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Breeding Bird Survey and West Nile Virus

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... Survey and West Nile Virus. Guide: Shannon LaDeau ... The West Nile virus was first seen ... Prediction: If West Nile virus has had catastrophic effects, the ... – PowerPoint PPT presentation

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Title: Breeding Bird Survey and West Nile Virus


1
Breeding Bird Survey and West Nile Virus
  • Guide Shannon LaDeau
  • Team Maggie, Rich, Nat, Hu, Aparna

2
The story so far
  • The West Nile virus was first seen in NY in 1999.
  • Many birds were found dead, and a lot of them
    tested positive for the presence of West Nile.
  • The effect of this disease on bird populations
    has not been quantified.

3
The question..
  • Has West Nile virus caused bird populations to
    decline?
  • Problem 1 We cannot conduct an experiment to
    answer this question.
  • Problem 2 Data on bird mortality are difficult
    to collect.
  • Problem 3 This process occurs over a large
    temporal and spatial scale and may be masked by
    other sources of variation, both internal to the
    population and otherwise.

4
One solution
  • Breeding Bird Survey (BBS) data.
  • Birds are counted along 25-mile routes each year
    in spring.
  • There are 3700 routes across continental US and
    Canada.
  • Qualified volunteer observers perform the
    surveys.
  • YAY!!

5
YAY???
6
More challenges..
The number of routes surveyed varies through the
study period
  • The bird counts are not corrected for observer
    ability.
  • The number of routes surveyed has been increasing
    the past 20 years.
  • (a) This leads to a lot of missing data.
  • (b) It might appear that the bird populations are
    declining.

Number of Routes Surveyed
Year
7
More solutions
  • Throw out routes with too many missing years of
    information, or
  • Throw out years with too many routes that were
    not surveyed.
  • BUT - Why waste the data?
  • Alternative Use MCMC to fill in the unobserved
    years/routes! ?

8
A population model to describe the variability in
counts
counts poisson(mu) muI,j,k observeri
route j year k observer normal(0,
tau.ob) route normal (0, tau.rt) year normal
(0, tau.yr) each tau gamma (0.001,0.001)
9
Uh-oh Two approaches to predicting unobserved
data
  • Idea - Model the counts as a function of the
    observer, the route and the year of observation.
  • More options
  • Routes are spatially independent.
  • Routes have spatially correlated error.
  • Which is better?

10
Population model to predict counts at BBS survey
routes for American Crow
Box plot of MCMC predictions Red circles are
observed data
Count per route
Year
11
A cross-validation approach
  • Randomly assign 10 of the bird counts as
    unmeasured.
  • Predict these counts using MCMC compare against
    the observed values.

12
Is there a West Nile signal?
  • Reminder West Nile virus was first reported in
    1999.
  • We want to know if there is evidence that
    population trends changed at this time.
  • We can use change point analysis to identify the
    most likely period that shows a change in trend.
  • This assumes
  • (1) a single change point.
  • (2) linear slope on either side of change point.
  • (3) lines intersecting at the change point.
  • Prediction If West Nile virus has had
    catastrophic effects, the change point should
    occur later than1999.

13
Doodle of the change-point models
  • Yi dnorm(mui, tau)
  • mui lt- alpha betaJ (xi - x.change)
  • where J is 1 if Xi gt x.change and 2 o/w.
  • tau dgamma(0.001, 0.001)
  • alpha dnorm(0.0,1.0E-6)
  • betaj dnorm(0.0,1.0E-6)
  • sigma lt- 1 / sqrt(tau)
  • x.change dunif(1980, 2005)

14
American Crow
House Finch
Eastern Bluebird
Black-capped Chickadee
Blue Jay
15
Change points
House Finch

Crow and Bluebird
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Mid WN arrival region
Early WN arrival region
Late WN arrival region
26
Summary
  • Two of five species showed distinct change points
    coincident with the arrival of West Nile virus.
  • The change point for American crows appears to be
    earlier in regions where West Nile arrived first.
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