The Generative Model

16 April, 2020

Appalachian salamanader surveys

For our project, we are designing a heirarchical model to analyze data from a case study on salamander
ecology in old-growth Appalachian forest. The data were collected from 4 repeated surveys for Southern
Ravine Salamanders (Plethodon richmondi) at 40 locations. Here’s a picture of the habitat and species:

Figure 1: Juvenile Southern Ravine salamander

Figure 2: Adult Southern Ravine salamander

Figure 3: Southern Ravine salamander Habitat

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The Observation Process

The observation model represents how salamander ecounter histories from repeated surveys (yij ) are not a
perfect translation of the true occupancy status of the sites (zi ). Because yij , in this case, represent a binary
condition (presence/absence) for each site i across sampling events j, it follows a Bernoulli distribution with
a parameter pij .
f (yij |ψi ) ∼ Bernoulli(Zi × pij )
This parameter pij is the conditional encounter probability. Recall that pij is a encounter probability
conditional on the availability of the species for detection, and is estimated across sites i and sample events
j:

logit(pij ) = αp + βCW Dp × CW Dp(ij)

where αp is an intercept and βCW Dp × CW Dp(ij) is a term that allows pij to vary with an evironmental
covariate. In this case, the covariate, CWD, is a abbreviation of “Coarse Woody Debris”. This covariates
represents the count of coarse woody debris objects within the site surveyed during each sampling event. This
covariate was chosen because woody debris are common habitat for small vertebrates in forested ecosystems.
For woodland salamanders, coarse woody debris is among the most preferred habitat. Thus, the ability to
detect a woodland salamanders is heavily influenced by the number of habitats present for searching.

The State Process

This state model represents the ecological patterns which produce variation in the occupancy of a species
in space. The data generated by this process are presence/absences, yi presence/absences of salamanders at
sites i = 1, .., a. The true occupancy status at each site zi is also represented by a Bernoulli distribution,
with parameter ψi :

g(zi |ψi ) ∼ Bernoulli(ψi )

logit(ψi ) = αψ + βCANψ × CANψ(i)

where αψ is an intercept and βCANψ × CANψ(i) is a slope term allowing ψ to vary with a covariate, canopy
openness. Canopy openness is a variable which describes the density of tree cover over the study site, an
important variable for salamanders because they require closed canopies. Therefore, our hypothesis is that
salamander occupancy probability (ψi ) will be negatively related to canopy openness.