setup basic no-op model with globals

README.md

 # Literate NetLogo
 
-This is an example project to demonstrate Literate Programming to create [NetLogo](https://ccl.northwestern.edu/netlogo/) models from ODD+C protocols. 
+This is an example project to demonstrate Literate Programming to create [NetLogo](https://ccl.northwestern.edu/netlogo/) models from ODD+C protocols.
 
 ## Rabies model - ODD protocol
 
 ### Purpose
 
+### Entities, state variables, and scales
 
+Each patch has a disease state.
 
-### Entities, state variables, and scales
+```netlogo
+;- State variables
+patches-own [
+  state
+]
+```
 
-### Process overview and scheduling
+```netlogo
+;- Disease states
+globals [
+  EMPTY
+  S
+  I
+  R
+]
+```
 
 ```netlogo
-;- file:Code.nls
-; ==> Setup.
-; ==> Go.
+;- Setup disease states
+set EMPTY 0
+set S 1
+set I 2
+set R 3
 ```
 
+### Process overview and scheduling
+
+
 ```netlogo
 ;- Go
 to go
+  update-patches
   tick
 end
+
+; ==> Update patches.
 ```
 
 ### Design concepts
@@ -32,6 +55,9 @@ end
 ```netlogo
 ;- Setup
 to setup
+  clear-all
+  ; ==> Setup disease states.
+  update-patches
   reset-ticks
 end
 ```
@@ -40,8 +66,35 @@ end
 
 ### Submodels
 
+#### Visualization
+
+```netlogo
+;- Update patches
+to update-patches   
+  ask patches [
+    ifelse state = EMPTY [ set pcolor white ]
+    [ ifelse state = S [ set pcolor blue ]
+    [ ifelse state = I [ set pcolor red ]
+    [ set pcolor green ] ] ]
+  ]
+end
+```
+
 ## Appendix
 
+### Code
+
+```netlogo
+;- file:Code.nls
+; ==> Disease states.
+
+; ==> State variables.
+
+; ==> Setup.
+
+; ==> Go.
+```
+
 ### NetLogo file
 
 In the main `nlogo` file, we only "include" an `nls` file to allow for the reverse mode.