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piLaboratory / GillesCom

Gillespie Simulation of Ecological Communities Dynamics
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run.bdm #5

Closed andrechalom closed 8 years ago

andrechalom commented 8 years ago

run.bdm should be adapted to use the new C++ code. We need to think about how to deal with the "abundance snapshots".

andrechalom commented 8 years ago

Abundance snapshots implemented via history matrix in C++, accessed via history() function. Speedup compared to R version is around 90%.

andrechalom commented 8 years ago

Some diagnostic plots after running bdm(1e8) with the default settings, i.e.,

> Init_Community(100)
> bdm(1e8)
> diagPlots()

diagplots

Species:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  71.00   78.00   80.00   80.09   82.00  100.00 
Individuals:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    100   11070   11150   11140   11230   11580 
Fishers alpha:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.   NAs 
  10.12   11.31   11.65   11.68   11.99   50.78       1 
Log-normal sd:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max.    NAs 
 0.7027  1.1700  1.2780  1.2720  1.3760  1.7810       1
andrechalom commented 8 years ago

Removed from main branch; latest version with original bdm and run.bdm is 24a50ad