Known Bugs

Things to change later

1. zeroBatch() to zero out egg batches is not called when using the emerge module; this is because egg laying has no effect on emergence (lambda is directly calculated from the “season” vector from seasonally forced emergence). For large simulations this will mean the eggQ will become excessively large. We should log the data from the eggQ periodically and then zero it out. Ask Dave his thoughts on this.
2. In EL4Pt (the daily difference equations) it is possible for population sizes to become arbitrarily small (but still non-zero) due to the nature of the equations. This is a problem because each “cohort” begins as an egg batch and starts moving through the EL4Pt equations but never fully leaves. Besides the logical issues, this creates a massive memory problem as the aquaPops object to store all the EL4P populations will have to become larger +1 every time a new eggBatch is laid in that site. We have to do some rounding/truncation. Ask Dave his thoughts on this.

Sean’s to-do

1. Rewrite rMove to be more generic: just take in M and output modified M. This is because we need a family of movement functions for when we update SEARCH component, rMove is a module of search; all modules need to take M as argument and return modified M. first new module is bMove (basic-Move) for MBITES-BASIC.
2. Check in original DHM files when eDefPreG or energyPreG is updated and checked for maturity; need to make sure it is consistent and logical (ie; if energyPreG = 0 at initialization then they are instantly mature). Also need to avoid weird conflicts; if energetics is called before the check would occur in boutS but energyPreG = 0 so they should be mature already (ie; mature in energetics).
3. Rewrite LANDSCAPE creation function to take P as input; make hazard and weight parameters directly adjustable by user (this has already been done to calculate mean values in order to run MBITES-Basic; need to implement for full M-BITES simulation).