Create experiments and replication

[eliotmcintire]

I think there are 3 options:

1. Push it all into the simList.
2. Add more args to spades()
3. Make a wrapper around spades call,with a new function name

I like option 2 or 3. It is too cumbersome to have to specify entirely new simList if only one parameter is different. Something like:
experiment(simList, replication=10L, params=list(spreadProb=c(0.22,0.23), growthExponent=c(2,2.2))

(These parameters will have to be module specific, I am just being lazy here)

Would also work with something like: modules=list("fireSense", "fireBEACONs")

(That is not fully formed thought for modules, how does it know which modules to use... Does it need entire list of modules twice if there are two levels to the experiment? )

The function would do several things:

1. Create as many simLists as needed to do a fully factorial experiment, in the parameter example above: 4 simLists. Don't need new simLists for replicates.
2. Create subdirectories inside outputPath corresponding to factors. I think these should be flat, i.e. 1 level inside outputPath, not 2, but with names that identify the factorial identity
3. Create sub-sub directories for replicates. No deeper.
4. Pass these as new outputPath to each simList
5. Use a mechanism similar to raster package for parallel calculations. If raster::makeCluster (need to verify actual function name) has been run and created, then experiment() will automatically run using cluster. If not then it is serial running.
6. All file saving will be exactly as in the saving of each of the modules and outputs, only outputPath is unique.

Thoughts? @achubaty @SteveCumming

[eliotmcintire]

Major first draft, with commit 02135d1
Needs more detailed documentation still. But it works for replication, plus full factorial experiments with parameters and modules.

[achubaty]

closing as this has been incorporated into the forthcoming v1.1.2 release