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casasglobal-org · Jan 22, 2025 · 452cec0 · 452cec0
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diff --git a/docs/examples/tutorials.md → docs/examples/index.md b/docs/examples/tutorials.md → docs/examples/index.md
@@ -14,22 +14,22 @@ These examples are arranged roughly in order of difficulty and complexity, with
 
     Population dynamics models, including exponential growth, the logistic equation, and predator-prey models.
 
-    [:octicons-arrow-right-24: Get started](./population_dynamics/population_modelling.md)
+    [:octicons-arrow-right-24: Get started](./population_dynamics/index.md)
 
 -   :material-roman-numeral-2:{ .lg .middle } __Mixing problems__
 
     ---
 
     Mixing of solutions in a single tank or across any number of tanks.
 
-    [:octicons-arrow-right-24: Get started](./mixing_problems/mixing_problems.md)
+    [:octicons-arrow-right-24: Get started](./mixing_problems/index.md)
 
 -   :material-roman-numeral-3:{ .lg .middle } __Second-order systems__
 
     ---
 
     How to simulate complex second-order or higher-order systems.
 
-    [:octicons-arrow-right-24: Get started](./second_order_odes/second_order_odes.md)
+    [:octicons-arrow-right-24: Get started](./second_order_odes/index.md)
 
 </div>
diff --git a/...amples/mixing_problems/mixing_problems.md → docs/examples/mixing_problems/index.md b/...amples/mixing_problems/mixing_problems.md → docs/examples/mixing_problems/index.md
diff --git a/...pulation_dynamics/population_modelling.md → docs/examples/population_dynamics/index.md b/...pulation_dynamics/population_modelling.md → docs/examples/population_dynamics/index.md
diff --git a/...es/second_order_odes/second_order_odes.md → docs/examples/second_order_odes/index.md b/...es/second_order_odes/second_order_odes.md → docs/examples/second_order_odes/index.md
diff --git a/docs/user_guide/getting_started.md → docs/index.md b/docs/user_guide/getting_started.md → docs/index.md
@@ -26,46 +26,46 @@ For most new users, going through the following resources in the suggested order
 
     Find out about the purpose and design principles of `psymple`.
 
-    [:octicons-arrow-right-24: Read more](../overview/introduction.md)
+    [:octicons-arrow-right-24: Read more](./overview/introduction.md)
 
 -   :material-roman-numeral-2:{ .lg .middle } __Modelling in psymple__
 
     ---
 
     Learn how to capture functions and differential equations in `psymple`, and combine these into complex models.
 
-    [:octicons-arrow-right-24: Start modelling](../components/functional_ported_objects.md)
+    [:octicons-arrow-right-24: Start modelling](./components/functional_ported_objects.md)
 
 -   :material-roman-numeral-3:{ .lg .middle } __Simulating models__
 
     ---
 
     Understand how to create and run simulations for `psymple` models.
 
-    [:octicons-arrow-right-24: Run simulations](./system.md)
+    [:octicons-arrow-right-24: Run simulations](system.md)
 
 -   :material-roman-numeral-4:{ .lg .middle } __Tutorials__
 
     ---
 
     Work through full examples of implementing, parametrising and simulating models.
 
-    [:octicons-arrow-right-24: See more](../examples/tutorials.md)
+    [:octicons-arrow-right-24: See more](./examples/tutorials.md)
 
 -   :material-roman-numeral-5:{ .lg .middle } __The mathematics__
 
     ---
 
     Learn more about the mathematical structures underneath psymple which tie everything together.
 
-    [:octicons-arrow-right-24: See the maths](../mathematics/ported_objects.md)
+    [:octicons-arrow-right-24: See the maths](./mathematics/ported_objects.md)
 
 -   :material-roman-numeral-6:{ .lg .middle } __Get involved__
 
     ---
 
     Find out how you can get involved in the community by using or developing `psymple`.
 
-    [:octicons-arrow-right-24: Get involved](../development/development.md)
+    [:octicons-arrow-right-24: Get involved](./development/development.md)
 
 </div>
diff --git a/docs/user_guide/simulation.md b/docs/user_guide/simulation.md
@@ -119,4 +119,4 @@ The time series used to plot each variable can also be accessed:
 
 ## Next steps
 
-Many more examples of creating and simulating models in `psymple` can be found in the [Examples](../examples/tutorials.md) section.
+Many more examples of creating and simulating models in `psymple` can be found in the [Examples](../examples/index.md) section.
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -15,6 +15,7 @@ theme:
     - content.code.annotate
     - navigation.tabs
     - navigation.tabs.sticky
+    - navigation.indexes
     - navigation.sections
     - navigation.footer
     - search.suggest
@@ -69,8 +70,14 @@ extra:
     default: latest
 
 nav:
+  - Home: index.md
+  - Overview:
+    - Introduction: overview/introduction.md
+    - Statement of need: overview/statement_of_need.md
+    - Hybrid systems modelling: overview/modelling_systems.md
+    - Mechanistic and correlative models: overview/modelling_types.md
+    - System design: overview/system_design.md
   - User guide:
-    - user_guide/getting_started.md
     - Building a model:
       - Defining functions: components/functional_ported_objects.md
       - Defining ODEs: components/variable_ported_objects.md
@@ -80,25 +87,19 @@ nav:
       - Building a system: user_guide/system.md
     - Running a simulation: 
       - Simulations: user_guide/simulation.md
-  - Overview:
-    - Introduction: overview/introduction.md
-    - Statement of need: overview/statement_of_need.md
-    - Hybrid systems modelling: overview/modelling_systems.md
-    - Mechanistic and correlative models: overview/modelling_types.md
-    - System design: overview/system_design.md
   - Examples:
-    - examples/tutorials.md
+    - Examples: examples/index.md
     - Population dynamics:
-      - Population modelling: examples/population_dynamics/population_modelling.md
+      - Population modelling: examples/population_dynamics/index.md
       - Malthusian growth: examples/population_dynamics/malthusian_population.md
       - Logistic growth: examples/population_dynamics/logistic_growth.md
       - Predator-prey systems: examples/population_dynamics/predator_prey.md
     - Mixing problems: 
-      - Mixing problems: examples/mixing_problems/mixing_problems.md
+      - Mixing problems: examples/mixing_problems/index.md
       - Single tank: examples/mixing_problems/single_tank.md
       - Multiple tanks: examples/mixing_problems/multiple_tanks.md
     - Second-order ODEs:
-      - Second-order ODEs: examples\second_order_odes\second_order_odes.md
+      - Second-order ODEs: examples\second_order_odes\index.md
       - Projectile motion: examples\second_order_odes\projectile_motion.md
       - Three body problem: examples\second_order_odes\three_body_problem.md
   - Mathematical components:
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Expand Up		@@ -119,4 +119,4 @@ The time series used to plot each variable can also be accessed:

		## Next steps

		Many more examples of creating and simulating models in `psymple` can be found in the [Examples](../examples/tutorials.md) section.
		Many more examples of creating and simulating models in `psymple` can be found in the [Examples](../examples/index.md) section.