Example tiger data for
These spatial capture-recapture data with a single mark type are summarized in a list of length 3 containing the following objects:
Enc.Mat is a 44 x (noccas*ntraps) matrix containing observed encounter histories for 44 tigers across
noccas=48 sampling occasions and
trapCoords is a matrix of dimension
ntraps x (2 +
noccas) indicating the Cartesian coordinates and operating occasions for the traps, where rows correspond to trap, the first column the x-coordinate, and the second column the y-coordinate. The last
noccas columns indicate whether or not the trap was operating on each of the occasions, where ‘1’ indciates the trap was operating and ‘0’ indicates the trap was not operating.
studyArea is a 3-column matrix containing the coordinates for the centroids of the contiguous grid of cells that define the study area and available habitat. Each row corresponds to a grid cell. The first 2 columns indicate the Cartesian x- and y-coordinate for the centroid of each grid cell, and the third column indicates whether the cell is available habitat (=1) or not (=0). The grid cells are 0.336 km^2 resolution.
These data were obtained from the R package
SPACECAP and modified by projecting onto a regular rectangular grid consisting of square grid cells (as is required by the spatial capture-recapture models in
We thank Ullas Karanth, Wildlife Conservation Society, for providing the tiger data for use as an example with this package.
Gopalaswamy, A.M., Royle, J.A., Hines, J.E., Singh, P., Jathanna, D., Kumar, N. and Karanth, K.U. 2012. Program SPACECAP: software for estimating animal density using spatially explicit capture-recapture models. Methods in Ecology and Evolution 3:1067-1072.
Royle, J.A., Karanth, K.U., Gopalaswamy, A.M. and Kumar, N.S. 2009. Bayesian inference in camera trapping studies for a class of spatial capture-recapture models. Ecology 90: 3233-3244.
1 2 3 4 5 6 7 8 9 10 11 12 13
data(tiger) #plot the traps and available habitat within the study area plotSpatialData(trapCoords=tiger$trapCoords,studyArea=tiger$studyArea) # This example is excluded from testing to reduce package check time # Example uses unrealistically low values for nchain, iter, and burnin # Fit spatial model to tiger data Enc.Mat<-tiger$Enc.Mat trapCoords<-tiger$trapCoords studyArea<-tiger$studyArea tiger.dot<-markClosedSCR(Enc.Mat,trapCoords,studyArea,iter=100,adapt=50,burnin=50) summary(tiger.dot$mcmc)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.