Added more example tests, doc update, and kwargs test

docs/source/PPP_pages/examples.rst

@@ -0,0 +1,28 @@
+========
+Examples
+========
+
+#################
+Function Examples
+#################
+
+PPP functions may be called at the command-line as shown in this example:
+
+.. code-block:: bash
+        
+        vcf_filter.py --vcf examples/files/merged_chr1_10000.vcf.gz --filter-only-biallelic --out-format bcf
+
+Details on the usage of a specific function may be found within the *Example usage* section of the function in question. In addition, all example files used may be found within **examples/files** directory.  
+
+
+##########################
+Jupyter Notebook Pipelines
+##########################
+
+All PPP functions may also be used within a `Jupyter Notebook <https://jupyter.org/>`_. We have included some examples below:
+
+.. toctree::
+   :maxdepth: 1
+   :hidden:
+
+   example_pipeline_pan.ipynb

docs/source/PPP_pages/model.rst

@@ -2,7 +2,10 @@
 Model File and Creation
 =======================
 
-A unique benefit of the PPP is the ability to use the Model files. Model files are JSON-based files used to store population models and their relevant details, such as: the populations within the model; the individuals in each population; the population tree; and other potential meta-data as needed. Model files allow the PPP functions to automatically assign various parameters and serves as the repository for all model-related information.
+A core aspect of the PPP is the use of Model files, JSON-based files used to assign and store **population models**. A population model primarily consists of: the populations within the model; the individuals in each population; and a population tree. Model files offer various benefits within the PPP: i) automatic assignment of relevant populations, individuals, or other potential meta-data; ii) simplifed process to examine multiple models; and iii) a single repository of all relevant meta-data. 
+
+
+Model files may be created and edited using our model creator. 
 
 .. toctree::
    :maxdepth: 1
@@ -17,6 +20,7 @@ An example Model file may be seen below:
     [
     {
         "name": "2Pop",
+        "tree": (Troglodytes,Verus);
         "pops": {
             "Verus": {
                 "inds": [

docs/source/index.rst

@@ -29,11 +29,11 @@ Please Note: This documentation is currently being devloped and will be updated
    :hidden:
 
    PPP_pages/install
+   PPP_pages/examples
    PPP_pages/functions
    PPP_pages/input_file_generators
    PPP_pages/analyses
    PPP_pages/utilities
    PPP_pages/model
    PPP_pages/contact
-   PPP_pages/citations
-   example_pipeline_pan.ipynb
+   PPP_pages/citations

examples/files/chr1_sites.1.bed

@@ -0,0 +1,21 @@
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examples/files/chr1_sites.2.bed

@@ -0,0 +1,32 @@
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examples/files/chr1_sites.3.bed

@@ -0,0 +1,41 @@
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examples/files/chr1_sites.4.bed

@@ -0,0 +1,30 @@
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examples/files/chr1_sites.unsorted.bed

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examples/files/chr_sizes.txt

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