SIMS_Launch_Script.m

%% LAUNCHER FOR SIMS
% Please see Readme and Example case of SIMS for more information

% Import data as row vectors [1xN]
x        =     ;      % depth in cm
z        =     ;      % tracer site fraction, distance corresponds to x

t        =     ;      % time associated with the SIMS dataset [1x1]


% Priors, or initial guesses at values

% k, surface reation rate
kmin     =     ; 
kmax     =     ;
k        =     ;
SIGMAk   =     ;
%D, bulk diffusion constant
Dmin     =     ;
Dmax     =     ;
D        =     ;
SIGMAD   =     ;

%SAMPLE OF VALUES FOR IG DISTRUBUTION; Experiment with your own values
ps       =     ;        % Best guess for Observational Error Standard Deviation
N        = 5000;        % Number of cycles to run the calibration
nu       = 4   ;        % Shape parameter of the ig prior
tau      = 5*ps^2;      % Scale Parameter of the ig prior

thinfact =     ;        % Thinning Factor between [0,1]

[kpost, Dpost, psipost, weights, successk, successD] = MCMCSIMSig(x, z, t, kmin, kmax, k, SIGMAk, Dmin, Dmax, D, SIGMAD, N, nu, tau, thinfact);

% Plots
figure
covdraws = 50;
drawind = randi(N-1000,1,covdraws);
plot(x,z, 'r.');
hold on

for i=1:covdraws
    y = SIMS(x,kpost(1000+drawind(i)), Dpost(1000+drawind(i)), t);
    plot(x, y, 'LineWidth', 0.4)
end

figure
scatdraws = 1000;
scatind = randi(N-1000,1,scatdraws);
scattervecs = zeros(scatdraws, 2);
for i=1:scatdraws
    scattervecs(i,:) = [kpost(scatind(i)+1000) Dpost(scatind(i)+1000)];
end
scatter(scattervecs(:,1), scattervecs(:,2), 'MarkerFaceAlpha', 0.2)