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

prab.sarestimate {prabclus} | R Documentation

## 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 chrish@stats.ucl.ac.uk http://www.homepages.ucl.ac.uk/~ucakche

### 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)

[Package prabclus version 2.2-6 Index]