Make these functions generic - Githubissues

KevinSee / DABOM

Dam Adult Branch Occupancy Model

https://kevinsee.github.io/DABOM/

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Make these functions generic #19

Closed KevinSee closed 1 year ago

KevinSee commented 3 years ago

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

KevinSee commented 3 years ago

I believe I have a generic writeDABOM() function now. With that, I have generic setInitialValues() and createJAGSinputs() functions that seem to work. They involve using the generic setBranchNums() and setSavedParams() functions.

However, now I need to think about how to generate a generic compileTransProbs() function.

KevinSee commented 1 year ago

I added a generic compileTransProbs() to the develop branch. It utilizes the parent-child table and PITcleanr's buildPaths() function to perform the appropriate multiplication. It also added black boxes for even the binomial transitions.