commOccu-class

Management and analysis of camera trap wildlife data through an integrated workflow. Provides functions for image/video organization and metadata extraction, species/individual identification. Creates detection histories for occupancy and spatial capture-recapture analyses, with support for multi-season studies. Includes tools for fitting community occupancy models in JAGS and NIMBLE, and an interactive dashboard for survey data visualization and analysis. Features visualization of species distributions and activity patterns, plus export capabilities for GIS and reports. Emphasizes automation and reproducibility while maintaining flexibility for different study designs.

Juergen Niedballa

camtrapR

Camera Trap Data Management and Analysis Framework

Alexandre Courtiol

Rahel Sollmann

John Mathai

Seth Timothy Wong

An The Truong Nguyen

Azlan bin Mohamed

Andrew Tilker

Roshan Guharajan

Ioannis Alexiou

Andreas Wilting

commOccu-class function

<dl>
<dt><code>modelText</code></dt>
<dd>JAGS model code as a character vector (made up of code chunks, use cat() to print)</dd></dl>
<dt><code>params</code></dt>
<dd>Parameters to monitor in the model runs</dd>
<dt><code>inits_fun</code></dt>
<dd>Function to create start values for the MCMC chains. It being a function ensures different values in each chain</dd>
<dt><code>data</code></dt>
<dd>List with data needed to run the model (detection &amp; effort matrices, site covariates, number of species / stations / occasions)</dd>
<dt><code>input</code></dt>
<dd>Input data_list (unchanged)</dd>
<dt><code>nimble</code></dt>
<dd>logical indicator for whether it is a Nimble model</dd>
<dt><code>modelFile</code></dt>
<dd>Path of the text file containing the model code</dd>
<dt><code>covariate_info</code></dt>
<dd>Data frame containing information about covariates. Only used internally in plot_* and predict methods</dd>
<dt><code>model</code></dt>
<dd>character indicating whether it is a standard "Occupancy" model or Royle-Nichols ("RN") occupancy model</dd>

Slots

commOccu objects — commOccu-class

<dl>
<dt><code>modelText</code></dt>
<dd>JAGS model code as a character vector (made up of code chunks, use cat() to print)</dd>


<dt><code>params</code></dt>
<dd>Parameters to monitor in the model runs</dd>


<dt><code>inits_fun</code></dt>
<dd>Function to create start values for the MCMC chains. It being a function ensures different values in each chain</dd>


<dt><code>data</code></dt>
<dd>List with data needed to run the model (detection &amp; effort matrices, site covariates, number of species / stations / occasions)</dd>


<dt><code>input</code></dt>
<dd>Input data_list (unchanged)</dd>


<dt><code>nimble</code></dt>
<dd>logical indicator for whether it is a Nimble model</dd>


<dt><code>modelFile</code></dt>
<dd>Path of the text file containing the model code</dd>


<dt><code>covariate_info</code></dt>
<dd>Data frame containing information about covariates. Only used internally in plot_* and predict methods</dd>


<dt><code>model</code></dt>
<dd>character indicating whether it is a standard "Occupancy" model or Royle-Nichols ("RN") occupancy model</dd>


</dl>

commOccu objects

commOccu-class: commOccu objects

Description

Arguments

Value

Slots