distance matrix generated by ade4::dist.kab (Pavoine et al. 2009). Default is NULL. Only needed if div = FD
tau	threshold for dij (Chao et al. 2019). Default is NULL, recommended value is mean(dij). Only needed if div = FD
q	the value of q to use, same used to compute the "observed" PD or FD
hilldiv	vector of hillnumber (qPD or qFD) for all assemblages
log_trans	logical. defaukt is FALSE. if TRUE, the SES if computed on the log of the index
nb	number of null models to generate (9999 is default)
mcores	number of cores to use

Value

a matrix of three columns : observed hillnumber, nb of species, SES hill number

JulietteLgls/aesthcorareef documentation built on Dec. 18, 2021, 2:32 a.m.