Implement relevant struct to handle SIRUS rule extraction #419
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Prototype worked by using $t$ to inform $t+1$, but ADRIAmod was developed such that $t-1$ is used to inform $t$.
Previous implementation worked on the assumption that increases to coral cover could be used to determine relative weights when mixing distributions. However, most scenario trajectories show a decline, meaning that distributions were never updated. This is resolved simply by pairing neighbouring size classes up (2 with 3, 3 with 4, etc) and using the current area covered to inform the weights/priors
Add additional detail in comments
Additional changes for performance
…oral cover array for ReefMod
ReefMod uses a log normal size distribution for initialising coral colonies with mean log(700cm^2) and standard deviation log(4cm^2). Coral cover is separated into ADRIA size classes using the cdf of this distribution and finding the density between each of the size class bin edges for ADRIA. These densities are then normalised and used to weight the distribution between size classes for each species.
Fix reference to AEDT to AEST
Update ReefMod interface to match new species list
Bin sizes are in diameter, not area
Shifting the minimum value as tolerance increases makes the distribution behave similarly to a log-normal representation. Discussed with K.B-N
Spawned larvae incorporates distribution mix of all reproductive size classes (see https://github.com/open-AIMS/ADRIA.jl/blob/df5d53c7c590a7c8250ddfc24a390d5a1ef67400/src/ecosystem/corals/Corals.jl#L177) TODO: Rather than hardcode the size classes, could use `corals.fecundity` to select relevant size classes.
Adjustments to heritability based on feedback
Missed this in earlier PR
Update docstrings with missing detail
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The struct Rule together with some functions to get information once a rule is extracted from SIRUS.