prabclus: prab.sarestimate – R documentation

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prab.sarestimate

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 christian.hennig@unibo.it https://www.unibo.it/sitoweb/christian.hennig/en

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

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

v2.3-2

GPL

Authors

Christian Hennig <christian.hennig@unibo.it>, Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>

Initial release

2020-01-06