prab.sarestimate: Estimates SAR model from log-abundance matrix of prab-object.

In prabclus: Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data

Estimates SAR model from log-abundance matrix of prab-object.

Description

This is either an interface for the function errorsarlm for abundance data stored in an object of class prab implemented for use in abundtest, or, in case that spatial information should be ignored, it estimates a two-way additive unreplicated linear model for log-abundances on factors species and region.

Usage

prab.sarestimate(abmat, prab01=NULL,sarmethod="eigen",
                             weightstyle="C",
                             quiet=TRUE, sar=TRUE,
                             add.lmobject=TRUE)

Arguments

abmat	object of class prab.
prab01	presence-absence matrix of same dimensions than the abundance matrix of prabobj. This specifies the presences and absences on which the presence/absence step of abundance-based tests is based (see details). If NULL (which is usually the only reasonable choice), prab01 is computed in order to indicate the nonzeroes of prabobj$prab.
sarmethod	this is passed on as parameter method to errorsarlm and documented there. We don't have experience with any other choice than "eigen".
weightstyle	can take values "W", "B", "C", "U", and "S" though tests suggest that "C" should be chosen. See nb2listw.
quiet	this is passed on as parameter quiet to errorsarlm and documented there.
sar	logical. If TRUE, a simultaneous autoregression model is fitted by calling errorsarlm. If FALSE, a two-way additive unreplicated linear model for log-abundances on factors species and region is computed by lm, ignoring the spatial arrangement of the regions.
add.lmobject	logical. If TRUE, the whole output object of errorsarlm (or lm) is given out.

Value

A list with the following components:

sar	see above.
intercept	numeric. Estimator of the intercept.
sigma	numeric. Estimator of error standard deviation.
regeffects	numeric vector. Estimator for region effects.
speceffects	numeric vector. Estimator for species effects.
lamda	numeric. Governs the degree of spatial autocorrelation. See errorsarlm.
size	integer. Length of neighborhood list generated by nb2listw used by errorsarlm.
nbweight	numeric. Average weight of neighbors.
lmobject	if add.lmobject=TRUE, output object of either lm or errorsarlm.

Author(s)

Christian Hennig [e-mail] https://www.unibo.it/sitoweb/christian.hennig/en

See Also

errorsarlm, abundtest

Examples

  options(digits=4)
  data(siskiyou)
  x <- prabinit(prabmatrix=siskiyou, neighborhood=siskiyou.nb,
             distance="none")
#  Not run; this needs package spdep 
#  prab.sarestimate(x)
  prab.sarestimate(x, sar=FALSE)

prabclus documentation built on Oct. 24, 2023, 1:06 a.m.