Data, code and manuscript 'Estimating invasive rodent abundance using removal data and hierarchical models'

• analyses
  • coypus.Rmd: R code for running the coypus analyses
  • muskrats.Rmd: R code for running the muskrats analyses
  • simulations.Rmd: R code for running the simulations
  • simulations-closure.Rmd: R code for running the simulations when the closure assumption is not met
  • data
    • coypus.rds: coypus data
    • temperature_netherlands.rds: temperature data for 2014
    • temperature_netherlands_allperiod.rds: temperature data for 1987-2014
• manuscript
  • rodent-abundance-from-removal.Rmd: master file to produce manuscript

Author:
Gimenez, Olivier – CNRS Montpellier, France

Abstract: Invasive rodents pose significant ecological, economic, and public health challenges. Robust methods are needed for estimating population abundance to guide effective management. Traditional methods such as capture-recapture are often impractical for invasive species due to ethical, legal and logistical constraints. Here, I showcase the application of hierarchical multinomial N-mixture models for estimating the abundance of invasive rodents using removal data. First, I perform a simulation study which demonstrates minimal bias, as well as good precision and reliable coverage of confidence intervals across a range of sampling scenarios. I also illustrate the consequences of violating the population closure assumption, showing how between-occasion dynamics can bias inference. Second, I analyze removal data for two invasive rodent species, namely coypus (Myocastor coypus) in France and muskrats (Ondatra zibethicus) in the Netherlands. Using hierarchical multinomial N-mixture models, I examine the effects of temperature on abundance while accounting for imperfect and time-varying capture probabilities. I also show how to accommodate spatial variability using random effects, quantify uncertainty in parameter estimates, and account for violations of closure by fitting an open-population model to multi-year data. Overall, I hope to demonstrate the flexibility and utility of hierarchical models in invasive species management.