find_bestq: find_bestq This function computes the hill numbers for...

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

Description

find_bestq This function computes the hill numbers for TD/PD/FD with q_nb different q between q_min and q_max it selects the q for wich the r² of lm(esth_score~hill_number) is maximized and finally compute the hill numbers for this q

Usage

find_bestq(
  div,
  data,
  tree = NULL,
  dij = NULL,
  tau = NULL,
  esth,
  q_min,
  q_max,
  q_nb,
  ncores,
  log_trans = FALSE
)

Arguments

div	the diversity worked with : c(TD,PD,FD)
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.
tau	threshold for dij (Chao et al. 2019). Default is NULL, recommended value is mean(dij).
esth	a two columns matrix of the aesthetic scores. rownames(esth) must be the same than rownames(data).
q_min	min value for q
q_max	max value for q
q_nb	number of values to test for q in range q_min;q_max
ncores	number of cores to use
log_trans	logical. Default is FALSE. if TRUE the tested relation is lm(log(esth)~log(hill_index))

Value

hill_number_q -> vector of the hill number with q maximizing the R² for all assemblages bestq -> the q maximizing the R² of lm(esth_score~hill_number) bestr2 -> max value of R² all_r2_q -> all q value tested and the associated R²

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