Convert glossary entries to pandoc format

learners/reference.md

@@ -4,22 +4,20 @@ title: 'Glossary of Terms: Epiverse-TRACE'
 
 ## A
 
-#### Airborne transmission
-
-Individuals become infected via contact with infectious particles in the air. Examples include influenza, COVID-19. [More information on airborne transmission](https://www.ncbi.nlm.nih.gov/books/NBK531468/).
+[Airborne transmission]{#airborne}
+: Individuals become infected via contact with infectious particles in the air. Examples include influenza, COVID-19. [More information on airborne transmission](https://www.ncbi.nlm.nih.gov/books/NBK531468/).
 
 <!--  ## B -->
 
 <!-- ## C -->
 
 ## D
 
-#### Deterministic models
-Models that will always have the same trajectory for given initial conditions and parameters. Examples include ordinary differential equations and difference equations. 
-
-#### Direct transmission
+[Deterministic model]{#deterministic}
+: Models that will always have the same trajectory for given initial conditions and parameters. Examples include ordinary differential equations and difference equations. 
 
-Individuals become infected via direct contact with other infected humans. Airborne transmitted infections are often modelled as directly transmitted infections as they require close contact with infected individuals for successful transmission. 
+[Direct transmission]{#direct}
+: Individuals become infected via direct contact with other infected humans. Airborne transmitted infections are often modelled as directly transmitted infections as they require close contact with infected individuals for successful transmission. 
 
 <!-- ## E -->
 
@@ -31,23 +29,20 @@ Individuals become infected via direct contact with other infected humans. Airbo
 
 ## I 
 
-#### Incubation period
-
-The time between becoming infected and the onset of infectiousness, same as 'Latent period'.
+[Incubation period]{#incubation}
+: The time between becoming infected and the onset of infectiousness, same as [latent period](#latent).
 
-#### Indirect transmission
-
-Indirectly transmitted infections are passed on to humans via contact with vectors, animals or contaminated environment. Vector-borne infections, zoonoses and water-borne infections are modelled as indirectly transmitted. 
+[Indirect transmission]{#indirect}
+: Indirectly transmitted infections are passed on to humans via contact with vectors, animals or contaminated environment. Vector-borne infections, zoonoses and water-borne infections are modelled as indirectly transmitted. 
 
 <!-- ## J -->
 
 <!-- ## K -->
 
 ## L
 
-#### Latent period
-
-The time between becoming infected and the onset of infectiousness, same as 'Incubation period'.
+[Latent period]{#latent}
+: The time between becoming infected and the onset of infectiousness, same as [incubation period](#incubation).
 
 
 <!-- ## M -->
@@ -64,8 +59,8 @@ The time between becoming infected and the onset of infectiousness, same as 'Inc
 
 ## S
 
-#### Stochastic model
-A model that includes some stochastic process resulting in variation in model simulations for the same initial conditions and parameters. Examples include stochastic differential equations, branching process models. For more detail see [Allen (2017)](https://doi.org/10.1016/j.idm.2017.03.001).
+[Stochastic model]{#stochastic}
+: A model that includes some stochastic process resulting in variation in model simulations for the same initial conditions and parameters. Examples include stochastic differential equations, branching process models. For more detail see [Allen (2017)](https://doi.org/10.1016/j.idm.2017.03.001).
 
 
 <!-- ## T -->
@@ -74,8 +69,8 @@ A model that includes some stochastic process resulting in variation in model si
 
 ## V
 
-#### Vector-borne transmission 
-Vector-borne transmission means an infection can be passed from a vector (e.g. mosquitoes) to humans. Examples of vector-borne diseases include malaria and dengue. [More information on vector-borne transmission](https://www.who.int/news-room/fact-sheets/detail/vector-borne-diseases).  
+[Vector-borne transmission]{#vectorborne}
+: Vector-borne transmission means an infection can be passed from a vector (e.g. mosquitoes) to humans. Examples of vector-borne diseases include malaria and dengue. [More information on vector-borne transmission](https://www.who.int/news-room/fact-sheets/detail/vector-borne-diseases).  
 
 
 <!-- ## W -->