diff --git a/README.md b/README.md
index 7a784be..3ee5ea6 100644
--- a/README.md
+++ b/README.md
@@ -1,21 +1,29 @@
 LAGOS GIS Toolbox
 ===================
 
-This is an ArcGIS toolbox for landscape limnology created from a collection of Python script tools. It was used to create the [LAGOS-NE database](https://lagoslakes.org/) and is currently being updated in 2017 and 2018 for the creation of the LAGOS-US database.
+This is an ArcGIS toolbox for landscape limnology created from a collection of Python script tools. It was used to create the [LAGOS-US database](https://lagoslakes.org/).
 
-This toolbox was created with ArcGIS 10.1. It is being maintained in ArcGIS 10.3. It may work for other versions of ArcGIS.
 
 ## Releases & Citation
+Release [v2.0](https://github.com/cont-limno/LAGOS_GIS_Toolbox/tree/v2.0) corresponds to the methods documented with the release of the LAGOS-US LOCUS and GEO modules
+
+LOCUS Data citation:
+Smith, N.J., K.E. Webster, L.K. Rodriguez, K.S. Cheruvelil, and P.A. Soranno. 2021. LAGOS-US LOCUS v1.0: Data module of location, identifiers, and physical characteristics of lakes and their watersheds in the conterminous U.S. ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/e5c2fb8d77467d3f03de4667ac2173ca (Accessed 2021-12-13).
+
+Data paper citation:
+Cheruvelil, K.S., Soranno, P.A., McCullough, I.M., Webster, K.E., Rodriguez, L.K. and Smith, N.J. (2021), LAGOS-US LOCUS v1.0: Data module of location, identifiers, and physical characteristics of lakes and their watersheds in the conterminous U.S. Limnol Oceanogr Letters 6: 270-292. https://doi-org.proxy1.cl.msu.edu/10.1002/lol2.10203
+
+GEO Data citation
+Smith, N.J., K.E. Webster, L. Rodriguez, K.S. Cheruvelil, and P.A. Soranno. 2021. LAGOS-US GEO: Data module of lake geospatial ecological context at multiple spatial and temporal scales in the conterminous U.S. Environmental Data Initiative. https://doi.org/??????. Dataset accessed XX/XX/2022.
+
 Release [v1.0](https://github.com/cont-limno/LAGOS_GIS_Toolbox/tree/v1.0) corresponds to the methods documented in the following manuscript:
 
 Soranno, P. A., Bissell, E. G., Cheruvelil, K. S., Christel, S. T., Collins, S. M., Fergus, C. E., ... & Scott, C. E. (2015). Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse. *GigaScience, 4*(1), 28.
 
 ## Requires
 * Spatial Analyst extension (some tools)
-* [RivEX software](http://www.rivex.co.uk/) (proprietary) to create the input (rivers with Strahler order assignment) to the Lake Order Tool.
-* While some steps in our workflow at Michigan State University are conducted in a supercomputing environment (ie Taudem
-pitremove & d8flowdir were ported to RHEL to get the data processed faster), you can do these steps on a workstation
-easily enough with ESRI tools or with the [Taudem](http://hydrology.usu.edu/taudem/taudem5/index.html) tool suite.
+* ArcGIS 10.3 or higher
+* [Taudem](http://hydrology.usu.edu/taudem/taudem5/index.html) tool suite (some tools).
 ## Installation
 
 ![](installation.png)
@@ -31,47 +39,37 @@ easily enough with ESRI tools or with the [Taudem](http://hydrology.usu.edu/taud
 ## Tools
 **Lake Analysis**
 * Lake Connectivity Classification
-* Lake Order Classification
-* Lake-Wetland Connections
 * Upstream Lakes
 
 **Summarize Data by Zones**
-* Lakes in Zones
-* Line Density
-* Point Density
-* Polygons in Zones
-* Streams in Zones
-* Subset Overlapping Zones
-* Wetlands in Zones
-* Zonal Attribution of Raster Data
+* Flatten Overlapping Zones
+* LAGOS-US Lake Density
+* LAGOS-US Stream Density
+* Line Density in Zones
+* Point Attribution of Raster Data
+* Point Density in Zones
+* Polygon Density in Zones
+* Pre-process PAD-US Dataset
+* Rasterize Zones
+* Zonal Summary of Classed Polygons
+* Zonal Summary of Raster Data
 
 **Utilities**
-* Add Unique Fields
-* Drop Fields and Calc Geometry
 * Export to CSV
-* Merge Many Feature Classes
-* Merge Many Shapefiles
-* Merge NHD Features
 * Merge NHD Features without Deduplication
-* Mosaic to Subregion
-* Prefix Field Names
+* Test LAGOS GIS Toolbox
 
 **Watershed Delineation**
-1. State and Mosaic Data for Subregion
-2. Burn Flowlines into DEM
-3. Clip DEM to HU8 Boundaries
-4. (Step 4 (Fill Pits) is not in toolbox)
-5. Create HU8 Walls
-6. (Step 6 (Flow Direction) is not in toolbox)
-7. Convert TauDEM Flow Direction Raster to ArcGIS Format
-8. Create Pour Points
-9. Create Lake Watersheds
-
-**Wetland Analysis**
-1. Preprocess NWI
-2. Wetland Order
+Plus-01. Add Waterbody NHDPlusID
+Plus-02. Update Grid Codes
+Plus-03. Add Lake Seeds (Pour Points/Outlets)
+Plus-04. Revise HydroDEM
+Plus-05. TauDEM Pit Remove
+Plus-06. Flow Direction
+Plus-07. Delineate Catchments
+Plus-08. Aggregrate Watersheds
 
 ---
 
-The toolbox is not formally supported. You can direct questions to the current maintainer, Nicole Smith (smithn78@msu.edu), or the project PI, Patricia Soranno (soranno@msu.edu).
+The toolbox is not formally supported. You can direct questions to the project PI, Kendra Cheruvelil (ksc@msu.edu).
 
