Added conversions to be in corals/site/year/species

[Rosejoycrocker]

Probably still a lot to fix here but I thought I'd create a PR so we can easily discuss resolving this issue, @KRNA01. What I currently have in place is:

• The preferred seeding sites are selected.
• The area and k for these sites are extracted.
• These are used to calculate the area available to coral at each site : site_area_seed=area(prefseedsites).*(k(prefseedsites)/100)
• The colony area is then extracted for the enhanced species, using col_area_seed1 = coral_params.colony_area_cm2(s1_idx)/(10^4) and the same for seed2 using s2_idx. (division by 10^4 is to convert to m^2)
• Seed1 and seed2 are divided by nsiteint to give the no. of corals per site.
• Finally the coral numbers are : seed1_scaled = ((seed1/nsiteint)*col_area_seed1)/site_area_seed and the same for seed2.

Something I am unsure of is the previous version multiplies seed1 and 2 by (pi^(((2-1)/2)^2)), so I'm not sure whether to also add this in (what is this for?). Additionally, should I also check the units of ```max_settler_density * basal_area_per_settler ...

• density_ratio_of_larvae_to_settlers``` ? I'm not sure if my changes will impact this calculation. (line 245 in coralScenario).

Sorry for the very long explanation.

[KRNA01]

@Rosejoycrocker and @ConnectedSystems , Just noted this line, and something looks off:

Additionally, should I also check the units of max_settler_density basal_area_per_settler ... density_ratio_of_larvae_to_settlers ? I'm not sure if my changes will impact this calculation. (line 245 in coralScenario).

_

There should no longer be a density_ratio_of_larvae_to_settlers

This should now be density_ratio_of_settlers_to larvae, and its value should be 1/2000.

I added this in my latest PR, but I don't know if this somehow got lost. Please see issue #100 and PR connected to branch corals_by_area

[ConnectedSystems]

@KRNA01 The change you refer to was merged into main sometime last week if I recall correctly.

In this case, git would have raised a merge conflict warning if there was an issue as the changes occurred across two different branches and it won't be able to determine which change to keep.

I've checked and your changes are in this branch too.

https://github.com/open-AIMS/ADRIA_repo/blob/652625ecdc66c7193fb593289028076e6f3d9fce/ADRIAfunctions/coralScenario.m#L230

[Rosejoycrocker]

Sorry about that @KRNA01, it was my typo when writing the PR commentary