Add toy model for Dmitri Aphid study.

WorkSpace/Dmitri/AphidModel.m

@@ -0,0 +1,57 @@
+close all
+clear all
+addpath(genpath('../../src'));
+
+Model = SSIT;
+% Model.species = {'aphid';'predator'};
+Model.species = {'aphid'};
+Model.initialCondition = [0];
+
+% Model.propensityFunctions = {'k1','g1*aphid','k2','g2*predator'};
+Model.propensityFunctions = {'k1+k2*aphid^eta/(M^eta+aphid^eta)','g1*aphid'};
+
+% Model.stoichiometry = [1,-1,0,0;...
+%     0,0,1,-1];
+Model.stoichiometry = [1,-1];
+
+% Model.parameters = ({'k1',5;'g1',0.5;'k2',2;'g2',0.3});
+Model.parameters = ({'k1',5;'g1',0.5;'k2',10;'eta',2;'M',100});
+
+Model.fspOptions.initApproxSS = false;
+Model.fittingOptions.modelVarsToFit = (1:2);
+
+Model = Model.formPropensitiesGeneral('DmitriAphids');
+
+[FSPGrSoln,Model.fspOptions.bounds] = Model.solve;
+
+%%
+% Model = Model.loadData("AphidsNewFormatB.csv",...
+%     {'aphid','sca'});
+Model = Model.loadData("AphidsNewFormatB.csv",...
+    {'aphid','sca'},...
+    {'plant_date','E';...
+    'seed_trtmt','U';...
+    'spray_trtmt','USP'});
+
+% {'Condition','GR_timesweep';'Dex_Conc',GRfitCases{i,2}}
+%%
+Model.tSpan = unique(Model.dataSet.times);
+Model.initialTime = Model.tSpan(1);
+
+Model.makeFitPlot
+set(gca,'xlim',[Model.tSpan(1),Model.tSpan(end)])
+
+%%
+% Model.parameters(1:2,2) = {2;0.1};
+Model.fspOptions.bounds(2) = 1000;
+
+Model.initialCondition = [0];
+fitOptions = optimset('Display','iter','MaxIter',300);
+pars = [Model.parameters{:,2}];
+for i = 1:1
+    fitOptions.suppressFSPExpansion = true;
+    pars = Model.maximizeLikelihood(...
+        pars, fitOptions);
+    Model.parameters(:,2) = num2cell(pars);
+end
+Model.makeFitPlot