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diff --git a/geo_job_control.csv b/geo_job_control.csv
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+++ b/geo_job_control.csv
@@ -1,6897 +1,6896 @@
 Line,Function,Arg1,Arg2,Arg3,Arg4,Arg5,Arg6,Arg7,Arg8,Output,CSV
-1,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,F:\Continental_Limnology\Data_Downloaded\Terrestrial_Ecosystems_Land_Surface_Forms\Pre-processed\landform.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_landform,TRUE,,hu12_landform,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_landform,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_landform.csv
-2,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu4_raster',hu4_zoneid,F:\Continental_Limnology\Data_Downloaded\Terrestrial_Ecosystems_Land_Surface_Forms\Pre-processed\landform.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_landform,TRUE,,hu4_landform,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_landform,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu4_landform.csv
-3,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu8_raster',hu8_zoneid,F:\Continental_Limnology\Data_Downloaded\Terrestrial_Ecosystems_Land_Surface_Forms\Pre-processed\landform.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_landform,TRUE,,hu8_landform,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_landform,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu8_landform.csv
-4,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatnws_raster',flatnws_zoneid,F:\Continental_Limnology\Data_Downloaded\Terrestrial_Ecosystems_Land_Surface_Forms\Pre-processed\landform.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_landform,TRUE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/nws_unflat',nws_landform,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_landform,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_landform.csv
-5,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatws_raster',flatws_zoneid,F:\Continental_Limnology\Data_Downloaded\Terrestrial_Ecosystems_Land_Surface_Forms\Pre-processed\landform.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/ws_landform,TRUE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/ws_unflat',ws_landform,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/ws_landform,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/ws_landform.csv
-6,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\bailey_raster',bailey_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/bailey_lith,TRUE,,bailey_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/bailey_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/bailey_lith.csv
-7,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\county_raster',county_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/county_lith,TRUE,,county_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/county_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/county_lith.csv
-8,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\epanutr_raster',epanutr_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/epanutr_lith,TRUE,,epanutr_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/epanutr_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/epanutr_lith.csv
-9,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_lith,TRUE,,hu12_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_lith.csv
-10,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu4_raster',hu4_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_lith,TRUE,,hu4_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu4_lith.csv
-11,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu8_raster',hu8_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_lith,TRUE,,hu8_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu8_lith.csv
-12,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\mlra_raster',mlra_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/mlra_lith,TRUE,,mlra_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/mlra_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/mlra_lith.csv
-13,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\neon_raster',neon_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_lith,TRUE,,neon_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/neon_lith.csv
-14,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\omernik3_raster',omernik3_zoneid,F:\Continental_Limnology\Data_Downloaded\Lithology\Pre-processed\lithology.tif,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/omernik3_lith,TRUE,,omernik3_lith,pct,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/omernik3_lith,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/omernik3_lith.csv
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-1983,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201401_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201401,FALSE,,hu12_tmean_201401,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201401,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201401.csv
-1984,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201402_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201402,FALSE,,hu12_tmean_201402,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201402,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201402.csv
-1985,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201403_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201403,FALSE,,hu12_tmean_201403,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201403,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201403.csv
-1986,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201404_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201404,FALSE,,hu12_tmean_201404,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201404,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201404.csv
-1987,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201405_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201405,FALSE,,hu12_tmean_201405,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201405,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201405.csv
-1988,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201406_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201406,FALSE,,hu12_tmean_201406,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201406,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201406.csv
-1989,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201407_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201407,FALSE,,hu12_tmean_201407,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201407,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201407.csv
-1990,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201408_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201408,FALSE,,hu12_tmean_201408,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201408,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201408.csv
-1991,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201409_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201409,FALSE,,hu12_tmean_201409,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201409,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201409.csv
-1992,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201410_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201410,FALSE,,hu12_tmean_201410,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201410,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201410.csv
-1993,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201411_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201411,FALSE,,hu12_tmean_201411,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201411,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201411.csv
-1994,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201412_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201412,FALSE,,hu12_tmean_201412,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201412,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201412.csv
-1995,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201501_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201501,FALSE,,hu12_tmean_201501,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201501,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201501.csv
-1996,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201502_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201502,FALSE,,hu12_tmean_201502,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201502,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201502.csv
-1997,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201503_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201503,FALSE,,hu12_tmean_201503,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201503,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201503.csv
-1998,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201504_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201504,FALSE,,hu12_tmean_201504,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201504,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201504.csv
-1999,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201505_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201505,FALSE,,hu12_tmean_201505,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201505,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201505.csv
-2000,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201506_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201506,FALSE,,hu12_tmean_201506,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201506,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201506.csv
-2001,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201507_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201507,FALSE,,hu12_tmean_201507,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201507,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201507.csv
-2002,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201508_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201508,FALSE,,hu12_tmean_201508,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201508,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201508.csv
-2003,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201509_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201509,FALSE,,hu12_tmean_201509,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201509,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201509.csv
-2004,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201510_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201510,FALSE,,hu12_tmean_201510,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201510,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201510.csv
-2005,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201511_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201511,FALSE,,hu12_tmean_201511,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201511,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201511.csv
-2006,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201512_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201512,FALSE,,hu12_tmean_201512,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201512,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201512.csv
-2007,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201601_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201601,FALSE,,hu12_tmean_201601,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201601,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201601.csv
-2008,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201602_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201602,FALSE,,hu12_tmean_201602,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201602,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201602.csv
-2009,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201603_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201603,FALSE,,hu12_tmean_201603,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201603,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201603.csv
-2010,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201604_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201604,FALSE,,hu12_tmean_201604,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201604,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201604.csv
-2011,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201605_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201605,FALSE,,hu12_tmean_201605,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201605,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201605.csv
-2012,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201606_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201606,FALSE,,hu12_tmean_201606,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201606,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201606.csv
-2013,zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\PRISM_Climate\tmean\Pre-processed\PRISM_tmean_stable_4kmM3_201607_bil_albers.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201607,FALSE,,hu12_tmean_201607,degc,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_tmean_201607,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tmean_201607.csv
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-6542,lake_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\neon',neon_zoneid,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\Lakes\LAGOS_US_All_Lakes_1ha',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_lakecount,,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_lakecount,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/neon_lakecount.csv
-6543,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\buff500',buff500_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/buff500_streams_all,buff500,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/buff500_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff500_streams_all.csv
-6544,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\nws',nws_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_streams_all,nws,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_streams_all.csv
-6545,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\ws',ws_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/ws_streams_all,ws,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/ws_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/ws_streams_all.csv
-6546,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\hu12',hu12_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_streams_all,hu12,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_streams_all.csv
-6547,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\hu8',hu8_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_streams_all,hu8,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu8_streams_all.csv
-6548,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\hu4',hu4_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_streams_all,hu4,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu4_streams_all.csv
-6549,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\county',county_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/county_streams_all,county,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/county_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/county_streams_all.csv
-6550,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\state',state_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/state_streams_all,state,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/state_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/state_streams_all.csv
-6551,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\epanutr',epanutr_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/epanutr_streams_all,epanutr,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/epanutr_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/epanutr_streams_all.csv
-6552,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\omernik3',omernik3_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/omernik3_streams_all,omernik3,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/omernik3_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/omernik3_streams_all.csv
-6553,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\wwf',wwf_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/wwf_streams_all,wwf,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/wwf_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/wwf_streams_all.csv
-6554,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\mlra',mlra_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/mlra_streams_all,mlra,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/mlra_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/mlra_streams_all.csv
-6555,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\bailey',bailey_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/bailey_streams_all,bailey,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/bailey_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/bailey_streams_all.csv
-6556,stream_density,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\neon',neon_zoneid,r'D:\Continental_Limnology\Data_Working\Default_Save.gdb\lagos_stream_minimal',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_streams_all,neon,,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_streams_all,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/neon_streams_all.csv
-6557,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\buff500',buff500_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/buff500_streams_rivers,,buff500_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/buff500_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff500_streams_rivers.csv
-6558,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\nws',nws_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_streams_rivers,,nws_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_streams_rivers.csv
-6559,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\ws',ws_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/ws_streams_rivers,,ws_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/ws_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/ws_streams_rivers.csv
-6560,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\hu12',hu12_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_streams_rivers,,hu12_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu12_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_streams_rivers.csv
-6561,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\hu8',hu8_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_streams_rivers,,hu8_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu8_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu8_streams_rivers.csv
-6562,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\hu4',hu4_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_streams_rivers,,hu4_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/hu4_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu4_streams_rivers.csv
-6563,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\county',county_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/county_streams_rivers,,county_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/county_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/county_streams_rivers.csv
-6564,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\state',state_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/state_streams_rivers,,state_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/state_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/state_streams_rivers.csv
-6565,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\epanutr',epanutr_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/epanutr_streams_rivers,,epanutr_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/epanutr_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/epanutr_streams_rivers.csv
-6566,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\omernik3',omernik3_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/omernik3_streams_rivers,,omernik3_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/omernik3_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/omernik3_streams_rivers.csv
-6567,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\wwf',wwf_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/wwf_streams_rivers,,wwf_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/wwf_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/wwf_streams_rivers.csv
-6568,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\mlra',mlra_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/mlra_streams_rivers,,mlra_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/mlra_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/mlra_streams_rivers.csv
-6569,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\bailey',bailey_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/bailey_streams_rivers,,bailey_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/bailey_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/bailey_streams_rivers.csv
-6570,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\neon',neon_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\rivers',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_streams_rivers,,neon_streams_rivers,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_streams_rivers,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/neon_streams_rivers.csv
-6571,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\buff500',buff500_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\midreaches',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/buff500_streams_midreaches,,buff500_streams_midreaches,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/buff500_streams_midreaches,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff500_streams_midreaches.csv
-6572,line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\nws',nws_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\midreaches',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_streams_midreaches,,nws_streams_midreaches,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/nws_streams_midreaches,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_streams_midreaches.csv
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+6883,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatnws_raster',flatnws_zoneid,r'F:\Continental_Limnology\Data_Downloaded\EDNA_CTI\Unzipped Original\us_cti\cti',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/nws_topographicwetness,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/nws_unflat',nws_topographicwetness,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/nws_topographicwetness,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_topographicwetness.csv
+6884,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'F:\Continental_Limnology\Data_Downloaded\EDNA_CTI\Unzipped Original\us_cti\cti',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/hu12_topographicwetness,FALSE,,hu12_topographicwetness,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/hu12_topographicwetness,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_topographicwetness.csv
+6885,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatbuff100_raster',flatbuff100_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\tri.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff100_tri,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/buff100_unflat',buff100_tri,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff100_tri,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff100_tri.csv
+6886,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatbuff500_raster',flatbuff500_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\tri.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff500_tri,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/buff500_unflat',buff500_tri,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff500_tri,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff500_tri.csv
+6887,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatws_raster',flatws_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\tri.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/ws_tri,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/ws_unflat',ws_tri,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/ws_tri,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/ws_tri.csv
+6888,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatnws_raster',flatnws_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\tri.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/nws_tri,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/nws_unflat',nws_tri,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/nws_tri,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_tri.csv
+6889,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\tri.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/hu12_tri,FALSE,,hu12_tri,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/hu12_tri,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_tri.csv
+6890,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatbuff100_raster',flatbuff100_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\elevation.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff100_elevation,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/buff100_unflat',buff100_elevation,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff100_elevation,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff100_elevation.csv
+6891,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatbuff500_raster',flatbuff500_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\elevation.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff500_elevation,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/buff500_unflat',buff500_elevation,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/buff500_elevation,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/buff500_elevation.csv
+6892,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatws_raster',flatws_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\elevation.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/ws_elevation,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/ws_unflat',ws_elevation,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/ws_elevation,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/ws_elevation.csv
+6893,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\flatnws_raster',flatnws_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\elevation.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/nws_elevation,FALSE,r'D:/Continental_Limnology/Data_Working/LAGOS_US_GIS_Data_v0.9.gdb/nws_unflat',nws_elevation,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/nws_elevation,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/nws_elevation.csv
+6894,lagosGIS.zonal_summary_of_raster_data,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9_RASTER.gdb\hu12_raster',hu12_zoneid,r'F:\Continental_Limnology\Data_Downloaded\3DEP_National_Elevation_Dataset\Zipped\elevation.tif',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/hu12_elevation,FALSE,,hu12_elevation,m,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2020-01-03_Zonal.gdb/hu12_elevation,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/hu12_elevation.csv
+6895,lagosGIS.line_density_in_zones,r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb\neon',neon_zoneid,r'D:\Continental_Limnology\Data_Downloaded\NHDPlus_High_Resolution_COMPLETE\Pre-processed\NHDPlus_HR_Streams.gdb\canals',D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_canals,,neon_canals,,,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/2021-01-12_Zonal.gdb/neon_canals,D:/Continental_Limnology/Data_Working/Tool_Execution/2020-01-03_Zonal/neon_canals.csv
diff --git a/lagosGIS/LAGOS_GIS_Toolbox.tbx b/lagosGIS/LAGOS_GIS_Toolbox.tbx
index 221e96f..086861e 100644
Binary files a/lagosGIS/LAGOS_GIS_Toolbox.tbx and b/lagosGIS/LAGOS_GIS_Toolbox.tbx differ
diff --git a/lagosGIS/__init__.py b/lagosGIS/__init__.py
index 9694ada..e4a3244 100644
--- a/lagosGIS/__init__.py
+++ b/lagosGIS/__init__.py
@@ -17,11 +17,10 @@
            "zonal_summary_of_raster_data",
            "zonal_summary_of_classed_polygons",
            "point_attribution_of_raster_data",
-           "summarize_raster_for_all_zones",
            "preprocess_padus",
 
-           "spatialize_lakes",
-           "georeference_lakes",
+           "spatialize_sites",
+           "georeference_lake_sites",
 
            "export_to_csv",
            "spatial_divisions_processing"
@@ -47,14 +46,13 @@
 from flatten_overlapping_zones import flatten as flatten_overlaps
 from rasterize_zones import rasterize as rasterize_zones
 from zonal_summary_of_raster_data import calc as zonal_summary_of_raster_data
-from summarize_raster_for_all_zones import summarize as summarize_raster_for_all_zones
 from preprocess_padus import preprocess as preprocess_padus
 
 from zonal_summary_of_classed_polygons import summarize as zonal_summary_of_classed_polygons
 from point_attribution_of_raster_data import attribution as point_attribution_of_raster_data
 
-from georeference import spatialize_lakes
-from georeference import georeference_lakes
+from georeference import spatialize_sites
+from georeference import georeference_lake_sites
 
 from export_to_csv import export as export_to_csv
 import spatial_divisions_processing
diff --git a/lagosGIS/calc_glaciation.py b/lagosGIS/calc_glaciation.py
index 95b153c..71abfe7 100644
--- a/lagosGIS/calc_glaciation.py
+++ b/lagosGIS/calc_glaciation.py
@@ -10,17 +10,33 @@
 from arcpy import analysis as AN, management as DM
 
 
-def calc(fc, glacial_extent_fc, zone_field, zone_name=''):
-    # tab area
-    if zone_name:
-        zone_name = zone_name
+def calc(zone_fc, glacial_extent_fc, zone_field, zone_prefix=''):
+    """ Calculates the percentage of the zonal polygon that was covered by the polygon extent of the glaciation dataset.
+    Modifies the original dataset.
+
+    :param zone_fc: Polygon feature class containing the zones to be characterized. The input will be modified.
+    :param glacial_extent_fc: Polygon feature class containing a single (multi-part permitted) polygon showing
+    maximum glacial extent
+    :param zone_field: Field name for the zone identifier
+    :param zone_prefix: (Optional) Short name or tag to use as prefix for all output column names and the table name
+    :return: The path to the modified zone polygon feature class
+    """
+
+    # Set-up names
+    if zone_prefix:
+        zone_prefix = zone_prefix
     else:
-        zone_name = os.path.basename(fc)
-    g_field = '{}_glaciatedlatewisc_pct'.format(zone_name)
-    AN.TabulateIntersection(fc, zone_field, glacial_extent_fc, 'in_memory/glacial_tab')
+        zone_prefix = os.path.basename(zone_fc)
+    g_field = '{}_glaciatedlatewisc_pct'.format(zone_prefix)
+
+    # Tabulate area and rename output field
+    AN.TabulateIntersection(zone_fc, zone_field, glacial_extent_fc, 'in_memory/glacial_tab')
     glacial_pct = {r[0]:r[1] for r in arcpy.da.SearchCursor('in_memory/glacial_tab', [zone_field, 'PERCENTAGE'])}
-    DM.AddField(fc, g_field, 'DOUBLE')
-    with arcpy.da.UpdateCursor(fc, [zone_field, g_field]) as u_cursor:
+    DM.AddField(zone_fc, g_field, 'DOUBLE')
+
+    # Cursor will essentially round to 2 decimal places, but also correct for TabulateArea percentages that slightly
+    # exceed 100 for whatever reason
+    with arcpy.da.UpdateCursor(zone_fc, [zone_field, g_field]) as u_cursor:
         for row in u_cursor:
             zoneid, glaciation = row
             if zoneid not in glacial_pct:
@@ -33,4 +49,8 @@ def calc(fc, glacial_extent_fc, zone_field, zone_name=''):
                 else:
                     glaciation = glacial_pct[zoneid]
             u_cursor.updateRow((zoneid, glaciation))
-    DM.Delete('in_memory/glacial_tab')
\ No newline at end of file
+
+    # Clean up
+    DM.Delete('in_memory/glacial_tab')
+
+    return zone_fc
\ No newline at end of file
diff --git a/lagosGIS/calc_relief_ratio.py b/lagosGIS/calc_relief_ratio.py
index eb11944..eff25ba 100644
--- a/lagosGIS/calc_relief_ratio.py
+++ b/lagosGIS/calc_relief_ratio.py
@@ -7,17 +7,31 @@
 import os
 import arcpy
 
