Notes for Logan

[adamreimer]

1. Instead of reading the data directly in the SR code it might be better to read directly from excel books Holly sends you (or create your own workbook for raw data which can be processed outside of the analysis code. One method is to store those in ".\data_raw" along with any R scrips you write to process the raw data and store the R datasets in ".\data". This way the jags data object can read from datasets which are easier to track wrt changes, version, exc.
2. I don't understand the advantage of Davids if(T){} method. You can comment out chucks if you don't want the run the entire section.
3. Preferable to draw initial values randomly from an appropriate distribution. If done inside of a function, you can just provide the function to jags and it will do the random draw for you. May not need to specify everything we specify here either.
4. I deleted the outputs you created under David's naming convention as I don't think they produced results we used or needed. My preference is to just save to posteriors to disk and then produce figures from those posteriors as needed.
5. function notes - most all of these functions are preceded by a standard header which was useful than I had them in a self-contained package. When they are read in as scripts that format is unnecessary, but it does contain some helpful info.
   table_age - need to remove the run argument.
   table_brood - need to remove the run argument.
   table_erindex - not sure if this is needed used to produce a table of abundance index information for reporting.
   table_state - remove run argument. modify as appropriate.
   plot_age - remove run argument.
   plot_chinBEGs - may work as is but the rugs on the horsetail plot may have made this function irrelevant.
   plot_ERfit - produces a plot like figure 4 in FMS17-02. Would need to be highly modified for the Anchor but likely useful.
   plot_ey - may work as is
   plot_horse_red / plot_horse_full - These worked but there was an issue with the brood year labels in the _full function. Might want to double check the _red function to make sure I made the correction in both places.
   plot_Swgoals - need to modify for a single run.
   get_BEGbounds - this is used internally within several of the plots. Probably should be in the internal file as I can't see why you would call it independently.
   get_ids - You don't need this but I left it in as an example of a function I have found very useful to run early in other SR scripts. Creates several of the default variables (Y, A, a.min, a.max) in your environment and can associate labels with jags indices that can be useful for later plots/tables. You can also use this to subset data so that you don't have to read in several version of the same dataset like we have here.
   get-Rhat - should run as it.