fitted.lfMsNMix

Method for extracting model fitted values and detection probability values from a fitted latent factor multi-species N-mixture (<code>lfMsNMix</code>) model.

model

Fits single-species (univariate) and multi-species (multivariate) non-spatial and spatial abundance models in a Bayesian framework using Markov Chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs). Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <doi:10.18637/jss.v103.i05>. Fits single-species and multi-species spatial and non-spatial versions of generalized linear mixed models (Gaussian, Poisson, Negative Binomial), N-mixture models (Royle 2004 <doi:10.1111/j.0006-341X.2004.00142.x>) and hierarchical distance sampling models (Royle, Dawson, Bates (2004) <doi:10.1890/03-3127>). Multi-species spatial models are fit using a spatial factor modeling approach with NNGPs for computational efficiency.

Jeffrey Doser

spAbundance

Univariate and Multivariate Spatial Modeling of Species
Abundance

Andrew Finley

fitted.lfMsNMix function

<dl> <dt>object</dt>
<dd>object of class <code>lfMsNMix</code>.</dd> <dt>type</dt>
<dd>a character string indicating whether fitted values should be generated conditional on the estimated latent abundance values (<code>type = 'conditional'</code>) estimated during the model or based on the marginal expected abundance values (<code>type = 'marginal'</code>).</dd> <dt>...</dt>
<dd>currently no additional arguments</dd></dl>

Arguments

Extract Model Fitted Values for lfMsNMix Object — fitted.lfMsNMix

<dl>

 <dt>object</dt>
<dd>object of class <code>lfMsNMix</code>.</dd>

 <dt>type</dt>
<dd>a character string indicating whether fitted values should be generated conditional on the estimated latent abundance values (<code>type = 'conditional'</code>) estimated during the model or based on the marginal expected abundance values (<code>type = 'marginal'</code>).</dd>

 <dt>...</dt>
<dd>currently no additional arguments</dd>

</dl>

fitted.lfMsNMix: Extract Model Fitted Values for lfMsNMix Object

Description

Usage

Value

Arguments

Details