+
 def calc_relief_ratio(elevation_stats_table):
+    """
+    Calculates watershed relief ratio using the mean, minimum, and maximum elevation for the zone polygon that was
+    calculated with Zonal Summary of Raster Data.
+    :param elevation_stats_table: Output table from Zonal Summary of Raster Data tool containing minimum, maximum,
+    mean elevation for each zone
+    :return: elevation_stats_table
+    """
+
+    # Find and add fields
     zone_prefix = os.path.basename(elevation_stats_table).split('_')[0]
     elev_mean = arcpy.ListFields(elevation_stats_table, '*elevation_mean*')[0].name
     elev_min = arcpy.ListFields(elevation_stats_table, '*elevation_min*')[0].name
     elev_max = arcpy.ListFields(elevation_stats_table, '*elevation_max*')[0].name
     ratio = '{}_reliefratio'.format(zone_prefix)
-    # arcpy.AddField_management(elevation_stats_table, ratio, 'DOUBLE')
+    arcpy.AddField_management(elevation_stats_table, ratio, 'DOUBLE')
+
+    # Calculate the "elevation relief ratio"
     with arcpy.da.UpdateCursor(elevation_stats_table, [ratio, elev_mean, elev_min, elev_max]) as cursor:
         for row in cursor:
             ratio, mean, min, max = row
             if mean and min != max:
                 ratio = (mean-min)/(max-min)
                 row = [ratio, mean, min, max]
-                cursor.updateRow(row)
\ No newline at end of file
+                cursor.updateRow(row)
+
+    return elevation_stats_table
\ No newline at end of file
diff --git a/lagosGIS/export_gis_and_info_tables.py b/lagosGIS/export_gis_and_info_tables.py
index c451483..e1ad6da 100644
--- a/lagosGIS/export_gis_and_info_tables.py
+++ b/lagosGIS/export_gis_and_info_tables.py
@@ -3,6 +3,8 @@
 # version: 2.0
 # LAGOS module(s): LOCUS, GEO
 # tool type: code journal, internal use only
+# purpose: Includes the specifications to export GIS layers and information tables from the internal spatial extents
+# file geodatabase. This was for LAGOS-US internal use.
 
 import os
 import arcpy
@@ -11,194 +13,151 @@
 arcpy.env.workspace = 'in_memory'
 arcpy.env.overwriteOutput = True
 CURRENT_WORKING_GDB = r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb'
-OUT_FOLDER = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-05-20_Export-LOCUS'
-OUT_GDB = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-05-20_Export-LOCUS\gis_locus_v1.0.gdb'
-
-#---------- LOCUS tables--------------
-
-# Lake information
-lake_info_fields = ['lagoslakeid',
-'lake_nhdid',
-'lake_nhdfcode',
-'lake_nhdftype',
-'lake_reachcode',
-'lake_namegnis',
-'lake_namelagos',
-'lake_onlandborder',
-'lake_ismultipart',
-'lake_missingws',
-'lake_shapeflag',
-'lake_lat_decdeg',
-'lake_lon_decdeg',
-'lake_elevation_m',
-'lake_centroidstate',
-'lake_states',
-'lake_county',
-'lake_countyfips',
-'lake_huc12',
-'buff100_zoneid',
-'buff500_zoneid',
-'ws_zoneid',
-'nws_zoneid',
-'hu12_zoneid',
-'hu8_zoneid',
-'hu4_zoneid',
-'county_zoneid',
-'state_zoneid',
-'epanutr_zoneid',
-'omernik3_zoneid',
-'wwf_zoneid',
-'mlra_zoneid',
-'bailey_zoneid',
-'neon_zoneid'
-          ]
+OUT_FOLDER_LOCUS = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-05-20_Export-LOCUS'
+OUT_GDB_LOCUS = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-05-20_Export-LOCUS\gis_locus_v1.0.gdb'
+OUT_FOLDER_GEO = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-11-28_Export-GEOGIS'
+OUT_GDB_GEO = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-11-28_Export-GEOGIS\gis_geo_v1.0.gdb'
+OUT_GDB_SIMPLE = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-11-28_Export-GEOGIS\simple_gis_geo_v1.0.gdb'
+FIELD_WARN_MSG = "WARNING: Specified fields missing from input dataset ({})"
 
+# ---SET UP EXPORT NAMES/REQUIREMENTS-----------------------------------------------------------------------------
 lake_fc = os.path.join(CURRENT_WORKING_GDB, 'LAGOS_US_All_Lakes_1ha')
+lake_fc_fields = [f.name for f in arcpy.ListFields(lake_fc)]
 
-print('lake info')
-fc_fields = [f.name for f in arcpy.ListFields(lake_fc)]
-for f in lake_info_fields:
-    if f not in fc_fields:
-        print f
-temp_lake_info = lagosGIS.select_fields(lake_fc, 'temp_lake_info', lake_info_fields, convert_to_table=True)
-lake_info = lagosGIS.export_to_csv('temp_lake_info', OUT_FOLDER, new_table_name = 'lake_information',
-                                   rename_fields=False, export_qa_version=False)
-
-print('lake shape')
-lake_shp_export = os.path.join(OUT_GDB, 'lake')
-lake_shape = lagosGIS.select_fields(lake_fc, lake_shp_export, ['lagoslakeid'])
-
-print('lake point')
-lake_shp_pt_export = os.path.join(OUT_GDB, 'lake_as_point')
-lake_shape = lagosGIS.select_fields(lake_fc + '_points', lake_shp_pt_export, ['lagoslakeid', 'nws_zoneid', 'ws_zoneid'])
-
+# lake information
+lake_info_fields = ['lagoslakeid',
+                    'lake_nhdid',
+                    'lake_nhdfcode',
+                    'lake_nhdftype',
+                    'lake_reachcode',
+                    'lake_namegnis',
+                    'lake_namelagos',
+                    'lake_onlandborder',
+                    'lake_ismultipart',
+                    'lake_missingws',
+                    'lake_shapeflag',
+                    'lake_lat_decdeg',
+                    'lake_lon_decdeg',
+                    'lake_elevation_m',
+                    'lake_centroidstate',
+                    'lake_states',
+                    'lake_county',
+                    'lake_countyfips',
+                    'lake_huc12',
+                    'buff100_zoneid',
+                    'buff500_zoneid',
+                    'ws_zoneid',
+                    'nws_zoneid',
+                    'hu12_zoneid',
+                    'hu8_zoneid',
+                    'hu4_zoneid',
+                    'county_zoneid',
+                    'state_zoneid',
+                    'epanutr_zoneid',
+                    'omernik3_zoneid',
+                    'wwf_zoneid',
+                    'mlra_zoneid',
+                    'bailey_zoneid',
+                    'neon_zoneid'
+                    ]
+lake_shp_export = os.path.join(OUT_GDB_LOCUS, 'lake')
+lake_shp_pt_export = os.path.join(OUT_GDB_LOCUS, 'lake_as_point')
 
-# Lake characteristics
+# lake characteristics
 lake_char_fields = [
-'lagoslakeid',
-'lake_waterarea_ha',
-'lake_totalarea_ha',
-'lake_islandarea_ha',
-'lake_perimeter_m',
-'lake_islandperimeter_m',
- 'lake_shorelinedevfactor',
-'lake_mbgconhull_length_m',
-'lake_mbgconhull_width_m',
-'lake_mbgconhull_orientation_deg',
-'lake_mbgrect_length_m',
-'lake_mbgrect_width_m',
-'lake_mbgrect_arearatio',
-'lake_meanwidth_m',
-'lake_connectivity_class',
-'lake_connectivity_fluctuates',
-'lake_connectivity_permanent',
-'lake_lakes4ha_upstream_ha',
-'lake_lakes4ha_upstream_n',
-'lake_lakes1ha_upstream_ha',
-'lake_lakes1ha_upstream_n',
-'lake_lakes10ha_upstream_n',
-'lake_lakes10ha_upstream_ha',
-'lake_glaciatedlatewisc',
+    'lagoslakeid',
+    'lake_waterarea_ha',
+    'lake_totalarea_ha',
+    'lake_islandarea_ha',
+    'lake_perimeter_m',
+    'lake_islandperimeter_m',
+    'lake_shorelinedevfactor',
+    'lake_mbgconhull_length_m',
+    'lake_mbgconhull_width_m',
+    'lake_mbgconhull_orientation_deg',
+    'lake_mbgrect_length_m',
+    'lake_mbgrect_width_m',
+    'lake_mbgrect_arearatio',
+    'lake_meanwidth_m',
+    'lake_connectivity_class',
+    'lake_connectivity_fluctuates',
+    'lake_connectivity_permanent',
+    'lake_lakes4ha_upstream_ha',
+    'lake_lakes4ha_upstream_n',
+    'lake_lakes1ha_upstream_ha',
+    'lake_lakes1ha_upstream_n',
+    'lake_lakes10ha_upstream_n',
+    'lake_lakes10ha_upstream_ha',
+    'lake_glaciatedlatewisc',
 ]
 
