Updates after Mandy's review (Thank you, Mandy!) (#13)

* Updates after Mandy's review (Thank you, Mandy!)

docs/emod/software-migration-creation-vector.rst

@@ -3,8 +3,8 @@ How to create vector migration files
 ====================================
 
 You can create the JSON metadata and binary migration files needed by |EMOD_s| to run simulations
-from CSV data using Python script below. You can assign the same probability of migration to
-each vector in a node or you can assign different migration rates based on gender or genetics of the vector.
+from CSV data using the Python script below. You can assign the same probability of migration to
+each vector in a :term:`node` or you can assign different migration rates based on gender or genetics of the vector.
 
 #.  Run the 'convert_csv_to_bin_vector_migration.py' script using the format below::
 
@@ -89,17 +89,17 @@ Actual csv:
 
 .. literalinclude:: ../csv/vector-migration-by-sex-input.csv
 
+.. _migration_vector_genetics:
 
 Different rates depending on genetics of the vector
 ---------------------------------------------------
 
 Header (required):  FromNodeID, ToNodeID, [], arrays denoting Allele_Combinations
-Allele_Combinations example: [["a1", "a1"], ["b1", "b1"]] or  [["X1","Y2"]] or [["*", "a0"], ["X1", "Y1"]]
-Due to use of commas in headers, it is best to use Excel to create them (or look at a sample text csv).
-This is to support VECTOR_MIGRATION_BY_GENETICS. Headers are required for this csv file.
+Allele_Combinations: [["a1", "a1"], ["b1", "b1"]] or  [["X1","Y2"]] or [["*", "a0"], ["X1", "Y1"]]
+Due to use of commas in headers, it is best to use Excel to create the csv input files.
 The first (empty, []) array is used as a "default rate" if the vector's genetics doesn't match any of the
 Allele_Combinations. The other column headers denote the rate that the vector will travel at if it matches the
-Allele_Combination listed. Vectors are checked against Allele_Combinations from most-specific, to least-specific,
+Allele_Combinations listed. Vectors are checked against Allele_Combinations from most-specific, to least-specific,
 regardless of the order in the csv file. Allele_Combinations can, but don't have to, include sex-alleles. Without
 specified sex-alleles, any vector that matches the alleles regardless of sex will travel at that rate. Use '*' as a
 wildcard if the second allele does not matter and can be matched with anything.
@@ -152,9 +152,10 @@ JSON metadata file
 ==================
 
 The metadata file is a JSON-formatted file that includes a metadata section and a node offsets
-section. The **Metadata** section contains a JSON object with parameters that help |EMOD_s| interpret the migration
-binary file. The users are encouraged to add their own parameters to the section to remind themselves about the source,
-reason, purpose of the binary file and the data it contains. Non-required parameters are ignored.
+section. The **Metadata** section contains a :term:`JSON (JavaScript Object Notation)` with parameters that help
+|EMOD_s| interpret the migration binary file. You are encouraged to add your own parameters to the section to remind
+your selves about the source, reason, and purpose of the binary file and the data it contains. Non-required parameters
+are ignored.
 
 
 Vector Migration Metadata File Parameters

docs/emod/software-migration-vector.rst

@@ -1,49 +1,42 @@
 =================
-Vector Migration
+Vector migration
 =================
 
-Vector migration file describes the rate of migration of vectors *out* of a geographic :term:`node`
-analogously to human migration (see :doc:`software-migration` for more information), the vector
+The vector migration file describes the rate of migration of vectors *out* of a geographic :term:`node`
+analogously to human migration (see :doc:`software-migration` for more information). The vector
 model does not support migration by age and age-based migration in the migration file will cause an
-error. Vector migration does support migration by gender as well as migration based on genetics (see below).
+error, but does support migration by vector gender as well as migration based on genetics (see below).
 Vector migration is one way, such that each trip made by a vector is independent of previous trips made
 by the vector.
 
 Note: If default geography is used (the configuration parameter **Enable_Demographics_Builtin** is set to 1,
 and **Default_Geography_Initial_Node_Population** and **Default_Geography_Torus_Size** are configured), 
-vector migration will be built internally and vectors will automatically migrate. It is a known issue,
-please see https://github.com/InstituteforDiseaseModeling/EMOD/issues/43
+vector migration will be built internally and vectors will automatically migrate.
 
-Vectors do not have a "MigrationType" as each species use only one file for all their migration needs.
+Vectors do not have a "MigrationType" as each species uses only one file for all their migration needs.
 
-Each vector species has its own **Vector_Migration_Filename**, if it is left as an empty string, no 
+Each vector species has its own **Vector_Migration_Filename**; if it is left as an empty string, no
 migration will happen for that species. The **Vector_Migration_Modifier_Equation** and its parameters 
 can influence female vector migration to particular nodes over others, while **x_Vector_Migration** is
-a multiplier affects the migration rates for both genders. See :doc:`parameter-configuration` for more
+a multiplier that affects the migration rates for both genders. See :doc:`parameter-configuration` for more
 information on the parameters governing vector migration.
 
+
 Vector Migration Using Genetics
 ===============================
 
-Vectors have a type of migration not available to humans set with "GenderDataType": VECTOR_MIGRATION_BY_GENETICS in the
+Vectors have a type of migration not available to humans set with **GenderDataType** = VECTOR_MIGRATION_BY_GENETICS in the
 migration metadata file (usually a .bin.json file).
 
-The way this migration works is that you can define a migration rate for each defined Allele_Combination.
-Allele_Combinations example: [ [], [["a1", "a1"], ["b1", "b1"]],  [["X1","Y2"]], [["*", "a0"], ["X1", "Y1"]]]
-The first (empty, []) array is used as a "default rate" if the vector's genetics doesn't match any of the
-Allele_Combinations. The other column Allele_Combinations will be associated with the rate that the vector will use
-if it matches with that Allele_Combination. Vectors are checked against Allele_Combinations from most-specific,
-to least-specific, regardless of the order in the Allele_Combinations parameter. Allele_Combinations can,
-but don't have to, include sex-alleles. Without specified sex-alleles, any vector that matches the alleles regardless
-of sex will travel at that rate. Please see Vector Migration File creation for more information.
+For information, see :ref:`migration_vector_genetics`.
 
 
 Vector Migration Files
 ======================
 
 The Binary file structure for the vector migration files is the same as it is for human files.
 The Allele_Combinations array, when present for vector VECTOR_MIGRATION_BY_GENETICS, is used in the same capacity as
-AgesYears array would be to maintain the same structure of the file. Please see migration file creation
+AgesYears array would be to maintain the same structure of the file. Please see :doc:`software-migration-creation`
 for more details.
 
 .. toctree::