User:Carl Boettiger/Notebook/Stochastic Population Dynamics/2010/06/01

Stochastic Population Dynamics

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Gamma Waiting times on individual level Wrote the proper record structure into C code to handle reporting to R, including ensemble data. Wrote the R interface to the dynamics. Needs exploration. Version-stable code for parameters. Run using defaults, graph as: <syntaxhighlight lang = "rsplus"> png("ibm_gamma.png") o <- gamma_beetles_ibm() plot(o$times, o$mv1,1, type='l', col="yellow") lines(o$times, o$mv1,2, col="yellowgreen") lines(o$times, o$mv1,3, col="lightgreen") lines(o$times, o$mv1,4, col="darkgreen") dev.off() o$parameters b ue ul up ua ae al ap cle cap 5.000 0.000 0.001 0.000 0.010 1.300 0.100 1.500 0.200 0.100 cae V 5.000 100.000 </syntaxhighlight> Simulation reports actual parameters above, chosen to match the theory results from last week (linear noise approximation). Comparisons using ensemble data against theory coming soon. Single replicate .c based IBM is currently faster than the ode system (with variance dynamics). Note: Entry and graph above actually added on June 3rd, parameters weren't named correctly on June 1st, so simulation wasn't oscillating.