-lake_fc = os.path.join(CURRENT_WORKING_GDB, 'LAGOS_US_All_Lakes_1ha')
-
-print('lake char')
-lake_fields = [f.name for f in arcpy.ListFields(lake_fc)]
-for f in lake_char_fields:
-    if f not in lake_fields:
-        print f
-temp_lake_char = lagosGIS.select_fields(lake_fc, 'temp_lake_char', lake_char_fields, convert_to_table=True)
-lake_char = lagosGIS.export_to_csv('temp_lake_char', OUT_FOLDER, new_table_name = 'lake_characteristics',
-                                   rename_fields=False, export_qa_version=False)
-
-# WS watersheds
-ws_fields = [
-'lagoslakeid',
-'ws_zoneid',
-'ws_subtype',
-'ws_equalsnws',
-'ws_onlandborder',
-'ws_oncoast',
-'ws_inusa_pct',
-'ws_includeshu4inlet',
-'ws_ismultipart',
-'ws_lat_decdeg',
-'ws_lon_decdeg',
-'ws_sliverflag',
-'ws_states',
-'ws_focallakewaterarea_ha',
-'ws_area_ha',
-'ws_perimeter_m',
-'ws_lake_arearatio',
-'ws_mbgconhull_length_m',
-'ws_mbgconhull_width_m',
-'ws_mbgconhull_orientation_deg',
-'ws_meanwidth_m'
-    ]
-
-# NWS watersheds
-nws_fields = [
-'lagoslakeid',
-'nws_zoneid',
-'nws_onlandborder',
-'nws_oncoast',
-'nws_inusa_pct',
-'nws_includeshu4inlet',
-'nws_ismultipart',
-'nws_lat_decdeg',
-'nws_lon_decdeg',
-'nws_states',
-'nws_focallakewaterarea_ha',
-'nws_area_ha',
-'nws_perimeter_m',
-'nws_lake_arearatio',
-'nws_mbgconhull_length_m',
-'nws_mbgconhull_width_m',
-'nws_mbgconhull_orientation_deg',
-'nws_meanwidth_m'
-    ]
-
+# watersheds
 ws = os.path.join(CURRENT_WORKING_GDB, 'ws')
 nws = os.path.join(CURRENT_WORKING_GDB, 'nws')
-
-print('ws')
 ws_fc_fields = [f.name for f in arcpy.ListFields(ws)]
-for f in ws_fields:
-    if f not in ws_fc_fields:
-        print f
-temp_lake_ws = lagosGIS.select_fields(ws, 'temp_lake_ws', ws_fields, convert_to_table=True)
-lake_sheds_ws = lagosGIS.export_to_csv('temp_lake_ws', OUT_FOLDER, new_table_name='lake_watersheds_ws',
-                                   rename_fields=False, export_qa_version=False)
-
-print('nws')
 nws_fc_fields = [f.name for f in arcpy.ListFields(nws)]
-for f in nws_fields:
-    if f not in nws_fc_fields:
-        print f
-temp_lake_nws = lagosGIS.select_fields(nws, 'temp_lake_nws', nws_fields, convert_to_table=True)
-lake_sheds_ws = lagosGIS.export_to_csv('temp_lake_nws', OUT_FOLDER, new_table_name='lake_watersheds_nws',
-                                   rename_fields=False, export_qa_version=False)
-
-print('ws shape')
-ws_shp_export = os.path.join(OUT_GDB, 'ws')
-ws_shape = lagosGIS.select_fields(ws, ws_shp_export, ['lagoslakeid', 'ws_zoneid'])
-
-print('nws shape')
-nws_shp_export = os.path.join(OUT_GDB, 'nws')
-nws_shape = lagosGIS.select_fields(nws, nws_shp_export, ['lagoslakeid', 'nws_zoneid'])
-
-# catchment layer
+ws_shp_export = os.path.join(OUT_GDB_LOCUS, 'ws')
+nws_shp_export = os.path.join(OUT_GDB_LOCUS, 'nws')
+
+ws_fields = [
+    'lagoslakeid',
+    'ws_zoneid',
+    'ws_subtype',
+    'ws_equalsnws',
+    'ws_onlandborder',
+    'ws_oncoast',
+    'ws_inusa_pct',
+    'ws_includeshu4inlet',
+    'ws_ismultipart',
+    'ws_lat_decdeg',
+    'ws_lon_decdeg',
+    'ws_sliverflag',
+    'ws_states',
+    'ws_focallakewaterarea_ha',
+    'ws_area_ha',
+    'ws_perimeter_m',
+    'ws_lake_arearatio',
+    'ws_mbgconhull_length_m',
+    'ws_mbgconhull_width_m',
+    'ws_mbgconhull_orientation_deg',
+    'ws_meanwidth_m'
+]
+
+nws_fields = [
+    'lagoslakeid',
+    'nws_zoneid',
+    'nws_onlandborder',
+    'nws_oncoast',
+    'nws_inusa_pct',
+    'nws_includeshu4inlet',
+    'nws_ismultipart',
+    'nws_lat_decdeg',
+    'nws_lon_decdeg',
+    'nws_states',
+    'nws_focallakewaterarea_ha',
+    'nws_area_ha',
+    'nws_perimeter_m',
+    'nws_lake_arearatio',
+    'nws_mbgconhull_length_m',
+    'nws_mbgconhull_width_m',
+    'nws_mbgconhull_orientation_deg',
+    'nws_meanwidth_m'
+]
+
+# catchments
 cat = os.path.join(CURRENT_WORKING_GDB, 'catchment')
-cat_shp_export = os.path.join(OUT_GDB, 'catchment')
-cat_shape = lagosGIS.select_fields(cat, cat_shp_export, ['lagoslakeid', 'Permanent_Identifier', 'NHDPlusID', 'SourceFC', 'Permanent_Identifier', 'VPUID'])
+cat_shp_export = os.path.join(OUT_GDB_LOCUS, 'catchment')
+cat_fields = ['lagoslakeid',
+              'Permanent_Identifier',
+              'NHDPlusID',
+              'SourceFC',
+              'Permanent_Identifier',
+              'VPUID']
 
-# # --------------------------GEO tables--------------
-arcpy.env.workspace = 'in_memory'
-CURRENT_WORKING_GDB = r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb'
-OUT_FOLDER = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-11-28_Export-GEOGIS'
-OUT_GDB = r'D:\Continental_Limnology\Data_Working\Tool_Execution\2021-11-28_Export-GEOGIS\gis_geo_v1.0.gdb'
+# great lakes
 
+
+# geo spatial divisions
 zones = ['buff100',
          'buff500',
          'nws',
@@ -214,79 +173,168 @@
          'neon',
          'omernik3',
          'epanutr']
-#
-CURRENT_WORKING_GDB = r'D:\Continental_Limnology\Data_Working\LAGOS_US_GIS_Data_v0.9.gdb'
 
 
-def export_zone(zone_name):
-    import os
-    import arcpy
-    zone_fc = os.path.join(CURRENT_WORKING_GDB, zone_name)
-    field_vars = ['zoneid',
-                  'sourceid',
-                  'name',
-                  'fips',
-                  'states',
-                  'area_ha',
-                  'perimeter_m',
-                  'originalarea_pct',
-                  'lat_decdeg',
-                  'lon_decdeg',
-                  'inusa_pct',
-                  'onlandborder',
-                  'oncoast',
-                  'ismultipart']
-    if not arcpy.ListFields(zone_fc, field_vars[3]):
-        field_vars.pop(3)
-    lake_zones = ['buff100', 'buff500', 'nws', 'ws']
-    if zone_name in lake_zones:
-        field_vars.remove('sourceid')
-        field_vars.remove('name')
-        field_vars.remove('originalarea_pct')
-    if zone_name == 'state':
-        field_vars.remove('states')
-    field_list = ['{}_{}'.format(zone_name, f) for f in field_vars]
-    if 'sourceid' in field_list[1]:
-        field_list[1] = arcpy.ListFields(zone_fc, '*sourceid*')[0].name
-    print field_list
-    for f in field_list:
-        if not arcpy.ListFields(zone_fc, f):
-            print f
-    temp_zone_fc = lagosGIS.select_fields(zone_fc, 'temp_zone_fc', field_list, convert_to_table=True)
-    lagosGIS.export_to_csv(temp_zone_fc, OUT_FOLDER,
-                                              new_table_name='{}_information'.format(zone_name),
-                                              rename_fields=False, export_qa_version=False)
-    arcpy.Delete_management(temp_zone_fc)
-    # zone_shp_export = os.path.join(OUT_GDB, zone_name)
-    # lagosGIS.select_fields(zone_fc, zone_shp_export, ['{}_zoneid'.format(zone_name)])
+# ---EXPORT LOCUS TABLES & GIS-------------------------------------------------------------------------------------
+def export_locus(export_info=True, export_gis=True):
+    """
+    Export the tables that comprise LAGOS-US LOCUS module.
+    :param export_info: Boolean. Whether to export *_information.csv tables
+    :param export_gis: Boolean. Whether to export GIS datasets
+    :return: None
+    """
+    if export_info:
+        # lake_information
+        print('lake_information')
+        for f in lake_info_fields:
+            if f not in lake_fc_fields:
+                print(FIELD_WARN_MSG.format(f))
+        temp_lake_info = lagosGIS.select_fields(lake_fc, 'temp_lake_info', lake_info_fields, convert_to_table=True)
+        lagosGIS.export_to_csv(temp_lake_info, OUT_FOLDER_LOCUS, new_table_name='lake_information',
+                               rename_fields=False, export_qa_version=False)
 
+        # lake_characteristics
+        print('lake_characteristics')
+        for f in lake_char_fields:
+            if f not in lake_fc_fields:
+                print(FIELD_WARN_MSG.format(f))
+        temp_lake_char = lagosGIS.select_fields(lake_fc, 'temp_lake_char', lake_char_fields, convert_to_table=True)
+        lagosGIS.export_to_csv(temp_lake_char, OUT_FOLDER_LOCUS, new_table_name = 'lake_characteristics',
+                               rename_fields=False, export_qa_version=False)
 
-for z in zones:
-        export_zone(z)
+        # lake_watersheds
+        print('watersheds')
+        for f in ws_fields:
+            if f not in ws_fc_fields:
+                print(FIELD_WARN_MSG.format(f))
+        temp_lake_ws = lagosGIS.select_fields(ws, 'temp_lake_ws', ws_fields, convert_to_table=True)
+        lagosGIS.export_to_csv(temp_lake_ws, OUT_FOLDER_LOCUS, new_table_name='lake_watersheds_ws',
+                               rename_fields=False, export_qa_version=False)
+
+        for f in nws_fields:
+            if f not in nws_fc_fields:
+                print(FIELD_WARN_MSG.format(f))
+        temp_lake_nws = lagosGIS.select_fields(nws, 'temp_lake_nws', nws_fields, convert_to_table=True)
+        lagosGIS.export_to_csv(temp_lake_nws, OUT_FOLDER_LOCUS, new_table_name='lake_watersheds_nws',
+                               rename_fields=False, export_qa_version=False)
+
+    if export_gis:
+        print('lake shape layers')
+        lagosGIS.select_fields(lake_fc, lake_shp_export, ['lagoslakeid'])
+        lagosGIS.select_fields(lake_fc + '_points', lake_shp_pt_export, ['lagoslakeid', 'nws_zoneid', 'ws_zoneid'])
+
+        print('watersheds shape layers')
+        lagosGIS.select_fields(ws, ws_shp_export, ['lagoslakeid', 'ws_zoneid'])
+        lagosGIS.select_fields(nws, nws_shp_export, ['lagoslakeid', 'nws_zoneid'])
+
+        # catchment layer
+        print('catchments shape layers')
+        lagosGIS.select_fields(cat, cat_shp_export, cat_fields)
+
+
+# ---EXPORT GEO INFORMATION & GIS-------------------------------------------------------------------------------------
+def export_zone(zone_name, export_info=True, export_gis=True, export_simple_gis=True, export_glaciation=True):
+    """
+    Exports a single spatial division's information table and GIS dataset for LAGOS-US GEO spatial divisions. Does not
+    export the rest of the GEO module!
+    :param zone_name: Shortname/prefix for the spatial division to be exported
+    :param export_info: Boolean. Whether to export *_information.csv table
+    :param export_gis: Boolean. Whether to export GIS database
+    :param export_simple_gis: Boolean. Whether to export simple GIS database
+    :param export_glaciation: Boolean. Whether to export glaciation metric to table named "*_glaciatedlatewisc"
+    :return: None
+    """
 
