Integrate R with Atlantis

[andybeet]

Add functionality to Atlantis to be able to shell out to R and run code that feeds back into Atlantis.
Use for

• alternative assessments models in R
• redistribution of effort
• harvest control rules

The trunk already has some code to address this (Calculating a TAC) but it has never been functional.

Add this new feature so that it is functional using a TAC for a set number of species.

[erlasturl]

I can make the code work for effort allocation using the current parameterization options. In order to allocate effort one needs to assess a species and put isTAC > 1 in the group csv file. This should then be done for a group which is not being assessed for TAC. The parameterization does not really make sense for effort allocation but it is possible to make it work.

We may want to add a parameter so instead of whichRAssess_XXX we would have RAssesseffortAllocation_YYY. Then I think we would need to call Do_RAssess (or just Run_RAssess() and Read_RAssess_output()) somewhere outside the loop Do_RAssess() is in. Maybe we would like to put it straight into RunNextTimeStep() after Manage_Calculate_Total_Effort(). It could be called before each season and the effort allocation for certain fleets will be updated.