fixes for merge

.gitignore

@@ -49,32 +49,6 @@ index.html
 
 AMICI.mlappinstall
 
-examples/example_1/simulate_model_example_1.m
-
-examples/example_2/simulate_model_example_2.m
-
-examples/example_3/simulate_model_example_3.m
-
-examples/example_4/simulate_model_example_4.m
-
-examples/example_5/simulate_model_example_5.m
-
-examples/example_6/simulate_model_example_6.m
-
-examples/geneExpression/simulate_geneExpression.m
-
-examples/example_1/html/*
-
-examples/example_2/html/*
-
-examples/example_3/html/*
-
-examples/example_4/html/*
-
-examples/example_5/html/*
-
-examples/example_6/html/*
-
 *.mat
 
 mtoc/makeExampleDoc.m
@@ -170,3 +144,9 @@ examples/example_dirac_adjoint/dxdotdp_model_dirac_adjoint.m
 examples/example_adjoint/J_model_adjoint.m
 
 examples/example_adjoint/dxdotdp_model_adjoint.m
+
+examples/example_jakstat_adjoint_hvp/simulate_model_jakstat_adjoint_hvp.m
+
+examples/example_dirac_adjoint_hessVecProd/simulate_model_dirac_adjoint_hessVecProd.m
+
+examples/example_adjoint_hessian/simulate_model_adjoint_hessian.m

@amimodel/amimodel.m

@@ -92,7 +92,7 @@
 
         % counter that allows enforcing of recompilation of models after
         % code changes
-        compver = 16;
+        compver = 18;
     end
 
     properties ( GetAccess = 'public', SetAccess = 'public' )

@amimodel/makeEvents.m

@@ -200,7 +200,7 @@ function makeEvents( this )
             trigger{ievent} = sym(symchar);
         end
     end
-
+    
     % update to prevent dirac functions.
     for ievent = 1:nevent
         dtriggerdt(ievent) = diff(trigger{ievent},sym('t')) + jacobian(trigger{ievent},this.sym.x)*this.sym.xdot(:);
@@ -242,23 +242,14 @@ function makeEvents( this )
 
     this.event = amievent.empty();
 
-
-    if(~isfield(this.sym,'Jz'))
-        this.sym.Jz = sym(0);
-        for iz = 1:length([this.event.z])
-            this.sym.Jz = this.sym.Jz + sym(['log(2*pi*sigma_z_' num2str(iz) '^2) + ((z_' num2str(iz) '-mz_' num2str(iz) ')/sigma_z_' num2str(iz) ')^2']);
-        end
-
     % update events
     for ievent = 1:nevent
-        this.event(ievent) = amievent(trigger{ievent},bolus{ievent}(:),z{ievent});
-        % do not add a (:) after z{ievent} this will transform an
-        % [ empty sym ] into Empty sym: 0-by-1 which will lead to a
-        % zero entry if we apply [this.event.z]
-        this.event(ievent) = this.event(ievent).setHflag(hflags(:,ievent));
-
+            this.event(ievent) = amievent(trigger{ievent},bolus{ievent}(:),z{ievent});
+            % do not add a (:) after z{ievent} this will transform an
+            % [ empty sym ] into Empty sym: 0-by-1 which will lead to a
+            % zero entry if we apply [this.event.z]
+            this.event(ievent) = this.event(ievent).setHflag(hflags(:,ievent));
     end
-
 end
 
 if(~isfield(this.sym,'sigma_z'))
@@ -271,7 +262,7 @@ function makeEvents( this )
 if(~isfield(this.sym,'Jz'))
     this.sym.Jz = sym(0);
     for iz = 1:length([this.event.z])
-        this.sym.Jz = this.sym.Jz + sym(['log(2*pi*sdz_' num2str(iz) '^2) + ((z_' num2str(iz) '-mz_' num2str(iz) ')/sdz_' num2str(iz) ')^2']);
+        this.sym.Jz = this.sym.Jz + sym(['log(2*pi*sigma_z_' num2str(iz) '^2) + ((z_' num2str(iz) '-mz_' num2str(iz) ')/sigma_z_' num2str(iz) ')^2']);
     end
 end
 