-def export_glaciation(zone_name):
-    import os
-    import arcpy
     zone_fc = os.path.join(CURRENT_WORKING_GDB, zone_name)
-    field_vars = ['zoneid',
-                  'glaciatedlatewisc_pct']
-    field_list = ['{}_{}'.format(zone_name, f) for f in field_vars]
-    print field_list
-    for f in field_list:
-        if not arcpy.ListFields(zone_fc, f):
-            print f
-    temp_zone_fc = lagosGIS.select_fields(zone_fc, 'temp_zone_fc', field_list, convert_to_table=True)
-    lagosGIS.export_to_csv(temp_zone_fc, OUT_FOLDER,
-                           new_table_name='{}_glaciatedlatewisc'.format(zone_name),
-                           rename_fields=False, export_qa_version=False)
-    arcpy.Delete_management(temp_zone_fc)
-
-for z in zones[2:4]:
-    export_glaciation(z)
-
-arcpy.env.workspace = CURRENT_WORKING_GDB
+
+    if export_info:
+        # Specify the right fields for this spatial division
+        field_vars = ['zoneid',
+                      'sourceid',
+                      'name',
+                      'fips',
+                      'states',
+                      'area_ha',
+                      'perimeter_m',
+                      'originalarea_pct',
+                      'lat_decdeg',
+                      'lon_decdeg',
+                      'inusa_pct',
+                      'onlandborder',
+                      'oncoast',
+                      'ismultipart']
+        if not arcpy.ListFields(zone_fc, field_vars[3]):
+            field_vars.pop(3)
+        lake_zones = ['buff100', 'buff500', 'nws', 'ws']
+        if zone_name in lake_zones:
+            field_vars.remove('sourceid')
+            field_vars.remove('name')
+            field_vars.remove('originalarea_pct')
+        if zone_name == 'state':
+            field_vars.remove('states')
+        field_list = ['{}_{}'.format(zone_name, f) for f in field_vars]
+        if 'sourceid' in field_list[1]:
+            field_list[1] = arcpy.ListFields(zone_fc, '*sourceid*')[0].name
+
+        # Check for missing fields
+        for f in field_list:
+            if not arcpy.ListFields(zone_fc, f):
+                print(FIELD_WARN_MSG.format(f))
+
+        # zone_information
+        print('zone_information (subset for division {})'.format(zone_name))
+        temp_zone_fc = lagosGIS.select_fields(zone_fc, 'temp_zone_fc', field_list, convert_to_table=True)
+        lagosGIS.export_to_csv(temp_zone_fc, OUT_FOLDER_GEO,
+                               new_table_name='{}_information'.format(zone_name),
+                               rename_fields=False, export_qa_version=False)
+
+    if export_gis:
+        # zone shape layers
+        if zone_name not in ('ws', 'nws'):  # which were published in LOCUS already
+            print('{} shape layer'.format(zone_name))
+            zone_shp_export = os.path.join(OUT_GDB_GEO, zone_name)
+            lagosGIS.select_fields(zone_fc, zone_shp_export, ['{}_zoneid'.format(zone_name)])
+
+    if export_simple_gis:
+        # simple shape layers
+        # created with
+        # SimplifyPolygon(zone_fc, out_fc, "BEND_SIMPLIFY, "2500 Meters", error_option="RESOLVE_ERRORS")
+        # or 5000 Meter tolerance for HU12
+        print('{} simple shape layer'.format(zone_name))
+        zone_fc = os.path.join(CURRENT_WORKING_GDB, 'simple_' + zone_name)
+        simple_shp_export = os.path.join(OUT_GDB_SIMPLE, 'simple_' + zone_name)
+        lagosGIS.select_fields(zone_fc, simple_shp_export, ['{}_zoneid'.format(zone_name)])
+
+        # HU12 gets two options because it's on the edge of usability
+        if zone_name == 'hu12':
+            zone_poly_fc = zone_fc + '_poly'
+            simple_poly_export = simple_shp_export + '_poly'
+            lagosGIS.select_fields(zone_poly_fc, simple_poly_export, ['{}_zoneid'.format(zone_name)])
+
+    if export_glaciation:
+        field_list = ['{}_{}'.format(zone_name, f) for f in ['zoneid', 'glaciatedlatewisc_pct']]
+        for f in field_list:
+            if not arcpy.ListFields(zone_fc, f):
+                print(FIELD_WARN_MSG.format(f))
+        temp_zone_fc = lagosGIS.select_fields(zone_fc, 'temp_zone_fc', field_list, convert_to_table=True)
+        lagosGIS.export_to_csv(temp_zone_fc, OUT_FOLDER_GEO,
+                               new_table_name='{}_glaciatedlatewisc'.format(zone_name),
+                               rename_fields=False, export_qa_version=False)
+
+
+# ---RUN ALL-----------------------------------------------------------------------------------------------------
+# RUN LOCUS
+export_locus()
+
+# RUN GEO
 for z in zones:
-    print z
-    shp_export = os.path.join(OUT_GDB, z)
-    zoneid = '{}_zoneid'.format(z)
-    shape = lagosGIS.select_fields(z, shp_export, [zoneid])
+    if z not in ['ws', 'nws']:
+        export_gis = False
+    else:
+        export_gis = True
+    export_zone(z, True, export_gis, True, True)
+
+
+# # add lake to simple gis
+simple_lake = os.path.join(OUT_GDB_SIMPLE, 'simple_lake')
+lagosGIS.select_fields(lake_fc + '_points', simple_lake, ['lagoslakeid'])
diff --git a/lagosGIS/export_to_csv.py b/lagosGIS/export_to_csv.py
index 4130c69..cc43463 100644
--- a/lagosGIS/export_to_csv.py
+++ b/lagosGIS/export_to_csv.py
@@ -13,17 +13,25 @@
 import arcpy
 
 
-def describe_arcgis_table_csv(in_table, out_path, field_list = [], rename_fields = True):
+def describe_arcgis_table_csv(in_table, out_path, field_list=[], rename_fields=True):
     """
-    :param in_table: A feature class or table used by ArcCatalog.
-    :param out_path: Where to save the output. Defaults to the input table named appended with "_cols.csv"
-    :return: None
+    Creates a companion table to a CSV table export that describes the field properties for each field as they were
+    stored in the file geodatabase table.
+    :param in_table: The feature class or table that will be exported to CSV
+    :param out_path: The output table location
+    :param field_list: (Optional) The list of fields to be described. Default is all fields.
+    :param rename_fields: Whether the fields are to be renamed in the exported CSV table
+    :return: The output table location
     """
+
+    # Identify fields to be described
     all_fields = arcpy.ListFields(in_table)
     if field_list:
         fields = [f for f in all_fields if f.name in field_list]
     else:
         fields = all_fields
+
+    # Define length for string fields as the longest character string value actually found in the table
     string_fields = [f.name for f in fields if f.type == 'String']
     if string_fields:
         try:
@@ -36,13 +44,20 @@ def describe_arcgis_table_csv(in_table, out_path, field_list = [], rename_fields
     else:
         string_lengths = {}
 
+    # Initialize  and populate output table with arcpy.Field object properties, unless string length
+
     with open(out_path, 'wb') as csv_file:
-        writer = csv.DictWriter(csv_file, fieldnames=[
-            'column_name', 'column_esri_type', 'column_esri_length', 'column_string_min'])
+        writer = csv.DictWriter(csv_file, fieldnames=['column_name',
+                                                      'column_esri_type',
+                                                      'column_esri_length',
+                                                      'column_string_min'
+                                                      ]
+                                )
         writer.writeheader()
 
         for f in fields:
-            if rename_fields: # this code is the duplicated part that I don't like that much.
+            # Re-name fields with necessary
+            if rename_fields: # duplicated from below, not my favorite way
                 if 'OBJECTID' in f.name:
                     continue
                 short_f_orig = os.path.splitext(os.path.basename(in_table))[0]
@@ -53,29 +68,46 @@ def describe_arcgis_table_csv(in_table, out_path, field_list = [], rename_fields
                 shortest = string_lengths[f.name]
             else:
                 shortest = ''
-            out_dict = {'column_name': f.name, 'column_esri_type': f.type, 'column_esri_length': f.length, \
-                        'column_string_min': shortest}
+
+            # Write out the results
+            out_dict = {'column_name': f.name,
+                        'column_esri_type': f.type,
+                        'column_esri_length': f.length,
+                        'column_string_min': shortest
+                        }
             writer.writerow(out_dict)
-    return(out_path)
 
-def rename_variables(file, prefix = ''):
+    return out_path
+
+
+def rename_variables(csv_file, prefix=''):
+    """
+    Renames all variables in a CSV file with the specified prefix or assumes the prefix from the file name.
+    :param csv_file: The CSV file in which to rename columns/fields
+    :param prefix: Text string of the prefix to use for all columns/fields
+    :return: None
+    """
+
     tempfile = NamedTemporaryFile(delete=False)
+
+    # Identify the prefix to use
     if prefix:
         short_f = prefix
     else:
-        short_f_orig = os.path.splitext(os.path.basename(file))[0]
+        short_f_orig = os.path.splitext(os.path.basename(csv_file))[0]
         short_f = short_f_orig.replace('_QA_ONLY', '')
 
-    with open(file, 'rb') as csv_file:
+    # Read and modify the column names
+    with open(csv_file, 'rb') as csv_file:
         reader = csv.DictReader(csv_file)
         header = reader.fieldnames
 
-        #update the header
+        # Update the header with new names
         desired_header = ['{}_{}'.format(short_f, name).lower() if 'zoneid' not in name else name for name in header]
         update_dict = dict(zip(header, desired_header))
         filtered_header = [name for name in desired_header if 'OBJECT' not in name]
 
-        # write out selected fields with new names
+        # Write out values for each field with new names
         with tempfile:
             writer = csv.DictWriter(tempfile, fieldnames = filtered_header)
             writer.writeheader()
@@ -83,10 +115,57 @@ def rename_variables(file, prefix = ''):
                 new_row = {update_dict[k]: row[k] for k in row if update_dict[k] in filtered_header}
                 writer.writerow(new_row)
 
-    shutil.move(tempfile.name, file)
+    # Update the original CSV file with the temp and delete the temp
+    shutil.move(tempfile.name, csv_file)
+    os.remove(tempfile.name)
 
-def export(in_table, out_folder, output_schema = True, prefix ='', new_table_name ='',
-           rename_fields = True, export_qa_version = True, field_list = []):
+
+def format_value(x):
+    """Prevent scientific notation in exports and change missing values to 'NULL' string."""
+    try:
+        if math.isnan(x):
+            return 'NULL'
+    except:
+        pass
+    if x is None:
+        return 'NULL'
+    elif isinstance(x, float):
+        x_10 = round(x, 10)
+        x_int = int(round(x, 0))
+        out_value = str(x_int if x_10 == x_int else '{:.10f}'.format(x_10))
+        if out_value == '-0':
+            out_value = '0'
+        return out_value
+    elif isinstance(x, int):
+        return str(x)
+    elif isinstance(x, unicode) or isinstance(x, str):
+        if ',' in x:
+            x = '"{}"'.format(x)  # quote-protection for commas
+        return x.encode('utf-8')
+    elif isinstance(x, datetime.datetime):
+        return str(x)
+
+
+def export(in_table, out_folder, output_schema=True, prefix='', new_table_name='',
+           rename_fields=True, export_qa_version=True, field_list=[]):
+    """
+    Exports a CSV with suppression of scientific notation and with options to rename fields and output a data schema
+    table.
+
+    You can use Export Rows to export tables instead of this tool if you do not need any of the specific functionality.
+    :param in_table: A table to be converted to CSV
+    :param out_folder: The directory in which the CSV output(s) will be located
+    :param output_schema: (Optional) Boolean, default True. Whether to create a descriptive data schema table.
+    :param prefix: (Optional) A text string containing a prefix to append to all output column names
+    :param new_table_name: (Optional) A new name to use for the output table, if desired. The table will have the same
+    name as the input table by default.
+    :param rename_fields: (Optional) Boolean, default True
+    :param export_qa_version: (Optional) Boolean, default True
+    :param field_list: A list of column names to save in the output
+    :return: None
+    """
+
+    # Get file basename without extension and specify auxiliary table output paths
     if arcpy.env.workspace == 'in_memory' and ':' not in in_table:
         name = os.path.basename(str(in_table))
     else:
@@ -95,9 +174,7 @@ def export(in_table, out_folder, output_schema = True, prefix ='', new_table_nam
     out_csv = os.path.join(out_folder, "{}.csv".format(name))
     arcpy.AddMessage("out csv is {}".format(out_csv))
 
-    # for rounding
-    places = 10
-
+    # Specify fields to use in outputs; select areas from Zonal Summary of Raster Data for special QA treatment
     if field_list:
         fields_qa = field_list
     else:
@@ -105,31 +182,7 @@ def export(in_table, out_folder, output_schema = True, prefix ='', new_table_nam
     ha_prefix = tuple(["Ha_{}".format(d) for d in range(10)])
     fields = [f for f in fields_qa if not f.startswith(ha_prefix) and f not in ['CELL_COUNT', 'ORIGINAL_COUNT']]
 
-    def format_value(x):
-        """PREVENTS scientific notation in exports and change null values"""
-        try:
-            if math.isnan(x):
-                return 'NULL'
-        except:
-            pass
-        if x is None:
-            return 'NULL'
-        elif isinstance(x, float):
-            x_10 = round(x, 10)
-            x_int = int(round(x, 0))
-            out_value = str(x_int if x_10 == x_int else '{:.10f}'.format(x_10))
-            if out_value == '-0':
-                out_value = '0'
-            return out_value
-        elif isinstance(x, int):
-            return str(x)
-        elif isinstance(x, unicode) or isinstance(x, str):
-            if ',' in x:
-                x = '"{}"'.format(x)  # quote-protection for commas
-            return x.encode('utf-8')
-        elif isinstance(x, datetime.datetime):
-            return str(x)
-
+    # Export QA version of file, if elected
     if export_qa_version:
         with open(out_qa_csv, 'w') as f:
             f.write(','.join(fields_qa) + '\n')  # csv headers
@@ -138,6 +191,7 @@ def format_value(x):
                     values = map(format_value, row)
                     f.write(','.join(values) + '\n')
 
