unmarked (version 1.2.5)

jay: European Jay data from the Swiss Breeding Bird Survey 2002

Description

The Swiss breeding bird survey ("Monitoring Haufige Brutvogel" MHB) has monitored the populations of 150 common species since 1999. The MHB sample consists of 267 1-km squares that are laid out as a grid across Switzerland. Fieldwork is conducted by about 200 skilled birdwatchers, most of them volunteers. Avian populations are monitored using a simplified territory mapping protocol, where each square is surveyed up to three times during the breeding season (only twice above the tree line). Surveys are conducted along a transect that does not change over the years.

The list jay has the data for European Jay territories for 238 sites surveyed in 2002.

Usage

data("jay")

Format

jay is a list with 3 elements:

caphist

a data frame with rows for 238 sites and columns for each of the observable detection histories. For the sites visited 3 times, these are "100", "010", "001", "110", "101", "011", "111". Sites visited twice have "10x", "01x", "11x".

Each row gives the number of territories with the corresponding detection history, with NA for the detection histories not applicable: sites visited 3 times have NAs in the last 3 columns while those visited twice have NAs in the first 7 columns.

References

Royle, J.A., Kery, M., Gauthier, R., Schmid, H. (2007) Hierarchical spatial models of abundance and occurrence from imperfect survey data. Ecological Monographs, 77, 465-481.

Kery & Royle (2016) Applied Hierarachical Modeling in Ecology Section 7.9

Examples

data(jay)
str(jay)

# Carry out a simple analysis, without covariates:
# Create a customised piFun (see ?piFun for details)
crPiFun <- function(p) {
   p1 <- p[,1] # Extract the columns of the p matrix, one for 
   p2 <- p[,2] #   each of J = 3 sample occasions
   p3 <- p[,3]
   cbind(      # define multinomial cell probabilities:
      "100" = p1 * (1-p2) * (1-p3),
      "010" = (1-p1) * p2 * (1-p3),
      "001" = (1-p1) * (1-p2) * p3,
      "110" = p1 * p2 * (1-p3),
      "101" = p1 * (1-p2) * p3,
      "011" = (1-p1) * p2 * p3,
      "111" = p1 * p2 * p3,
      "10x" = p1*(1-p2),
      "01x" = (1-p1)*p2,
      "11x" = p1*p2)
}
# Build the unmarkedFrame object
mhb.umf <- unmarkedFrameMPois(y=as.matrix(jay$caphist),
  obsToY=matrix(1, 3, 10), piFun="crPiFun")
# Fit a model
( fm1 <- multinomPois(~1 ~1, mhb.umf) )