kevinsee / dabom Goto Github PK

Because fall Chinook are included in STADEM estimates, any valid tags from fall Chinook should NOT be excluded before running DABOM. Presumably they all end up in the main black box, but that should be checked.

After cleaning up the "Installation and Setup" instructions in the DABOM vignette, perhaps we could move those to a fragment to be included in both the vignette and the README file.

In the Asotin, in 2010 and 2011, the Asotin weir (ASOTIC) was located upstream of the instream array ACB. After that, it has been placed downstream of ACB. DABOM should reverse the ASOTIC and ACB nodes if being run in 2010 and 2011.

Add an argument to this function to have different versions: TRT, GSI, etc.

Probably move this function to PITcleanr, so it can be used to summarize biological information

The following functions have separate versions for each version of DABOM (_xxx). Seems worth attempting to consolidate them into a single generic function:

• createJAGSinputs_xxx: look to createJAGSinputs_PRO() for a possible starting point.
• compileTransProbs_xxx: look to compileTransProbs_PRO() for an example that doesn't require a renameTransParams_xxx() function. Using a parent-child table of sites, can we build a loop that goes through each parent site and multiplies the child transitions by the parent transition?
• setBranchNums_xxx: ensure that the generic setBranchNums() works for all versions
• setSavedParams_xxx: I believe that the generic setSavedParams() works for all versions, so the others can be deleted

Include at least 2 vignettes in the package:

• Walk a user through how to use the package to generate escapement estimates for a single spawn year.
• Detail all the updates needed if a new site is added to the model
  • Which functions need to be updated?
  • How should each of them be changed?
  • Try to provide a checklist somewhere

For versions of DABOM with wild and hatchery fish (e.g. Priest Rapids steelhead), the createJAGSinputs_PRA() function sets some of the Dirichlet priors on all the multinomials to 0, if no fish moved along that branch. It allows those priors to be different for hatchery and wild fish, so it can turn a branch "off" for hatchery fish but "on" for wild fish.

However, the fixNoFishNodes() function doesn't do something similar for the phi parameters. If no fish are observed past a node with a phi parameter leading up to it, then it sets that phi parameter to 0. However, if some wild fish but no hatchery fish are observed at that node, the phi parameters for both wild and hatchery fish will be estimated. This is inconsistent with the multinomial nodes described above, and could be corrected for consistency.

Since JDA is an actual site, use that. Change all the various functions that have "BelowJD1" in them to match "JDA".

When STADEM drops some weeks due to window and trap seem to be closed, the week number labels from STADEM output won't match those of DABOM, so the calcTribEscape_LGD function won't work properly (when time-varying movement parameters are being estimated).

Thanks @ryankinzer for noting this!