+    # Export table with original names to the output location
     with open(out_csv, 'w') as f:
         f.write(','.join(fields)+'\n') #csv headers
         with arcpy.da.SearchCursor(in_table, fields) as cursor:
@@ -145,14 +199,17 @@ def format_value(x):
                 values = map(format_value, row)
                 f.write(','.join(values)+'\n')
 
+    # Modify the field names in place, if elected
     if rename_fields:
         rename_variables(out_csv, prefix)
         rename_variables(out_qa_csv, prefix)
 
+    # Create the data schema description table, if elected
     if output_schema:
         out_schema = os.path.join(out_folder, "{}_schema.csv".format(name))
         out_schema = describe_arcgis_table_csv(in_table, out_schema, field_list, rename_fields=rename_fields)
 
+    # Modify the table file name, if elected
     if new_table_name:
         out_qa_csv_rename = os.path.join(out_folder, "{}_QA_ONLY.csv".format(new_table_name))
         out_csv_rename = os.path.join(out_folder, "{}.csv".format(new_table_name))
@@ -173,5 +230,6 @@ def main():
     new_table_name = arcpy.GetParameterAsText(5)
     export(in_table, out_folder, output_schema, rename_fields=rename_fields, prefix=prefix, new_table_name=new_table_name)
 
+
 if __name__ == '__main__':
     main()
diff --git a/lagosGIS/flatten_overlapping_zones.py b/lagosGIS/flatten_overlapping_zones.py
index 595c075..ae2f662 100644
--- a/lagosGIS/flatten_overlapping_zones.py
+++ b/lagosGIS/flatten_overlapping_zones.py
@@ -10,30 +10,37 @@
 from arcpy import analysis as AN
 
 
-def flatten(zone_fc, zone_field, output_fc, output_table, cluster_tolerance=' 3 Meters'):
+def flatten(zone_fc, zone_field, output_fc, output_table, cluster_tolerance='3 Meters'):
+    """
+    Converts overlapping zone polygons into non-overlapping regions (first output) and provides a table of identifiers
+    to link between input and output polygons (second output).
+    :param zone_fc: A polygon feature class containing overlapping zones
+    :param zone_field: The unique identifier for each zone
+    :param output_fc: The output feature class location
+    :param output_table: The output table location
+    :param cluster_tolerance: Cluster tolerance passed to Union function (The minimum distance separating all feature
+    coordinates (nodes and vertices) as well as the distance a coordinate can move in X or Y (or both).)
+    :return: Output feature class path
+    """
+
+    # Set-up workspace and naming conventions
     orig_env = arcpy.env.workspace
     arcpy.env.workspace = 'in_memory'
 
     objectid = [f.name for f in arcpy.ListFields(zone_fc) if f.type == 'OID'][0]
-    zone_type = [f.type for f in arcpy.ListFields(zone_fc, zone_field)][0]
+    zoneid_dict = {r[0]: r[1] for r in arcpy.da.SearchCursor(zone_fc, [objectid, zone_field])}
+    zone_field_type = [f.type for f in arcpy.ListFields(zone_fc, zone_field)][0]
     fid1 = 'FID_{}'.format(os.path.basename(zone_fc))
     flat_zoneid = 'flat{}'.format(zone_field)
     flat_zoneid_prefix = 'flat{}_'.format(zone_field.replace('_zoneid', ''))
 
-    # Union with FID_Only (A)
+    # Self-union with FID_Only (A). This step identifies overlapping regions and creates a new feature for them.
     arcpy.AddMessage("Splitting overlaps in polygons...")
-    zoneid_dict = {r[0]: r[1] for r in arcpy.da.SearchCursor(zone_fc, [objectid, zone_field])}
     self_union = AN.Union([zone_fc], 'self_union', 'ONLY_FID', cluster_tolerance=cluster_tolerance)
 
-    # #If you don't run this section, Find Identical fails with error 999999. Seems to have to do with small slivers
-    # #having 3 vertices and/or only circular arcs in the geometry.
+    # Delete features with null geometry. Some kind of geometry repair is commonly helpful following a Union analysis.
     arcpy.AddMessage("Repairing self-union geometries...")
-    # DM.AddGeometryAttributes(self_union, 'POINT_COUNT; AREA')
-    # union_fix = DM.MakeFeatureLayer(self_union, 'union_fix', where_clause='PNT_COUNT <= 10 OR POLY_AREA < 5000')
-    # arcpy.Densify_edit(union_fix, 'DISTANCE', distance = '1 Meters', max_deviation='1 Meters')  # selection ON, edits self_union disk
-    DM.RepairGeometry(self_union, 'DELETE_NULL')  # eliminate empty geoms. selection ON, edits self_union disk
-    # for field in ['PNT_COUNT', 'POLY_AREA']:
-    #     DM.DeleteField(self_union, field)
+    DM.RepairGeometry(self_union, 'DELETE_NULL')
 
     # Find Identical by Shape (B)
     if arcpy.Exists('identical_shapes'):
@@ -52,7 +59,7 @@ def flatten(zone_fc, zone_field, output_fc, output_table, cluster_tolerance=' 3
     # Add the original zone ids and save to table (E)
     arcpy.AddMessage("Assigning temporary IDs to split polygons...")
     unflat_table = DM.CopyRows(self_union, 'unflat_table')
-    DM.AddField(unflat_table, zone_field, zone_type)  # default text length of 50 is fine if needed
+    DM.AddField(unflat_table, zone_field, zone_field_type)  # default text length of 50 is fine if needed
     with arcpy.da.UpdateCursor(unflat_table, [fid1, zone_field]) as u_cursor:
         for row in u_cursor:
             row[1] = zoneid_dict[row[0]]  # assign zone id
@@ -81,6 +88,7 @@ def flatten(zone_fc, zone_field, output_fc, output_table, cluster_tolerance=' 3
 
     return output_fc
 
+
 def main():
     zone_fc = arcpy.GetParameterAsText(0)
     zone_field = arcpy.GetParameterAsText(1)
@@ -89,5 +97,6 @@ def main():
     cluster_tolerance = arcpy.GetParameterAsText(4)
     flatten(zone_fc, zone_field, output_fc, output_table, cluster_tolerance)
 
+
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()
diff --git a/lagosGIS/georeference.py b/lagosGIS/georeference.py
index bd23791..9cf0155 100644
--- a/lagosGIS/georeference.py
+++ b/lagosGIS/georeference.py
@@ -3,6 +3,9 @@
 # version: 2.0
 # LAGOS module(s): LIMNO
 # tool type: limited re-usability as code (change constants by hand for your computer)
+# purpose: Identify the lakes being sampled with water quality observation data.
+# Convert lake sampling data to point features using an appropriate coordinate system and spatially link the
+# point features to the best matching LAGOS-US lake polygon, if possible.
 
 import os
 import arcpy
@@ -11,31 +14,34 @@
 from arcpy import management as DM
 import lagosGIS
 
-# Change these to match your computer. Yes, this is a crap way to code this.
-MASTER_LAKES_FC = 'NHDWaterbody_LAGOS'
-MASTER_LAKES_LINES = 'NHDWaterbody_LAGOS_Line'
-MASTER_STREAMS_FC = 'NHDArea_LAGOS'
-MASTER_XWALK = 'LAGOS_Lake_Link_v1_legacy_only'
+# Features to use for geographic linking.
+# Change these to match your computer. It's not very elegant.
+MASTER_LAKES_FC = 'NHDWaterbody_LAGOS'  # population of valid lakes
+MASTER_LAKES_LINES = 'NHDWaterbody_LAGOS_Line'  # artificial paths associated with lakes in MASTER_LAKES_FC
+MASTER_STREAMS_FC = 'NHDArea_LAGOS'  # merged NHDArea polygon features from NHD with StreamRiver feature type
+MASTER_XWALK = 'LAGOS_Lake_Link_v1_legacy_only'  # lake identifier crosswalk, see lake_link in LAGOS-US LOCUS
 
 # Can change but probably don't need to
 MASTER_LAKE_ID = 'lagoslakeid'
 MASTER_GNIS_NAME = "GNIS_Name"
-#MASTER_STREAM_ID = 'Permanent_Identifier' #hard-coded below
+# MASTER_STREAM_ID = 'Permanent_Identifier' #hard-coded below
 MASTER_COUNTY_NAME = 'COUNTY_NAME'
 MASTER_STATE_NAME = 'STATE'
-STATES = ("AK","AL","AR","AZ","CA","CO","CT","DC","DE","FL","GA","GU","HI","IA","ID", "IL","IN","KS","KY","LA","MA",
-          "MD","ME","MH","MI","MN","MO","MS","MT","NC","ND","NE","NH","NJ","NM","NV","NY", "OH","OK","OR","PA","PR",
-          "PW","RI","SC","SD","TN","TX","UT","VA","VI","VT","WA","WI","WV","WY")
-LAGOSNE_STATES = ("CT","IA","IL","IN","MA","ME","MI","MN","MO","NH","NJ","NY", "OH","PA","RI","VT","WI")
-CRS_DICT = {'NAD83':4269,
-            'WGS84':4326,
-            'NAD27':4267,
-            'NAD_1983_StatePlane_Washington_North_FIPS_4601_Feet':102748,
+STATES = ("AK", "AL", "AR", "AZ", "CA", "CO", "CT", "DC", "DE", "FL", "GA", "GU", "HI", "IA", "ID", "IL", "IN", "KS",
+          "KY", "LA", "MA", "MD", "ME", "MH", "MI", "MN", "MO", "MS", "MT", "NC", "ND", "NE", "NH", "NJ", "NM", "NV",
+          "NY", "OH", "OK", "OR", "PA", "PR", "PW", "RI", "SC", "SD", "TN", "TX", "UT", "VA", "VI", "VT", "WA", "WI",
+          "WV", "WY"
+          )
+LAGOSNE_STATES = ("CT", "IA", "IL", "IN", "MA", "ME", "MI", "MN", "MO", "NH", "NJ", "NY", "OH", "PA", "RI", "VT", "WI")
+CRS_DICT = {'NAD83': 4269,
+            'WGS84': 4326,
+            'NAD27': 4267,
+            'NAD_1983_StatePlane_Washington_North_FIPS_4601_Feet': 102748,
             'NAD_1983_HARN_UTM_Zone_15N': 3745,
             }
 
 
-def spatialize_lakes(lake_points_csv, out_fc, in_x_field, in_y_field, in_crs = 'NAD83'):
+def spatialize_sites(lake_points_csv, out_fc, in_x_field, in_y_field, in_crs='NAD83'):
     """
     Casts xy data as spatial points.
     :param lake_points_csv: The lake water quality dataset containing coordinates as text columns.
@@ -54,31 +60,60 @@ def spatialize_lakes(lake_points_csv, out_fc, in_x_field, in_y_field, in_crs = '
     arcpy.env.outputCoordinateSystem = arcpy.SpatialReference(102039)
     DM.CopyFeatures('xylayer', out_fc)
     arcpy.Delete_management('xylayer')
-    return(out_fc)
+    return out_fc
 
