epizootic

An R package for process-explicit models of wildlife disease

July Pilowsky

What is machine learning?

What is a process-explicit model?

What do you need to make one?

  • Theory about how the study system works
  • This is all you really need, because process-explicit models can be data-free

OK, July, but not all models can or should be data-free

  • Data on processes (such as nitrogen fixation rate or replication fidelity)
  • Data on drivers (such as temperature or % impervious surface)
  • Observed patterns that can be compared to model outputs for validation

How do these models apply to disease ecology?

Introducing epizootic

The structure of epizootic

Choosing a study system

I needed to choose a study system on which to test out epizootic based on these criteria:

  • Verena-scale problem (continental)
  • Enough data to parameterize and independently validate the model
  • Enough theory about the system that we know which processes to include

Case study: house finch conjunctivitis

Image credit: Kerry Hargrove

epizootic in practice

epizootic in practice

Processes included in the model:

  • Transmission dynamics (discrete time SIRI models, parameters differing by season and life cycle stage)
  • Density-dependent dispersal, parameters differing by life cycle stage
  • Density-dependent fecundity and mortality, with mortality differing by infection status

epizootic in practice

Drivers included in the model:

  • Environmental change (climate and land use)
  • Invasion dynamics (introduction of house finches to NY)
  • Initial spillover event from poultry in 1994

Parameterization for epizootic

  • House finch demography
  • House finch banding survey data on dispersal
  • Transmission, recovery, and partial immunity for the disease
  • Spatially explicit breeding season length (inferred from eastern bluebird data)
  • Historical climate data
  • Historical land use data

Validation for epizootic

  • Presence of house finches in Washington DC in 1994
  • Date of arrival of house finch conjunctivitis in Northeast regions
  • Spatiotemporal point prevalence of conjunctivitis
  • Rate of change in house finch abundance
  • Date of arrival of house finches east of the Rockies
  • Presences and true absences of house finches in North America

Validation for epizootic

epizootic and you

How can epizootic integrate with the research that you do at Verena?

epizootic and you

epizootic and you

epizootic and you

I believe that process-explicit modeling is an excellent and rigorous way to model ecological processes at multiple scales. How can it help you? Let’s discuss!