Add documentation for various parts of software

docs/_toc.yml

@@ -1,23 +1,32 @@
-# Table of contents
-# Learn more at https://jupyterbook.org/customize/toc.html
-
-format: jb-book
-root: index
-parts:
-# - file: markdown
-- caption: Documentation
-  chapters:
-  - file: classes-datastructures
-  - file: example_notebooks/workflow_minimal.ipynb
-  - file: input-files
-- caption: Notebooks
-  chapters:
-  - file: example_notebooks/echopro_workflow.ipynb
-  - file: example_notebooks/reports_workflow.ipynb
-  - file: example_notebooks/semi_variogram_workflow.ipynb
-  - file: example_notebooks/kriging_mesh_walkthrough.ipynb
-  - file: example_notebooks/transect_selection_workflow.ipynb
-  - file: example_notebooks/bootstrapping_walkthrough.ipynb
-- caption: Help & reference
-  chapters:
-  - file: api
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: index
+parts:
+# - file: markdown
+- caption: Documentation
+  chapters:
+  - file: core_data_structure
+  - file: input-files
+  - file: workflow_minimal.ipynb
+  - file: glossary
+    title: theory
+    sections: 
+      - file: theory/ts_length_conversion
+      - file: theory/acoustics_to_biomass_conversion
+      - file: theory/semivariograms
+      - file: theory/kriging
+      - file: theory/stratified_statistics
+      - file: theory/general_equations
+- caption: Notebooks
+  chapters:
+  - file: example_notebooks/echopro_workflow.ipynb
+  - file: example_notebooks/reports_workflow.ipynb
+  - file: example_notebooks/semi_variogram_workflow.ipynb
+  - file: example_notebooks/kriging_mesh_walkthrough.ipynb
+  - file: example_notebooks/transect_selection_workflow.ipynb
+  - file: example_notebooks/bootstrapping_walkthrough.ipynb
+- caption: Help & reference
+  chapters:
+  - file: api

docs/classes-datastructures.md → docs/core_data_structure.md

@@ -1,38 +1,40 @@
-# Classes and data structures
-
-## Classes
-
-Python EchoPro is designed using an object-oriented approach where data are stored in core classes and computations are called as methods (functions) on those classes.
-
-- Core class
-  - survey.Survey
-  - All actions and computations are orchestrated from this class
-- computation
-  - computation.transect_results.ComputeTransectVariables
-  - computation.semivariogram.SemiVariogram
-  - computation.kriging.Kriging
-  - computation.kriging_variables.ComputeKrigingVariables
-  - computation.bootstrapping.Bootstrapping
-- data loaders
-  - data_loader.kriging_mesh.KrigingMesh
-  - data_loader.biological_data.LoadBioData
-  - data_loader.stratification_data.LoadStrataData
-- report generation
-  - reports.Reports
-
-### Other notes
-
-- `bio_calc`: From `computation.transect_results.ComputeTransectVariables`; and also from Kriging?
-  - Categorize the long list of df's and gdf's available on `bio_calc`; eg, `kriging`, `kriging_bin`, `transect`, `weight_fraction`, etc. These can be categorized either by prefix or suffix
-  - Only the 6 "results" tables are gdf's: transect vs kriging, and sex (all[empty]/male/female). eg, `transect_results_male_gdf`
-  - `bin_ds` is an xarray dataset
-  - Most of the other objects are dataframes (`_df`), but there are a few others that don't have a clarifying suffix: `strata_sig_b`, `all_strata`, `missing_strata`, `percentage_transects_selected`, `sel_tran_strata_choice` (a dict), `stratum_choices` (a dict)
-
-
-## Data structures
-
-- df's acessible from the `survey`
-    - innputs
-    - others
-- `bin_ds` 
+# Classes and data structures
+
+![ text ](images/core_data_structure.jpg)
+
+## Classes
+
+Python EchoPro is designed using an object-oriented approach where data are stored in core classes and computations are called as methods (functions) on those classes.
+
+- Core class
+  - survey.Survey
+  - All actions and computations are orchestrated from this class
+- computation
+  - computation.transect_results.ComputeTransectVariables
+  - computation.semivariogram.SemiVariogram
+  - computation.kriging.Kriging
+  - computation.kriging_variables.ComputeKrigingVariables
+  - computation.bootstrapping.Bootstrapping
+- data loaders
+  - data_loader.kriging_mesh.KrigingMesh
+  - data_loader.biological_data.LoadBioData
+  - data_loader.stratification_data.LoadStrataData
+- report generation
+  - reports.Reports
+
+### Other notes
+
+- `bio_calc`: From `computation.transect_results.ComputeTransectVariables`; and also from Kriging?
+  - Categorize the long list of df's and gdf's available on `bio_calc`; eg, `kriging`, `kriging_bin`, `transect`, `weight_fraction`, etc. These can be categorized either by prefix or suffix
+  - Only the 6 "results" tables are gdf's: transect vs kriging, and sex (all[empty]/male/female). eg, `transect_results_male_gdf`
+  - `bin_ds` is an xarray dataset
+  - Most of the other objects are dataframes (`_df`), but there are a few others that don't have a clarifying suffix: `strata_sig_b`, `all_strata`, `missing_strata`, `percentage_transects_selected`, `sel_tran_strata_choice` (a dict), `stratum_choices` (a dict)
+
+
+## Data structures
+
+- df's acessible from the `survey`
+    - innputs
+    - others
+- `bin_ds` 
 - results gdf's

docs/glossary.md

@@ -0,0 +1,3 @@
+Glossary of all symbols, indices, and notations used for mathematical equations and variables contained within the `Survey` class object. 
+
+![ text ](images/symbols.jpeg)