BC_model: ESTIMATE BC MODEL

In agarciaEE/NINA: Niche Interaction Network Analyses

ESTIMATE BC MODEL

Description

Transforms environmental niche in base to species interactions

Usage

BC_model(
  x,
  y,
  A.matrix = NULL,
  C.matrix = NULL,
  D = 1,
  method = c("composition", "densities"),
  eval = TRUE,
  relative.niche = T,
  K = NULL,
  sample.pseudoabsences = TRUE,
  R = 100,
  res = NULL,
  plot.eval = FALSE,
  rep = 100,
  th = NULL,
  ras = NULL,
  best.th = c("accuracy", "similarity"),
  combine.regions = F,
  cor = F,
  type = c("region", "global")
)

Arguments

x	NINA EN model object for species group one
y	NINA EN model object for species group two
A.matrix	m by n matrix indicating the association coefficient (-1 to 1). m are species to be modeled as rows and n interactions as columns
C.matrix	n by n matrix indicating the competition coefficient between interactions (0 to 1).
D	Numeric value indicating independence from biotic associations. Value must be comprised between 0 and 1.
method	Method; abundances or composition
eval	Boolean whether to evaluate the model
relative.niche	Logical
K	= Carrying capacity of each environmental cell
sample.pseudoabsences	Boolean to whether sample pseudo-absences
R	Integer. size of the grid for the niche space estimate. R represents number of columns and rows
res	spatial resolution
plot.eval	Logical to whether plot the evaluation
rep	number of randomzation tests
th	threshold to perform cut off for model evaluation
ras	raster to constrain pseudoabsences sampling in model evalluation
best.th	method to select the best thresholt. Default is "similarity"
combine.regions	Logical. Whether to combine regional niche models into a global one
cor	Logical
type	String indicating whether to perform at a region or a global level. Note that if models have not been estimated at a region level and it is selected it will produce an error

Value

NINA model

Examples

## Not run: 
EN1 <- EN_model(env_data, occ_data1, cluster = "env", n.clus = 5)
EN2 <- EN_model(env_data, occ_data2, cluster = "env", n.clus = 5)
BC <- BC_model(EN1, EN2, A.matrix = int_matrix)

## End(Not run)

agarciaEE/NINA documentation built on Jan. 9, 2025, 10:09 a.m.