-def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
-                       lake_name_field, lake_county_field = '', state = '',
-                       master_gdb=r'C:\Users\smithn78\Dropbox\CL_HUB_GEO\Lake_Georeferencing\Masters_for_georef.gdb'
-                       ):
+
+def georeference_lake_sites(sample_sites_point_fc, out_fc, site_id_field,
+                            lake_name_field, lake_county_field='', state='',
+                            master_gdb=r'C:\Users\smithn78\Dropbox\CL_HUB_GEO\Lake_Georeferencing\Masters_for_georef.gdb'
+                            ):
     """
     Evaluate water quality sampling point locations and either assign the point to a lake polygon or flag the
-    point for manual review.
-    :param lake_points_fc:
-    :param out_fc:
-    :param lake_id_field:
-    :param lake_name_field:
-    :param lake_county_field:
-    :param state:
-    :param master_gdb: Location of master geodatabase used for linking
-    :return:
+    point for manual review. This function is meant to be used as the first of two steps in a semi-automated linking
+    process, in which a possible linked lake for each site is calculated and then a reviewer visually inspects each
+    site in context with corroborating information in order to accept or reject the links.
+    :param sample_sites_point_fc: A point feature class containing water quality sampling data (see spatialize_sites)
+    :param out_fc: An output feature class to save the result to
+    :param site_id_field: The column/field determined by the user to be the unique identifier associated with one
+    or more observations at a single location (i.e. a "site"). If a lake can have multiple sites in the dataset,
+    choose the "site" identifier, not the lake identifier.
+    :param lake_name_field: The lake name recorded with the observation
+    :param lake_county_field: (Optional) The county name recorded with the observation, if available, which will be
+    used to limit name-based matches to lakes in the same county to avoid mis-identifying lakes with common names
+    :param state: (Optional) The 2-letter abbreviation of the U.S. state the dataset is limited to
+    :param master_gdb: Location of master geodatabase used for linking that contains the collateral matching information
+    described in the variables MASTER_LAKES_FC, MASTER_LAKES_LINES, MASTER_STREAMS_FC, and MASTER_XWALK in this script
+    :return: A point feature class containing the original input rows with the following fields added to document and
+    control the semi-automated linking process.
+        -Auto_Comment: Match status of site suggested by georeference_lakes. Permitted values:
+            'Exact location link'
+            'Linked by common name and location'
+            'Linked by common location'
+            'Not linked because represented as river in NHD'
+            'LAGOS-NE legacy link'
+            'Not linked"
+        -Comment: Match status of site finalized after review. (Edit this field during review.)
+        -Manual_Review: Numeric value indicating level of scrutiny to apply to suggested link, with higher values
+        indicating matches with less confidence.
+        -Shared_Words: Lake name elements common to the site and the linked lake
+        -Linked_lagoslakeid: The lagoslakeid for the LAGOS-US lake polygon linked to the sampling site. (Edit this field
+        during review.)
+        -GEO_Discovered_Name: A column to add any additional names for the lake discovered during lake linking review.
+        -Duplicate_Candidate: A Y/N flag indicating whether multiple suggested links are included in the dataset (Delete
+        one of the rows after choosing the best one in manual review.)
+        -Is_Legacy_Link: A Y/N flag indicating whether the site identifier was detected in the LAGOS-NE legacy site
+        identifiers list provided in the LAGOS-US lake_link crosswalk.
+        -Total_points_in_lake_poly: The number of unique site identifiers suggested to be linked to the same LAGOS-US
+        lake as this site, including this site in the count.
+        -Note: A field provided for any free-form notes and comments about linking determinations during manual review.
     """
+
+    # ---SETUP----------------------------------------------------------------------------------------------------
     master_lakes_fc = os.path.join(master_gdb, MASTER_LAKES_FC)
     master_lakes_lines = os.path.join(master_gdb, MASTER_LAKES_LINES)
     master_streams_fc = os.path.join(master_gdb, MASTER_STREAMS_FC)
     master_xwalk = os.path.join(master_gdb, MASTER_XWALK)
 
-    # setup
-    arcpy.AddMessage("Joining...")
     state = state.upper()
     if state not in STATES:
         raise ValueError('Use the 2-letter state code abbreviation')
@@ -87,64 +122,71 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
     join1 = '{}_1'.format(out_short)
     join2 = '{}_2'.format(out_short)
     join3 = '{}_3'.format(out_short)
-    join3_select = join3 + '_select'
     join4 = '{}_4'.format(out_short)
-    join5 = '{}_5'.format(out_short)
-    joinx = '{}_x'.format(out_short)
-
-    county_name_results = arcpy.ListFields(lake_points_fc, '{}*'.format(lake_county_field))[0].name
-    if lake_county_field and not lake_county_field in county_name_results:
-        print('{} field does not exist in dataset.'.format(lake_county_field))
-        raise Exception
-
-    point_fields = [f.name for f in arcpy.ListFields(lake_points_fc)]
+    point_fields = [f.name for f in arcpy.ListFields(sample_sites_point_fc)]
 
-    # update the lake id to a text field if not already
-    lake_id_field_type = arcpy.ListFields(lake_points_fc, lake_id_field)[0].type
+    # If the lake ID is not a text/string value type, change to string
+    lake_id_field_type = arcpy.ListFields(sample_sites_point_fc, site_id_field)[0].type
     if lake_id_field_type != 'String':
-        temp_id_field = '{}_t'.format(lake_id_field)
-        arcpy.AddField_management(lake_points_fc, '{}_t'.format(lake_id_field), 'TEXT', '255')
-        expr = '!{}!'.format(lake_id_field)
-        arcpy.CalculateField_management(lake_points_fc, temp_id_field, expr, 'PYTHON')
-        arcpy.DeleteField_management(lake_points_fc, lake_id_field)
-        arcpy.AlterField_management(lake_points_fc, temp_id_field, new_field_name = lake_id_field)
-
-
-
-    # Try to make some spatial connections and fulfill some logic to assign a link
-    join1 = AN.SpatialJoin(lake_points_fc, master_lakes_fc, join1, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option = 'INTERSECT')
-    join2 = AN.SpatialJoin(join1, master_streams_fc, join2, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option = 'INTERSECT')
-    join3 = AN.SpatialJoin(join2, master_lakes_fc, join3, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option = 'INTERSECT', search_radius = '10 meters')
-    join4 = AN.SpatialJoin(join3, master_lakes_fc, join4, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option = 'INTERSECT', search_radius =  '100 meters')
-
-    # setup for editing lake assignment values
-    DM.AddField(join4, 'Auto_Comment', 'TEXT', field_length = 100)
+        temp_id_field = '{}_t'.format(site_id_field)
+        arcpy.AddField_management(sample_sites_point_fc, '{}_t'.format(site_id_field), 'TEXT', '255')
+        expr = '!{}!'.format(site_id_field)
+        arcpy.CalculateField_management(sample_sites_point_fc, temp_id_field, expr, 'PYTHON')
+        arcpy.DeleteField_management(sample_sites_point_fc, site_id_field)
+        arcpy.AlterField_management(sample_sites_point_fc, temp_id_field, new_field_name=site_id_field)
+
+    # ---SPATIAL LINK EVIDENCE GATHERING ----------------------------------------------------------------------
+    # Perform joins to gather spatial link information to apply rules later
+    # Join 1: point inside lake
+    # Join 2: point inside double-banked stream polygon (not lake)
+    # Join 3: point within 10m of lake border
+    # Join 4: point within 100m of lake border
+    join1 = AN.SpatialJoin(sample_sites_point_fc, master_lakes_fc, join1, 'JOIN_ONE_TO_MANY', 'KEEP_ALL',
+                           match_option='INTERSECT')
+    join2 = AN.SpatialJoin(join1, master_streams_fc, join2, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option='INTERSECT')
+    join3 = AN.SpatialJoin(join2, master_lakes_fc, join3, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option='INTERSECT',
+                           search_radius='10 meters')
+    join4 = AN.SpatialJoin(join3, master_lakes_fc, join4, 'JOIN_ONE_TO_MANY', 'KEEP_ALL', match_option='INTERSECT',
+                           search_radius='100 meters')
+
+    # ---APPLY DISTANCE & NAME-BASED LOGIC TO CHOOSE LINK---------------------------------------------------------
+    # Set-up for editing lake assignment values
+    DM.AddField(join4, 'Auto_Comment', 'TEXT', field_length=100)
     DM.AddField(join4, 'Manual_Review', 'SHORT')
-    DM.AddField(join4, 'Shared_Words', 'TEXT', field_length = 100)
+    DM.AddField(join4, 'Shared_Words', 'TEXT', field_length=100)
     DM.AddField(join4, 'Linked_lagoslakeid', 'LONG')
-    DM.AddField(join4, 'GEO_Discovered_Name', 'TEXT', field_length = 255)
-    DM.AddField(join4, 'Duplicate_Candidate', 'TEXT', field_length = 1)
-    DM.AddField(join4, 'Is_Legacy_Link', 'TEXT', field_length = 1)
-
-    update_fields = [lake_id_field, lake_name_field,  MASTER_LAKE_ID, MASTER_GNIS_NAME, # 0m match
-                     'PERMANENT_IDENTIFIER_1', 'GNIS_NAME_1', # stream match
-                     MASTER_LAKE_ID + '_1', MASTER_GNIS_NAME +'_12', # 10m match
-                     MASTER_LAKE_ID + '_12', MASTER_GNIS_NAME + '_12_13', # 100m match
-                     'Auto_Comment', 'Manual_Review', 'Shared_Words',
+    DM.AddField(join4, 'GEO_Discovered_Name', 'TEXT', field_length=255)
+    DM.AddField(join4, 'Duplicate_Candidate', 'TEXT', field_length=1)
+    DM.AddField(join4, 'Is_Legacy_Link', 'TEXT', field_length=1)
+    update_fields = [site_id_field,
+                     lake_name_field,
+                     MASTER_LAKE_ID,
+                     MASTER_GNIS_NAME,  # 0m match
+                     'PERMANENT_IDENTIFIER_1', 'GNIS_NAME_1',  # stream match
+                     MASTER_LAKE_ID + '_1', MASTER_GNIS_NAME + '_12',  # 10m match
+                     MASTER_LAKE_ID + '_12', MASTER_GNIS_NAME + '_12_13',  # 100m match
+                     'Auto_Comment',
+                     'Manual_Review',
+                     'Shared_Words',
                      'Linked_lagoslakeid']
 
