Further Capabilities And Future Extensions
  • Further capabilities (examples to come)

- Model integrating habitat and species occupancy dynamics (e.g. (MacKenzie et al. 2011))
- Prediction of unobserved state via Viterbi (Fiske, Royle, & Gross 2013) using the R package HMM (http://cran.r-project.org/web/packages/HMM/HMM.pdf).
- Missing data: the appropriate detection probabilities need to be fixed to 1 in IVFV.
- Get SEs and confidence intervals for derived parameters (e.g., (occupancy, growth rate and turnover in dynamic models); use the delta-method as implemented in the R package msm for example (http://cran.r-project.org/web/packages/msm/msm.pdf), or resort to non-parametric bootstrap in E-SURGE.
- Trap-dependence: use a site- and survey-specific covariate with value 1 for all surveys after first detection at a site, and 0 otherwise.
- Time-specific covariates applied to colonisation-extinction probabilities.

  • Future extensions

- Removal occupancy design (Mackenzie & Royle 2005); use censorship in the Headed format?
- Spatial autocorrelation (Hines et al. 2010) and second-order Markov chain in occupancy (Green, Bailey, & Nichols 2011); using similar ideas to the capture-recapture memory model (Rouan, Choquet, & Pradel 2009).
- Royle-Nichols model (Royle & Nichols 2003).

  • References

Fiske, I.J., Royle, J.A. & Gross, K. (2013) Inference for finite-sample trajectories in dynamic multi-state site-occupancy models using hidden Markov model smoothing. Environmental and Ecological Statistics.
Green, A.W., Bailey, L.L. & Nichols, J.D. (2011) Exploring sensitivity of a multistate occupancy model to inform management decisions. Journal of Applied Ecology, 48, 1007–1016.
Hines, J.E., Nichols, J.D., Royle, J.A., MacKenzie, D.I., Gopalaswamy, A.M., Kumar, N.S. & Karanth, K.U. (2010) Tigers on trails: occupancy modeling for cluster sampling. Ecological Applications, 20, 1456–1466.
MacKenzie, D.I., Bailey, L.L., Hines, J.E. & Nichols, J.D. (2011) An integrated model of habitat and species occurrence dynamics. Methods in Ecology and Evolution, 2, 612–622.
Mackenzie, D.I. & Royle, J.A. (2005) Designing occupancy studies: general advice and allocating survey effort. Journal of Applied Ecology, 42, 1105–1114.
Rouan, L., Choquet, R. & Pradel, R. (2009) A General Framework for Modeling Memory in Capture-Recapture Data. Journal of Agricultural Biological and Environmental Statistics, 14, 338–355.
Royle, J.A. & Nichols, J.D. (2003) Estimating abundance from repeated presence-absence data or point counts. Ecology, 84, 777–790.

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