setupSuperSymbionts.m

function [startSymFractions, superStartYear, superSeedFraction, oneShot] = ...
    setupSuperSymbionts(superMode, RCP, E, superAdvantage, superStart, maxReefs)
%SETUPSUPERSYMBIONTS Set symbiont internal variables based on input choices.

% Summary of superMode options, rules for adding symbionts.
%
% Advantage: 
% 0, 5, and 6: Fixed advantage relative to historical temperature.
% 1, 3: Advantage relative to mean of the last 10 years before introduction.
% 2, 4: Advantage relative to max of the last 10 years before introduction.
% 7, 8, 9: Advantage is dynamic, added relative to the native symbiont.
% 
% Introduction date:
% 0, 1, 2, 7, 9: Fixed year as specified.
% 3, 4, 5: After 5 years of mortality.
% 6: At the first year of bleaching.
% 8: As determined by bleaching events in timeIteration.

% Note that 7 and 9 are the same in terms of this logic.  The difference is that
% in mode 9 there is a growth penalty against the coral when there are more
% tolerant than sensitive symbionts.

% For now (January 2020) assume that in mode 9 only we combine both symbiont
% populations in a single coral population.
% TODO If the other modes are used again, this should be revisited.

    % Some MATLAB doesn't like mixing int32 and double, so
    superStart = double(superStart);
    if superMode == 9
        startSymFractions = [1.0-10^-6 10^-6];  % Starting fraction for native and shuffled symbionts.
    else
        startSymFractions = [1.0 0.0];  % Starting fraction for native and super symbionts.
    end
    if strcmp(RCP, 'control400')
        last = 1860+400+1;
    else
        last = 2100 + 1;
    end
    if superMode >= 3 && superMode <=5
        fn = strcat('longMortYears_', RCP, '_', num2str(E));
        load(fn, 'longMortYears');
        superStartYear = longMortYears;
        % XXX - next two lines for testing only!!!
        %subFrom = (superStartYear > 1882);
        %superStartYear = superStartYear - 20*subFrom;
    elseif superMode == 6
        fn = strcat('firstBleachYears_', RCP, '_', num2str(E));
        load(fn, 'firstBleachYears');
        superStartYear = firstBleachYears;
    elseif superAdvantage == 0.0
        % If there's no advantage it's a case where there's no addition.
        % Delay to the end or we'll end up "seeding" extra symbionts.

        superStartYear = last*ones(maxReefs, 1); % Until this date set S(:, 3:4) to zero.  Use 1861 to start from the beginning.
    else  
        % Start the symbionts in this fixed year for all reefs.
        superStartYear = superStart*ones(maxReefs, 1); % Until this date set S(:, 3:4) to zero.  Use 1861 to start from the beginning.
    end
    assert(length(superStartYear) == maxReefs, 'By-year symbiont starts should have a start year for every reef.');

    % superStartYear may be zero if a reef never bleached - this should be
    % treated as beyond the end of the run.
    superStartYear(superStartYear < 1800) = last;
    
    %superInitYears = [2025 2035]; % Years from which adaptation temp is selected.
    superSeedFraction = 10^-3;      % Fraction of S_seed to use for seeding super symbionts.
    % sizing notes: for massive,
    % KSm = 3000000
    % seed = 100000
    % KSm/seed = 30
    % the seed fraction is a fraction of this value.
    % for 0.01 -> KSm/introduced = 3000
    % for 0.0001 -> KSm/introduced = 300000
    oneShot = false;  % After supersymbiont introduction, set its seed to zero.
    assert(superMode == 9 || startSymFractions(2) == 0, 'Start with no symbionts if they are to be suppressed at first.');
    assert(sum(startSymFractions) == 1.0, 'Start fractions should sum to 1.');
end