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

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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:

  png("ibm_gamma.png")
  o <- gamma_beetles_ibm()
  plot(o$times, o$mv[[1,1]], type='l', col="yellow")
  lines(o$times, o$mv[[1,2]], col="yellowgreen")
  lines(o$times, o$mv[[1,3]], col="lightgreen")
  lines(o$times, o$mv[[1,4]], 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
  • 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.



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