Added code block captions.

Documentation.org

@@ -241,6 +241,7 @@ def select_Xi_parsimony_sweep(msindyc):
 #+end_src
 
 #+NAME: c0
+#+CAPTION: This code block is associated with the upper subplot in Figure 1.
 #+begin_src python :noweb strip-export :exports both :tangle ./Scripts/c0.py :results file :return filepath
 cluster=0
 
@@ -265,6 +266,7 @@ filepath = plot_clusterModels(
 #+end_src
 
 #+NAME: c1
+#+CAPTION: This code block is associated with the lower subplot in Figure 1.
 #+begin_src python :noweb strip-export :exports both :tangle ./Scripts/c1.py :results file :return filepath
 cluster=1
 <<sindyc_header>>
@@ -298,7 +300,9 @@ filepath = plot_clusterModels(
 
 #+end_src
 
+
 #+NAME: cosimulate_ID_c0
+#+CAPTION: This code block is associated with Figure 2.
 #+begin_src python :results file :exports both :return filename :tangle ./Scripts/cosimulate_ID_c0.py :noweb yes
 import copy
 import numpy as np
@@ -362,6 +366,7 @@ filename = plot_sns(
 #+end_src
 
 #+NAME: one_step_prediction_surface
+#+CAPTION: This code block is associated with Figure 3.
 #+begin_src python :tangle ./Scripts/one_step_prediction_surface.py :exports both :results file :return filepath :noweb yes
 <<paper_simulation_header>>
 <<paper_simulation_class>>
@@ -479,7 +484,8 @@ filepath = plot_one_step_prediction_map(mp, xs, us, cluster=[0])
 * TODO Markov Chain Monte Carlo
 
  #+NAME: c0_stan
- #+begin_src python :noweb strip-export :exports none :results file :tangle ./Scripts/c0_stan.py :return filepath
+ #+CAPTION: This code block is associated with subfigure (a) in Figure 4.
+ #+begin_src python :noweb strip-export :exports both :results file :tangle ./Scripts/c0_stan.py :return filepath
 cluster=0
 <<sindyc_header>>
 <<code_stan_fitModel>>
@@ -529,10 +535,9 @@ filepath = Plotter.plot_density(
 
  #+end_src
 
-
 #+NAME: c0_stan_ppc
-#+CAPTION: Posterior-Predictive check.
-#+begin_src python :exports none :results file :tangle ./Scripts/c0_stan_ppc.py :noweb yes :return filepath
+#+CAPTION: This code block is associated with subfigure (a) in Figure 5.
+#+begin_src python :exports both :results file :tangle ./Scripts/c0_stan_ppc.py :noweb yes :return filepath
 import numpy as np
 <<paper_plotting_header>>
 import arviz as az
@@ -581,9 +586,57 @@ filepath = Plotter.plot_ppc(
 
 #+end_src
 
+#+NAME: c1_stan
+#+CAPTION: This code block is associated with subfigure (b) in Figure 4.
+#+begin_src python :noweb strip-export :exports both :results file :tangle ./Scripts/c1_stan.py :return filepath
+cluster=1
+<<simo_IDCL_sindy_header>>
+<<code_stan_fitModel>>
+<<paper_simulation_header>>
+
+data = read_from_disc('data_simo_IDCL_c1.pkl')
+msindy = data['msindy']
+
+Xistar = select_Xi_parsimony_sweep(msindy)
+print(Xistar)
+
+df = data['df'][0]
+obs = df
+
+sigma_y_init = df.filter(regex='y').iloc[0, :].std()
+stan_results = Simulator.identify_stan(obs,
+                                       Xistar,
+                                       sigma_y_init=sigma_y_init,
+                                       name='c1',
+                                       fitnewmodel=True)
+
+var_names = {'plot_labels': [], 'labels': []}
+nXi = Xistar[Xistar != 0].shape[0]
+for n in range(nXi):
+    subscript = f'{n+2}'  # Only valid for this scenario
+    # var_names.append(r'\xi_' + subscript)
+    var_names['plot_labels'].append(r'$\xi_' + subscript + r'$')
+    var_names['labels'].append(f'Xi[{n+1}]')
+filename = 'simo_IDCL_c1_stan.pdf'
+filepath = os.path.join(PLOTPATH, filename)
+filepath = Plotter.plot_density(stan_results,
+                                var_names=var_names,
+                                var_prior=Xistar,
+                                labels=[[
+                                    'True parameter', 'Posterior',
+                                    'SINDyc (prior mean)',
+                                    r'95% confidence interval',
+                                    'MAP'
+                                ], None],
+                                original_model_obj=mp,
+                                show=False,
+                                save=True,
+                                filename=filepath)
+
+#+END_SRC
 
 #+NAME: c1_stan_ppc
-#+CAPTION: Posterior-Predictive check.
+#+CAPTION: This code block is associated with subfigure (b) in Figure 5.
 #+begin_src python :exports none :results file :tangle ./Scripts/c1_stan_ppc.py :noweb yes :return filepath
 import numpy as np
 <<paper_plotting_header>>
@@ -632,8 +685,8 @@ filepath = Plotter.plot_ppc(
 
 #+end_src
 
-
 #+NAME: stan_cosimulate_ID_c0
+#+CAPTION: This code block is associated with Figure 6.
 #+begin_src python :results file :exports results :return filename :tangle ./Scripts/stan_cosimulate_ID_c0.py :noweb yes
 from collections import OrderedDict
 import numpy as np