Chapter 1 Introduction

This vignette outlines how to create migratory networks using the R package mignette (migratory network tools ensemble). mignette was developed to facilitate conservation and management decision-making for migratory wildlife populations using migratory networks (Ruegg et al. 2020; Taylor and Norris 2010). Spatial migratory networks are graph-based models that incorporate migratory connectivity and abundance data to define the degree of connectivity between stages of the annual cycle, defined as breeding and nonbreeding nodes. These models are useful for a wide variety of applications because they can accommodate, and combine, different types of common tracking data used to infer individual and population movement across the annual cycle. We designed mignette to facilitate the creation and visualization of migratory networks for users with a wide-range of data sources and study species.

1.1 Tutorial structure

For an introductory demonstration of creating a migratory network with mignette, see the quick start example. This demonstrates the core functionality of mignette using data from a recent study of the American Redstart (Setophaga ruticilla), a widespread Nearctic-Neotropical migratory songbird (DeSaix et al. 2023).

Subsequent chapters of the vignette provide more detailed instructions and are broken up into three main steps:

  1. Define breeding and nonbreeding nodes
  2. Assemble abundance and migratory connectivity data
  3. Modeling the migratory network

1.2 Installation

While mignette is an R package, it uses JAGS (Just Another Gibbs Sampler) to actually implement the migratory network model. JAGS is a specific software for conducting analysis of Bayesian hierarchical models using Markov Chain Monte Carlo simulation. JAGS needs to be installed for mignette to function and can be downloaded here.

Once you have installed JAGS, you can install mignette from GitHub with:

# install.packages("remotes")
remotes::install_github("mgdesaix/mignette")

The primary packages for this vignette are:

library(mignette)
library(sf)
library(terra)
library(tidyverse)
library(ebirdst) # for avian abundance data from eBird Status and Trends
library(rjags) # for network model
library(jagsUI) # for network model
library(ggnewscale) # for network visualization
library(tidyterra) # for plotting terra objects with ggplot

References

DeSaix, Matthew G, Eric C Anderson, Christen M Bossu, Christine E Rayne, Teia M Schweizer, Nicholas J Bayly, Darshan S Narang, et al. 2023. “Low-Coverage Whole Genome Sequencing for Highly Accurate Population Assignment: Mapping Migratory Connectivity in the American Redstart (Setophaga Ruticilla).” Molecular Ecology.
Ruegg, Kristen C, Ryan J Harrigan, James F Saracco, Thomas B Smith, and Caz M Taylor. 2020. “A Genoscape-Network Model for Conservation Prioritization in a Migratory Bird.” Conservation Biology 34 (6): 1482–91.
Taylor, Caz M, and D Ryan Norris. 2010. “Population Dynamics in Migratory Networks.” Theoretical Ecology 3: 65–73.