StateSpace: Runs and reports on a generic state space model of population...
In USFWS/AKaerial: Analysis of Alaska Region Aerial Survey Data

StateSpace

R Documentation

Runs and reports on a generic state space model of population growth

Description

StateSpace will search the internal AKaerial index estimates and run a generic state space model over the range selected

Usage

StateSpace(
  area,
  index,
  years,
  species,
  N1 = c(1000, 1e+05),
  r = c(-0.3, 0.3),
  sigma = c(0, 0.3),
  n.chains = 3,
  n.thin = 1,
  n.iter = 5000,
  n.burnin = 1000,
  output = "object"
)

Arguments

`area`	The area code for dedicated MBM Alaska region surveys. Either folder.path or area must be specified. Acceptable values include: YKD - Yukon Kuskokwim Delta, ducks YKG - Yukon Kuskokwim Delta, geese ACP - Arctic Coastal Plain CRD - Copper River Delta WBPHS - The North American Waterfowl Breeding Population Habitat Survey
`index`	The index used. Acceptable values include: itotal - indicated total; singles and pairs doubled, flocks added, flkdrake added, flkdrake 2-4 doubled ibb - indicated breeding birds; singles and pairs doubled total - total birds observed; pairs doubled, others added
`years`	- The years to run the model over
`species`	- The accepted `sppntable` species code for which to model
`N1`	- Initial population size in the format c(min, max) to establish log-scale uniformly-distributed prior
`r`	- Range of growth rate parameter in the format c(min, max) to establish normally-distributed prior
`sigma`	- Range of the process standard deviation parameter in the format c(min, max) to establish uniformly-distributed prior
`n.chains`	- Number of Monte Carlo chains
`n.thin`	- Model thin rate
`n.iter`	- Model iterations
`n.burnin`	- Burn-in iteration length

Details

A state-space model is a general term that usually refers to a model containing the true underlying (and unobserved) time-dependent state of the system and imperfect time-dependent observations. The states change with time so that the state at time t depends on the state at time t-1 (and potentially other factors). Here, the state is defined as the unobserved total population of geese or ducks in the survey area, and observations depend just on the state. A formal description is contained in GenericStateSpaceModel.Rmd, which is provided as the output to this function.

The current index objects in the package are ACPHistoric, CRDHistoric, YKDHistoric, and YKGHistoric.