Updates and model example additions (#19)

* updates and model example additions

* Updated funding information

* Removed Cheat sheet and Styleguide for updating work

* Improving model examples, making them more standardized

Author: vresbok

docs/examples/clads.md

@@ -0,0 +1,26 @@
+---
+id: div
+title: Diversification models
+sidebar_label: Diversification models
+---
+# Diversification models
+
+# Constant rate birth-death
+
+  - **Model file:** `models/phylo/crbd.tppl`
+
+  - **Example input data:** `models/phylo/crbd.json`
+
+  - **Brief info:** The model simulates the constant rate birth-death process over a phylogenetic tree. The speciation rate is returned.
+
+# ClaDS
+
+  - **Model file:** `models/phylo/clads.tppl`
+
+  - **Example input data:** `models/phylo/clads.json`
+
+  - **Brief info:** The model simulates the ClaDS process over a phylogenetic tree. This implementation of the ClaDS model is a simple version that returns the speciation rate λ; however, it does not return the branch-specific rates.
+
+  - **Reference:**
+    Maliet, O., Hartig, F. & Morlon, H. A model with many small shifts for estimating species-specific diversification rates. Nat Ecol Evol 3, 1086–1092 (2019). 
+    https://doi.org/10.1038/s41559-019-0908-0

docs/examples/crbd.md

@@ -1,7 +1,7 @@
 ---
 id: hostrep
 title: Host-repertoire model
-sidebar_label: Host-repertorire
+sidebar_label: Host-repertoire model
 ---
 
 <meta http-equiv="refresh" content="0; url=https://treeppl.org/treepplr/articles/hostrep-example.html" />

docs/examples/div.md

@@ -1,5 +1,4 @@
 # Model examples
 
-A library of models has been created as part of TreePPL.  
+A library of models has been created as part of TreePPL, see the `models` directory.  
 
-Phylogenetic models can be found under `models/phylo`.

docs/examples/host-repertoire.md

@@ -0,0 +1,22 @@
+---
+id: tree_inference
+title: Tree inference
+sidebar_label: Tree inference models
+---
+
+# Tree inference models
+
+# Jukes-Cantor
+
+  - **Model files:** `models/phylo/tree_inference.tppl`, `models/phylo/tree_inference_pruning.tppl`, `models/phylo/tree_inference_scaled.tppl`
+
+  - **Example input data:** `models/phylo/tree_inference.json`
+
+  - **Brief info:** The model version `tree_inference.tppl` is a simple backwards tree reconstruction based on aligned DNA sequence data (converted to integers) as input, and using the Jukes-Cantor model of nucleotide substitution. There are also other and more computationally efficient model versions:  `tree_inference_pruning.tppl` using hard-coded pruning (Felsenstein's pruning algorith) and `tree_inference_scaled.tppl` with pruning and a scaled approach to the messages. Use the scaled version for efficient inference on larger datasets.
+
+# GTR
+  - **Model file:** `models/phylo/tree_inference_pruning_gtr.tppl`
+
+  - **Example input data:** `models/phylo/tree_inference.json`
+
+  - **Brief info:** The basic models using Jukes-Cantor above can easily be extended to adhere other models of nucleotide substitution. As an example, this is the GTR model with pruning.

docs/examples/index.md

@@ -7,9 +7,9 @@ sidebar_position: 1
 
 The TreePPL documentation consists of:
 
- - [Tutorials](docs/tutorials), in which the user learns by doing something meaningful, towards some achievable goal;
  - [Model examples](docs/examples), which illustrate each model available in TreePPL;
-  - [Reference](docs/reference), which is material that contains the technical details of functions, compiler flags, options, etc.
-  - System, which is documentation for the people who would like to develop the TreePPL language itself
+ - [Reference](docs/reference), which is material that contains the technical details of functions, compiler flags, options, etc.
+ - [Tutorials](docs/tutorials), in which the user learns by doing something meaningful, towards some achievable goal;
+<!-- - To be added: System, which is documentation for the people who would like to develop the TreePPL language itself -->
 
 If you are new to TreePPL, we recommend beginning looking at our [Getting started pages](getting-started/getting-started).