Revision post review comments

PlotSpecificFigures.m

@@ -28,12 +28,13 @@ try
     disp('3. Effects of removing insulin actions (Fig. 5)')
     disp('4. All figure after diabetes was introduced (Fig. 6, 7, S3, S4)')
     disp('5. Best agreement when insulin action 3 was removed (Fig. S2)')
+    disp('6. Figures related to using the alternative epi data set (Doc. SX)')
     disp('Note that figures numbered 5X corresponds to supplementary figures SX.')
-    choice = input('\nChoice (1, 2, 3, 4 or 5): ');
+    choice = input('\nChoice (1, 2, 3, 4, 5  or 6): ');
     
-    if ~ismember(choice, [1,3,5])
+    if ~ismember(choice, [1,3,5, 6])
         fprintf('\n\nWhat resolution do you want?\n')
-        disp('High resolution (as in the papers) or low resolution (faster)?')
+        disp('High resolution (as in the paper) or low resolution (faster)?')
         disp('1. High resolution')
         disp('2. Low resolution')
         choice2 = input('\nChoice (1 or 2): ');
@@ -41,11 +42,11 @@ try
         choice2 = 1;
     end
     fprintf('\n\n')
-    if ~ismember(choice,[1 2 3 4 5]) && ~ismember(choice2,[1 2])
+    if ~ismember(choice,[1 2 3 4 5 6]) && ~ismember(choice2,[1 2])
         error('Invalid choice of plots. Invalid choice of resolution')
-    elseif ~ismember(choice,[1 2 3 4 5]) && ismember(choice2,[1 2])
+    elseif ~ismember(choice,[1 2 3 4 5 6]) && ismember(choice2,[1 2])
         error('Invalid choice of plots. Valid choice of resolution')
-    elseif ismember(choice,[1 2 3 4 5]) && ~ismember(choice2,[1 2])
+    elseif ismember(choice,[1 2 3 4 5 6]) && ~ismember(choice2,[1 2])
         error('Valid choice of plots. Invalid choice of resolution')
     elseif choice2==1
         res=0.01;
@@ -66,6 +67,10 @@ try
         PlotUncertainty(1, res)
     elseif choice == 5
         PlotUncertainty(0,res, 'lipolysis_noIns3')
+    elseif choice == 6
+        PlotPL('lipolysis', 0)
+        PlotUncertainty(0,res, 'lipolysis', 0)
+        PlotInsulinActions(0)
     else
         disp('Invalid choice if plots')
     end

PlotSupplementaryAlternativeData.m

+if ~(exist('./Model equations.txt','file') && exist('./Scripts and data','dir'))
+    cdChoice=input('Warning! You are likely running the file from the wrong directory.\nDo you want to attempt to switch to the correct directory automatically?\n  1. yes\n  2. no\nChoice (1 or 2): ','s');
+    if cdChoice == 1
+        cd(fileparts(mfilename('fullpath')))
+    elseif cdChoice == 2
+        disp('Warning! The script will most likely not run from this directory.')
+        disp('If you encounter errors, please change the directory to the folder with the files.' )
+    else
+        disp('Invalid choice')
+    end
+end
+assert(exist('./Model equations.txt','file') && exist('./Scripts and data','dir'),'Error! Likely running from the wrong directory.')
+currentDir = pwd;
+
+try
+    run('./Scripts and data/Setup.m')
+    res = 0.01;
+    cd('Scripts and data')
+    PlotPL('lipolysis', 0)
+    PlotUncertainty(0,res, 'lipolysis', 0)
+    PlotInsulinActions(0)
+    cd(currentDir)
+catch err
+    disp('Something went wrong.')
+    cd(currentDir)
+    rethrow(err)
+end
\ No newline at end of file

Scripts and data/CostInVivo.m

-function [cost, responses] = CostInVivo(params, model, data, tol)
+function [cost, responses] = CostInVivo(params, model, data, tol, useFig2EpiData)
 if nargin<4, tol = 0; end
 try
     ind = ismember(data.Fig1.Time(1):data.Fig1.Time(30), data.Fig1.Time);
@@ -11,18 +11,32 @@ try
     SEM=data.Fig1.SEM;
     costFig1 = sum((yh-y).^2 ./SEM.^2);
     
-    %% Fig2
-    yh=[responses.Gly.Fig2Epi(ind); responses.Gly.Fig2Iso(ind)];
-    y=[data.Fig2Epi.Mean; data.Fig2Iso.Mean];
-    SEM=[data.Fig2Epi.SEM; data.Fig2Iso.SEM];
-    costFig2 = sum((yh-y).^2 ./SEM.^2);
-    
-    %% Fig3
-    yh=responses.Gly.Fig3EpiPhe(ind);
-    y=data.Fig3EpiPhe.Mean;
-    SEM=data.Fig3EpiPhe.SEM;
-    costFig3 = sum((yh-y).^2 ./SEM.^2);
-    
+    if useFig2EpiData
+        %% Fig2
+        yh=[responses.Gly.Fig2Epi(ind); responses.Gly.Fig2Iso(ind)];
+        y=[data.Fig2Epi.Mean; data.Fig2Iso.Mean];
+        SEM=[data.Fig2Epi.SEM; data.Fig2Iso.SEM];
+        costFig2 = sum((yh-y).^2 ./SEM.^2);
+        
+        %% Fig3
+        yh=responses.Gly.Fig3EpiPhe(ind);
+        y=data.Fig3EpiPhe.Mean;
+        SEM=data.Fig3EpiPhe.SEM;
+        costFig3 = sum((yh-y).^2 ./SEM.^2);
+    else
+        %% Fig2
+        yh=responses.Gly.Fig2Iso(ind);
+        y=data.Fig2Iso.Mean;
+        SEM=data.Fig2Iso.SEM;
+        costFig2 = sum((yh-y).^2 ./SEM.^2);
+
+        %% Fig3
+        yh=[responses.Gly.Fig3Epi(ind); responses.Gly.Fig3EpiPhe(ind)];
+        y=[data.Fig3Epi.Mean; data.Fig3EpiPhe.Mean];
+        SEM=[data.Fig3Epi.SEM; data.Fig3EpiPhe.SEM];
+        costFig3 = sum((yh-y).^2 ./SEM.^2);
+    end
+
     %% Total cost
     cost=costFig1+costFig2+costFig3+steady;
     

Scripts and data/Init.m

@@ -90,7 +90,7 @@ lb=repmat(log(1e-6), 1, expInd); % set lower bound for all "InVitro" parameters
 ub=repmat(log(1e6), 1, expInd); % set upper bound for all "InVitro" paramters
 
 lb=[lb 0.6   8   0   0   0   -5   log(0.5) -5 0.5  0.5 0.5];
-ub=[ub 1    12   8 20  20    3    log(1.1)  3   2    2   2];
+ub=[ub 1    12   20 20  20    3    log(1.1)  3   2    2   2];
 
 if contains(modelName, '_noIns1')
     lb([28 31])=[];