Updating environmental input layers and functions for Moore and Hastings Clusters

[KRNA01]

UPDATES 31 JAN 22

Starting this issue to flag a set of hurdles we need to jump to get DHW, connectivity, site carrying capacity(k), depth, and waves streamlined as new RECOM data are coming in for the Moore and Hastings reef clusters.

• [X] 1. ~DHW distribution potentially needs correcting for Moore (flipped lats and lons)~ - WIP by @KRNA01. NOW SOLVED
• [x] 2. DHW calculation methods applied generally need to be reviewed. New AIMS method versus historical/conventional. Just pinging @BarbaraRobson to remind us we need to have this discussion asap because the choice of method affects the spatial DHW variation.
• [ ] 3. Suggest we upgrade routine waves to include cyclone impacts (stochastic function imported from IPMF). Suggest @KRNA01 works on this with @ConnectedSystems - and with outside help from Cresswell and Puotinen. EDIT: pulling this out as separate issue
• [X] 4. ~Need to double-check orientation of connectivity (transition-probability) matrices. Suspect we need to transpose such that rows are sources.~ NOW SOLVED
• [x] 5. Initial coral cover pulled in from data or other models.
• [x] 6. Site depth pulled in from tables or maps and used in updated bleaching function
• [x] 7. Site area pulled in from tables or maps and used in estimates of absolute coral cover and RCI..

[ConnectedSystems]

For prosterity, reproducing some notes I sent here. I will eventually put this into documentation somewhere.

Site depth and initial coral cover is pulled in from the spatial data layer.

The spatial data is fed in to coralScenario() as the new site_data input.

This is currently read in from a CSV file with ai.loadSiteData() (see here for an example).

The second argument to ai.loadSiteData() is to indicate which columns to use for base coral cover. Please note: This is currently very fragile - it only expects two columns that always map to Corymbose Acropora and Small Massives. Change the order or number and it will break.

• k values are assumed to always be in a "k" column
• depth values are assumed to always be in a "sitedepth" column
• area is also included, but currently unused.

[KRNA01]

Thanks all. Closing this. Waves are still a current issue, but will address separately