Title: Breeding Bird Survey and West Nile Virus
1Breeding Bird Survey and West Nile Virus
- Guide Shannon LaDeau
- Team Maggie, Rich, Nat, Hu, Aparna
2The 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.
3The 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.
4One 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!!
5YAY???
6More 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
7More 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! ?
8A 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)
9Uh-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?
10Population 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
11A cross-validation approach
- Randomly assign 10 of the bird counts as
unmeasured. - Predict these counts using MCMC compare against
the observed values.
12Is 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.
13Doodle 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)
14American Crow
House Finch
Eastern Bluebird
Black-capped Chickadee
Blue Jay
15Change points
House Finch
Crow and Bluebird
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25Mid WN arrival region
Early WN arrival region
Late WN arrival region
26Summary
- 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.