updating model_setup docs

docs/source/model_setup.rst

@@ -3,10 +3,12 @@
 Model Setup
 ===========
 
-Geography/World
+.. _setup-geography:
 
+Geography/World
+---------------
 
-``JUNE`` operates on a threetiered geographical hierarchy:
+``JUNE`` operates on a three tiered geographical hierarchy:
 1. Regions: the highest level
 2. Super areas: the middle level
 3. Areas: the lowest level
@@ -20,12 +22,12 @@ Much of the code handling the creation of the geography is using that
 of the ``JUNE`` code. Some modifications have been made to allow for a
 simpler input format.
 
-On the :ref:`datainputs` page we discussed the :ref:`datageography` data required. Here we set up the heirarchy and provide the
+On the :ref:`data-inputs` page we discussed the :ref:`data-geography` data required. Here we set up the heirarchy and provide the
 coordinates for the super areas and areas.
 
 These files are utilised by the :class:`.CampGeography` class which
-generates the geography. This class inherits from the make ``JUNE``
-class ``Geography``. If you want to only generate a subset of the
+generates the geography. This class inherits from the ``june.Geography``
+class. If you want to only generate a subset of the
 possible geographic areas then the ``filter_key`` option can be used
 to pass a list of areas, super areas or regions which you want to
 initialise. An example of doing this is in the ``Notebooks/quickstart camps.ipynb`` notebook.
@@ -40,69 +42,66 @@ in the :func:`.generate_empty_world` function which also initialises
 an empty ``Population`` class (imported from ``JUNE``). We will cover
 this the :ref:`setupdemography` section.
 
-.. _setupdemography: 
+.. _setup-demography: 
 
 Demography
-
-
-TODO:
- Reference back to data inputs
- Add something on code to set up demography
+----------
 
 Households/Shelters
+-------------------
 
+The households in the camp are initialised based the data contained within ``camp_data/input/households/``.
+This folder contains three files:
 
-TODO:
- Reference back to data inputs page
+**1.** ``area_residents_families.csv`` informs the distributor of the demography of the population
+**2.** ``area_household_structure.csv`` informs the distributor of household types and household properties 
+   in each area
+**3.** ``household_structure.yaml`` informs the distributor of the distribution of household sizes across the camp
 
-The households in the camp are initialised based the data contained within camp_data/input/households/.
-This folder contains three files;
+Given the number of households provided in ``area_household_structure.csv`` per venue we initialise empty households of sizes
+of the correct frequency determined by ``household_structure.yaml``.
 
-**1.** area_residents_families.csv informs the distributor of the demography of the population
-**2.** area_household_structure.csv informs the distributor of household types and household properties 
-   in each area
-**3.** household_structure.yaml informs the distributor of the distribution of household sizes across the camp
-
-Given the number of households provided in area_household_structure.csv per venue we initialise empty households of sizes
-of the correct frequency determined by household_structure.yaml household_sizes distribution. Each of these households
-is placed into a sublists of each household type::
-   Houses with children
-   Houses without children
-   Houses with single occupants
-   Houses with multigenerational families
+Each of these households is placed into a sublist of each household
+type:
+
+- Houses with children
+- Houses without children
+- Houses with single occupants
+- Houses with multigenerational families
+
 The length of each of these lists is proportionate to the relevent fractions of households of each type determined from 
-area_household_structure.csv. For each household we generate the following parameters (where appropitate for the household type)
-   Spousal age gap (area_household_structure.csv "avgAgeDiff")
-   First child mother age gap (area_household_structure.csv "MotherFirst Child Age Diff")
-   Number of children (area_household_structure.csv "children per family")
-   mother grandmother age gap (First child mother age gap)
-   Age gap between children = 1 year
-In each of these parameters we allow for a small deviation. First we place random young adults, and if appropiate add a spousal 
+``area_household_structure.csv``.
+
+For each household we generate the following parameters (where
+appropitate for the household type):
+
+- Spousal age gap (``avgAgeDiff``)
+- First child mother age gap (``MotherFirst Child Age Diff``)
+- Number of children (``children per family``)
+- Mother grandmother age gap (``First child mother age gap``)
+- Age gap between children is set to 1 year
+
+In each of these parameters we allow for a small deviation. First, we place random young adults, and if appropiate add a spousal 
 partner of the oposite sex. Then children are distributed obeying the appropiate age gaps between children and parents and siblings.
-Lastly we distribute older adults to multigenerational households.
+Lastly, we distribute older adults to multigenerational households.
 
 After this procedure there can be a small number of leftover individuals which we place in households randomly in which there remains 
 space.
 
-To form shelters we randomly combine two of 75% of the total households to form a shared multiple family shelter of two households. The remaining 25% of households form 
-a single household shelter. 
-
+To form shelters we combine multiple households to form a shared multiple family shelter of two households.
 
 
 Activities/Locations
+--------------------
 
-
-TODO:
- Reference back to data inputs page
- Add something on construction of locations  referencing back to
-  main JUNE
-
-.. _setupinteractions:
+.. _setup-interactions:
 
 Interactions
+------------
 
 
 Policies
+--------
 
 
 

docs/source/symptoms.rst

@@ -3,10 +3,6 @@
 Disease Characteristics
 =======================
 
-TODO:
-- Be clear which ones of these can be set from the camps model itself
-  as there are some which are set in the model running script.
-
 By default, the ``JUNE`` framework is set up to model COVID-19. It has the
 capacity to model multiple variants, where different parameters are
 set relative to the wild-type (original) variant. however, the disease is able