Add in automation for 100 data sets for spatial model

[brianlangseth-NOAA]

The current set up for running the spatial models does not yet have the lines for automating running of the 100 datasets.

To do so, add this section of code for the 1 area model, adapted for the spatial datasets. This includes the option to redo bad runs, which may or may not be applicable (though I assume it will be)

An important step will be to add to the mungeData function to incorporate our most up to data model. Currently, mungeData does not have employ the most uptodate movement dynamics. These will need to be added within the function to automate for running the 100 datasets.

[brianlangseth-NOAA]

The catalog of changes Jon made is on github in the ChangeLog.txt file. Fit ending in ...18alk is the best mult-area model.

[brianlangseth-NOAA]

Based on my read of juv_age and ph_T_YR_AGE_ALT_FREQ as described in the OM, youve handled the interplay between them correctly. ph_T_YR_AGE_ALT_FREQ governs that there are 2 age parameters (28 ages / 14), and juv_age = 9 specifies that the first age parameter is fixed up to age 9 at the one for age 1.

[brianlangseth-NOAA]

@JDeroba I have the 100 dataset script up. I am going to test tonight and see how far it gets by the morning.

Right now, I am not estimating a hessian. Is this consistent with how we did the 100 datasets for the single area model? I forget if your 1.5 hrs run time included the hessian or not but I would assume it did not.

It appears that your script for rerunning the bad runs required some additional step. It looks like you identified these using some code pulled from SIM_TIM.R. Im assuming that code works after we do the runs, so have commented out that code in commit 78047a4