In ecohealthalliance/metaflu: Functions for Avian Influenza Metapopulation Simulation

library(knitcitations)
cite_options(citation_format = 'pandoc')
P <- rprojroot::find_rstudio_root_file

Questions

Movement Rate ($\omega$)

• How often do small / large farms exchange chickens?

• How many chickens are at a market?

• How many people would be at a market?

• Do chickens that go to market return to farms?

Network

• Is a large farm realistically one large node, or a clustering of small nodes?

• If large farms have separate sections, how are they connected and what are the movement patterns between sections?

Culling Parameters ($\tau$, $\iota$, $\pi$, t-detect)

• How long does it take between knowing a farm is infected and culling the farm?

• How common is it for a farmer to report an infected farm?

• What is a realistic threshold of deaths or infections for a farmer to notice a problem? What is a realistic time frame for this process?

• What is the actual culling protocol?

• Is there government oversight?

• Is there some standard culling procedure?

• How good are your diagnostic tools? Are there false alarms? (to get at pi-detect)

Direct Transmission ($\beta$, $\rho$)

• How does transmission change per strain?

• How does it change based on farm size?

Recovery Rate ($\gamma$)

• What is the recovery rate per strain?

• Does this change based on farm size (due to attention / resources)?

Base Mortality Rate ($\mu$)

• What is the base mortality rate for chickens?

• Does this change in different locales?

• Does this differ based on the size or type of farm (due to attention / resources)?

Disease Mortality Rate ($\alpha$)

• What is the disease mortality per strain?

• Does the disease mortality change during the course of an outbreak?

Previous Model Parameters r citep('10.1371/journal.pone.0080091'):

Direct Transmission $\beta = 0.004$

Recovery Rate $\upsilon = (0-0.167)$

Disease Mortality Rate $\alpha = (0 - 0.4)$

Environmental Uptake Rate $\nu = 0.001$

Virion Infectiousness $\phi = 1.96 * 10^{-4}$

Virus Degradation Rate $\eta = 0.14$

Virion Shedding Rate $\sigma = 10^5$

Movement Rate $\omega = 0.30$

References

ecohealthalliance/metaflu documentation built on May 15, 2019, 7:56 p.m.