examples/example_adjoint_hessian/simulate_model_adjoint_hessian.m

@@ -1,6 +1,7 @@
 % simulate_model_adjoint_hessian.m is the matlab interface to the cvodes mex
 %   which simulates the ordinary differential equation and respective
 %   sensitivities according to user specifications.
+%   this routine was generated using AMICI commit 8e3f5d50faeacd3f16d95839fea1182ef5417611 in branch stable in repo https://github.com/FFroehlich/AMICI.
 %
 % USAGE:
 % ======
@@ -71,8 +72,8 @@
 %        1: Hermite (DEFAULT for problems without discontinuities)
 %        2: Polynomial (DEFAULT for problems with discontinuities)
 %    .ordering   ... online state reordering.
-%        0: AMD reordering
-%        1: COLAMD reordering (default)
+%        0: AMD reordering (default)
+%        1: COLAMD reordering
 %        2: natural reordering
 %
 % Outputs:
@@ -218,6 +219,7 @@
     sol.sx = bsxfun(@times,sol.sx,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.sy = bsxfun(@times,sol.sy,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.sz = bsxfun(@times,sol.sz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
+    sol.srz = bsxfun(@times,sol.srz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.ssigmay = bsxfun(@times,sol.ssigmay,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.ssigmayz = bsxfun(@times,sol.ssigmaz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
 end

examples/example_dirac_adjoint_hessVecProd/simulate_model_dirac_adjoint_hessVecProd.m

@@ -1,6 +1,7 @@
 % simulate_model_dirac_adjoint_hessVecProd.m is the matlab interface to the cvodes mex
 %   which simulates the ordinary differential equation and respective
 %   sensitivities according to user specifications.
+%   this routine was generated using AMICI commit 8e3f5d50faeacd3f16d95839fea1182ef5417611 in branch stable in repo https://github.com/FFroehlich/AMICI.
 %
 % USAGE:
 % ======
@@ -71,8 +72,8 @@
 %        1: Hermite (DEFAULT for problems without discontinuities)
 %        2: Polynomial (DEFAULT for problems with discontinuities)
 %    .ordering   ... online state reordering.
-%        0: AMD reordering
-%        1: COLAMD reordering (default)
+%        0: AMD reordering (default)
+%        1: COLAMD reordering
 %        2: natural reordering
 %
 % Outputs:
@@ -229,6 +230,7 @@
     sol.sx = bsxfun(@times,sol.sx,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.sy = bsxfun(@times,sol.sy,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.sz = bsxfun(@times,sol.sz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
+    sol.srz = bsxfun(@times,sol.srz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.ssigmay = bsxfun(@times,sol.ssigmay,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.ssigmayz = bsxfun(@times,sol.ssigmaz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
 end

examples/example_events/model_events_syms.m

@@ -3,6 +3,7 @@
 % set the parametrisation of the problem options are 'log', 'log10' and
 % 'lin' (default).
 model.param = 'log10';
+
 %%
 % STATES
 

examples/example_jakstat_adjoint_hvp/example_jakstat_adjoint_hvp.m

@@ -2,7 +2,7 @@ function example_jakstat_adjoint_hvp()
 
     % compile the model
     [exdir,~,~]=fileparts(which('example_jakstat_adjoint_hvp.m'));
-    % amiwrap('model_jakstat_adjoint_hvp','model_jakstat_adjoint_hvp_syms',exdir,2)
+    amiwrap('model_jakstat_adjoint_hvp','model_jakstat_adjoint_hvp_syms',exdir,2)
     num = xlsread(fullfile(exdir,'pnas_data_original.xls'));
 
     D.t = num(:,1);

examples/example_jakstat_adjoint_hvp/simulate_model_jakstat_adjoint_hvp.m

@@ -1,6 +1,7 @@
 % simulate_model_jakstat_adjoint_hvp.m is the matlab interface to the cvodes mex
 %   which simulates the ordinary differential equation and respective
 %   sensitivities according to user specifications.
+%   this routine was generated using AMICI commit 8e3f5d50faeacd3f16d95839fea1182ef5417611 in branch stable in repo https://github.com/FFroehlich/AMICI.
 %
 % USAGE:
 % ======
@@ -71,8 +72,8 @@
 %        1: Hermite (DEFAULT for problems without discontinuities)
 %        2: Polynomial (DEFAULT for problems with discontinuities)
 %    .ordering   ... online state reordering.
-%        0: AMD reordering
-%        1: COLAMD reordering (default)
+%        0: AMD reordering (default)
+%        1: COLAMD reordering
 %        2: natural reordering
 %
 % Outputs:
@@ -226,6 +227,7 @@
     sol.sx = bsxfun(@times,sol.sx,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.sy = bsxfun(@times,sol.sy,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.sz = bsxfun(@times,sol.sz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
+    sol.srz = bsxfun(@times,sol.srz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.ssigmay = bsxfun(@times,sol.ssigmay,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
     sol.ssigmayz = bsxfun(@times,sol.ssigmaz,permute(theta(options_ami.sens_ind),[3,2,1])*log(10));
 end