NEON-NIWO-misclass

Here we develop a joint classification-occupancy model for multispecies survey datasets. We illustrate the model using carabid pitfall trap data from the National Ecological Observatory Network (NEON) collected at Niwot Ridge, CO, USA.

Publication

https://doi.org/10.1111/2041-210X.13858

The manuscript describing this work is published in Methods in Ecology & Evolution

Estimating species misclassification with occupancy dynamics and encounter rates: A semi-supervised, individual-level approach Anna I. Spiers, J. Andrew Royle, Christa L. Torrens, Maxwell B. Joseph

Code is archived on Zenodo at https://doi.org/10.5281/zenodo.6394878

Prerequisites

To run this compendium, you'll need R installed.

Quickstart

This compendium produces the article's figures based off of the carabid case study results.

It does not produce the paper nor simulation output. For simulation output, run simulations.R. This will take a long time depending on your CPU bandwidth. For simulation figures, run sim_figs.R

Navigate to repository

Download the repository. In terminal, navigate to the repository.

Execute the compendium

To run the analysis run GNU Make from the terminal:

make

Details

Here's what's inside:

data/

A place for local storage of publicly available NEON data. Data are ignored by version control.

figures/

A location for generated figures.

output/

JAGS model output

source/

custom functions

Makefile

This file contains instructions for how to execute the compendium.