fitPNB: Fit using Probabilistic niche model

In TheoreticalEcosystemEcology/alien: Comparative analysis of interaction inference methods

Description

Model adegency matrix using probabilistic niche model

Usage

fitPNB(
  data,
  type,
  optimum,
  optimumMin,
  optimumMax,
  range,
  rangeMin,
  rangeMax,
  verbose = TRUE
)

Arguments

data	An object of the class alienData, see alienData.
type	Method to be used to estimate the model. Either 'P' (presence-only) or 'PA' (presence-absence), respectively.
optimum	A vector of two values defining the optimum intercept (first value) and slope (second value).
optimumMin	A vector of two values giving the minimum values the optimum intercept and slope can have, respectively.
optimumMax	A vector of two values giving the maximum values the optimum intercept and slope can have, respectively.
range	A vector of two values defining the range intercept (first value) and slope (second value).
rangeMin	A vector of two values giving the minimum values the range intercept and slope can have, respectively.
rangeMax	A vector of two values giving the maximum values the range intercept and slope can have, respectively.
verbose	Logical. Whether messages from the algorithm are shown (TRUE) or not (FALSE). Default is TRUE.

Details

This function is only designed to handle presence-only and presence-absence data. In addition, the function can only handle a single continuous trait for each species.

If there are any NAs in the species interaction data (the adjacency matrix), they will be automatically removed to estimate the presence-absence (PA) model parameters. If there are NAs in the traits, an error message will be sent.

Value

An object with a class alienFit and a class fitPNB.

Author(s)

Dominique Gravel and F. Guillaume Blanchet

TheoreticalEcosystemEcology/alien documentation built on Dec. 25, 2021, 5:57 p.m.