Continuous-time Markov models
Continuous-time Markov models for species interactions M. Spencer and E. Susko (2005). Ecology 86: 3272-3278 (the authoritative version is here).
Estimation code to accompany this paper. Matlab code for estimating continuous-time Markov models. This code is also available at Ecological Archives.
Sensitivity analysis
Sensitivity analysis of Markov models for communities of competing sessile organisms M. Spencer (2006), Journal of Animal Ecology 75: 1024-1033 (the authoritative version is here).
Sensitivity code Zip archive of Matlab code for sensitivity analyses of the stationary distribution of continuous-time Markov models. See readme for details.
Past states
Past states of continuous-time Markov models for ecological communities M. Spencer (2008). Mathematical Biosciences 211: 299-313 (the authoritative version is here).
Lotka-Volterra models for permanent quadrat data
Lotka-Volterra competition models for sessile organisms, Matthew Spencer and Jason Tanner (2008). Ecology 89: 1134-1143 (the authoritative version is here). Also has an appendix.
Linear models code Tar archive of Matlab code used in this manuscript for fitting continuous-time linear Markov models. See README.txt for details.
LVfit0.2.tgz Tar archive of C code used in this manuscript for fitting continuous-time Lotka-Volterra competition models. See README.txt for details. Version 0.2, 2/2/09: minor bug fixes.
Empirical models of transitions between coral reef states
More details here.
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