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.
Ibm gamma.png

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.