-    # use a cursor to go through each point and evaluate its assignment
+    # Evaluate match criteria for each lake and transfer the linked lagoslakeid value to the Linked_lagoslakeid field
+    # if the match is accepted.
+    # Update the comment to describe the match type.
+    # Update the manual review flag to indicate only superficial review needed (-1) for convincing matches, and review
+    # needed (>=1, higher values need more scrutiny) if the match is less convincing or needs discrimination
+    # These criteria flow from most convincing (inside lake) to least convincing link.
     cursor = arcpy.da.UpdateCursor(join4, update_fields)
     arcpy.AddMessage("Calculating link status...")
     for row in cursor:
         id, name, mid_0, mname_0, stream_id, streamname_0, mid_10, mname_10, mid_100, mname_100, comment, review, words, lagosid = row
-        if mid_0 is not None: # if the point is directly in a polygon
+        if mid_0 is not None:  # if the point is directly in a polygon
             if name and mname_0:
                 words = lagosGIS.list_shared_words(name, mname_0, exclude_lake_words=False)
             comment = 'Exact location link'
             lagosid = mid_0
             review = -1
-        elif mid_0 is None and mid_10 is not None: # if the point is only within 10m of a lake
+        elif mid_0 is None and mid_10 is not None:  # if the point is only within 10m of a lake
             if name and mname_10:
                 words = lagosGIS.list_shared_words(name, mname_10, exclude_lake_words=False)
             if words:
@@ -156,14 +198,13 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
                 lagosid = mid_10
                 review = 1
         elif mid_0 is None and mid_10 is None:
-            if stream_id is not None: # if there is a stream match
+            if stream_id is not None:  # if there is a stream match
                 comment = 'Not linked because represented as river in NHD'
                 review = 2
             else:
-                if mid_100 is not None: # if the point is only within 100m of lake(s)
+                if mid_100 is not None:  # if the point is only within 100m of lake(s)
                     if name and mname_100:
                         words = lagosGIS.list_shared_words(name, mname_100, exclude_lake_words=True)
-                # TODO: Frequency check
                     if words:
                         comment = 'Linked by common name and location'
                         lagosid = mid_100
@@ -172,83 +213,18 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
                         comment = 'Linked by common location'
                         lagosid = mid_100
                         review = 2
-        cursor.updateRow((id, name, mid_0, mname_0, stream_id, streamname_0, mid_10, mname_10, mid_100, mname_100, comment, review, words, lagosid))
-
-    # # So I haven't been able to get the county logic to work and it hasn't been that important yet, ignore for now
-    # Select down to a minimum set because we're about to join on county, which will create lots of duplicate matches
-    # Then join calculated results back to full set
-    # if lake_county_field:
-    #     join5 = AN.Select(join4, join5, 'Manual_Review IS NULL')
-    #     lakes_state = AN.Select(MASTER_LAKES_FC, 'lakes_state', "{0} = '{1}'".format(MASTER_STATE_NAME, state))
-    #     lakes_state_lyr = DM.MakeFeatureLayer(lakes_state, 'lakes_state_lyr')
-    #     join5_lyr = DM.MakeFeatureLayer(join5, 'join5_lyr')
-    #     DM.AddJoin(join5_lyr, lake_county_field, lakes_state_lyr, MASTER_COUNTY_NAME)
-    #     join5_with_county = DM.CopyFeatures(join5_lyr, 'join5_with_cty')
-    #     j5 = 'DEDUPED_CA_SWAMP_data_linked_5.'
-    #
-    #     county_update_fields = [j5 + lake_id_field, j5 + lake_name_field, j5 + lake_county_field,
-    #                             'lakes_state.' + MASTER_LAKE_ID, 'lakes_state.' + MASTER_GNIS_NAME, 'lakes_state.' + MASTER_COUNTY_NAME,
-    #                             j5 + 'Auto_Comment', j5 + 'Manual_Review', j5 + 'Shared_Words',
-    #                             j5 + 'Linked_lagoslakeid']
-    #     with arcpy.da.UpdateCursor(join5_lyr, county_update_fields) as cursor:
-    #         for row in cursor:
-    #             id, name, county, mid_cty, mname_cty, mcounty, comment, review, words, lagosid = row
-    #             if county is not None and mcounty is not None:
-    #                 if name and mname_cty:
-    #                     words = lagosGIS.list_shared_words(name, mname_cty, exclude_lake_words=True)
-    #                 if words:
-    #                     comment = 'PRELIMINARY: Linked by common name and location'
-    #                     lagosid = mid_cty
-    #                     review = 2
-    #             cursor.updateRow((id, name, county, mid_cty, mname_cty, mcounty, comment, review, words, lagosid))
-    #     DM.RemoveJoin(join5_lyr)
-    #     join5_with_county = DM.CopyFeatures(join5_lyr, 'join5_with_county')
-    #
-    #     # join5 = DM.JoinField(join5, lake_county_field, lakes_state, MASTER_COUNTY_NAME,
-    #                          fields = [MASTER_COUNTY_NAME, MASTER_LAKE_ID, MASTER_GNIS_NAME])
-    #
-    #     # This is a long way to make a join
-    #     join_dict = {}
-    #     with arcpy.da.SearchCursor(lakes_state, [MASTER_COUNTY_NAME, MASTER_LAKE_ID, MASTER_GNIS_NAME]) as cursor:
-    #         for row in cursor:
-    #             join_value, val1, val2 = row
-    #             join_dict[join_value] = [val1, val2]
-    #
-    #     arcpy.AddField_management(join5, MASTER_LAKE_ID + 'cntyj', 'LONG')
-    #     arcpy.AddField_management(join5, MASTER_GNIS_NAME + 'cntyj', 'TEXT', 255)
-    #
-    #     with arcpy.da.SearchCursor(join5, [lake_county_field, MASTER_LAKE_ID + 'cntyj', MASTER_GNIS_NAME + 'cntyj']) as cursor:
-    #         for row in cursor:
-    #             key_value = row[0]
-    #             words = lagosGIS.list_shared_words()
-    #             if join_dict.has_key(key_value):
-    #                 row[1] = join_dict[key_value][0]
-    #                 row[2] = join_dict[key_value][1]
-    #             else:
-    #                 row[1] = None
-    #                 row[2] = None
-    #             cursor.updateRow(row)
-    #
-    #
-    #     county_update_fields = [lake_id_field, lake_name_field, lake_county_field,
-    #                 MASTER_LAKE_ID + '_12_13_14', MASTER_GNIS_NAME + '_12_13',  MASTER_COUNTY_NAME + '_12_13', # county
-    #                  'Auto_Comment', 'Manual_Review', 'Shared_Words',
-    #                  'Linked_lagoslakeid']
-    #     cursor = arcpy.da.UpdateCursor(join5, county_update_fields)
-    #     for row in cursor:
-    #         id, name, county, lagosid_cty, lagosname_cty, mcounty, comment, mreview, words, linked_lagosid = row
-    #         if mcounty is not None:
-    #             words = lagosGIS.list_shared_words()
-    # else:
-    #     join5 = join4
-    #
-
+        cursor.updateRow((id, name, mid_0, mname_0, stream_id, streamname_0, mid_10, mname_10, mid_100, mname_100,
+                          comment, review, words, lagosid))
 
+    # --- LEGACY LINKING TO LAGOS-NE IDENTIFIERS-------------------------------------------------------------------
+    # If the dataset is from a state that was in LAGOS-NE, flag site for manual review if the match type above was
+    # not 'Exact location link' and transfer the lake info that was linked previously for LAGOS-NE (so that sites
+    # already matched in LAGOS-NE are not forgotten or over-written by this process for LAGOS-US)
     if state in LAGOSNE_STATES:
-        DM.JoinField(join4, lake_id_field, master_xwalk, 'lagosne_legacyid',
+        DM.JoinField(join4, site_id_field, master_xwalk, 'lagosne_legacyid',
                      ['lagoslakeid', 'lagos_lakename', 'lagos_state'])
-        update_fields = [lake_id_field, lake_name_field,
-                         MASTER_LAKE_ID + '_12_13', 'lagos_lakename', 'lagos_state', # crosswalk match
+        update_fields = [site_id_field, lake_name_field,
+                         MASTER_LAKE_ID + '_12_13', 'lagos_lakename', 'lagos_state',  # crosswalk match
                          'Auto_Comment', 'Manual_Review', 'Shared_Words',
                          'Linked_lagoslakeid', 'Is_Legacy_Link']
 
@@ -258,36 +234,30 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
                 # fields are populated already from links above. Revise only if legacy links
                 if mid_x is not None:
                     if state == state_x:
-                        legacy_flag = 'Y' # set to Y regardless of whether using legacy comment if state matches
+                        legacy_flag = 'Y'  # set to Y regardless of whether using legacy comment if state matches
                     if comment != 'Exact location link':
                         review = 1
                         if state != state_x:
-                            review = 3 # downgrade if states mismatch--border lakes OK, random common IDs NOT. Check.
+                            review = 3  # downgrade if states mismatch--border lakes OK, random common IDs NOT. Check.
                         legacy_flag = 'Y'
-                        comment = 'LAGOS-NE legacy link' # only comment non-exact location matches
+                        comment = 'LAGOS-NE legacy link'  # only comment non-exact location matches
                         lagosid = mid_x
                         if name and mname_x:
-                            words = lagosGIS.list_shared_words(name, mname_x) # update words only if legacy comment
+                            words = lagosGIS.list_shared_words(name, mname_x)  # update words only if legacy comment
 
                 new_row = id, name, mid_x, mname_x, state_x, comment, review, words, lagosid, legacy_flag
                 uCursor.updateRow(new_row)
 
-
-
-
-        # # Undo the next line if you ever bring this chunk back.
-    join5 = join4
-
-    # then re-code the no matches as a 3 and copy comments to the editable field
-    # compress the joined lake ids into one field
-    # having two fields lets us keep track of how many of the auto matches are bad
-    if arcpy.ListFields(join5, 'Comment'):
+    # ---ASSIGN REVIEW FLAGS FOR EXTREMES--------------------------------------------------------------------------
+    # No match
+    # Assign high scrutiny, assign and/or copy the no-match comment
+    if arcpy.ListFields(join4, 'Comment'):
         comment_field_name = 'Comment_LAGOS'
     else:
         comment_field_name = 'Comment'
 
-    DM.AddField(join5, comment_field_name, 'TEXT', field_length=100)
-    with arcpy.da.UpdateCursor(join5, ['Manual_Review', 'Auto_Comment', 'Comment']) as cursor:
+    DM.AddField(join4, comment_field_name, 'TEXT', field_length=100)
+    with arcpy.da.UpdateCursor(join4, ['Manual_Review', 'Auto_Comment', 'Comment']) as cursor:
         for flag, ac, comment in cursor:
             if flag is None:
                 flag = 3
@@ -295,8 +265,8 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
             comment = ac
             cursor.updateRow((flag, ac, comment))
 
-    # Re-code points more than 100m into the polygon of the lake as no need to check
-    DM.MakeFeatureLayer(join5, 'join5_lyr')
+    # Assign lowest scrutiny value for points more than 100m inside lake, very convincing match
+    DM.MakeFeatureLayer(join4, 'join5_lyr')
     DM.MakeFeatureLayer(master_lakes_lines, 'lake_lines_lyr')
     DM.SelectLayerByAttribute('join5_lyr', 'NEW_SELECTION', "Auto_Comment = 'Exact location link'")
     DM.SelectLayerByLocation('join5_lyr', 'INTERSECT', 'lake_lines_lyr', '100 meters', 'SUBSET_SELECTION', 'INVERT')
@@ -311,21 +281,21 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
     copy_fields.remove('Shape')
     copy_fields.remove('OBJECTID')
 
-    lagosGIS.select_fields(join5, out_fc, copy_fields)
+    lagosGIS.select_fields(join4, out_fc, copy_fields)
+    DM.AssignDomainToField(out_fc, 'Comment', 'Comment')  # prevent manual editor from entering bad comments
 
-    DM.AssignDomainToField(out_fc, 'Comment', 'Comment')
+    # ---MANAGE ONE-TO-MANY SCENARIOS------------------------------------------------------------------------------
 
-    DM.AddField(out_fc, 'Total_points_in_lake_poly', 'Short')
-
-    # Remove any duplicates. (These originate from the join3/join4 transition because a point can be both
-    # within 10m and 100m of lakes, this code takes the closest lake as true for my current sanity.)
-    # Or, in other words, this is a hack solution.
+    # Remove any duplicates on all non-OID fields.
+    # (These originate from the join3/join4 transition because a point can be both
+    # within 10m and 100m of lakes, this code takes the closest lake as true for my current sanity.
+    # Or, in other words, this is a hack solution.)
     out_fc_fields = [f.name for f in arcpy.ListFields(out_fc) if f.name != 'OBJECTID']
     DM.DeleteIdentical(out_fc, out_fc_fields)
 
     # Get the join_count for each limno lake ID
     # De-dupe anything resulting from limno ID duplicates first before counting
-    id_pairs = list(set(arcpy.da.SearchCursor(out_fc, [lake_id_field, 'Linked_lagoslakeid'])))
+    id_pairs = list(set(arcpy.da.SearchCursor(out_fc, [site_id_field, 'Linked_lagoslakeid'])))
     # THEN pull out LAGOS id. Any duplicate now are only due to multiple distinct points within lake
     lagos_ids = [ids[1] for ids in id_pairs]
     sample_ids = [ids[0] for ids in id_pairs]
@@ -333,6 +303,7 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
     linked_multiple_lake_counts = Counter(sample_ids)
 
     # Get the count of points in the polygon
+    DM.AddField(out_fc, 'Total_points_in_lake_poly', 'Short')
     with arcpy.da.UpdateCursor(out_fc, ['Linked_lagoslakeid', 'Total_points_in_lake_poly']) as cursor:
         for lagos_id, join_count in cursor:
             join_count = lagos_lake_counts[lagos_id]
@@ -340,7 +311,7 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
 
     # Mark any samples linked to more than one lake so that the analyst can select the correct lake in the
     # manual process
-    with arcpy.da.UpdateCursor(out_fc, [lake_id_field, 'Duplicate_Candidate']) as cursor:
+    with arcpy.da.UpdateCursor(out_fc, [site_id_field, 'Duplicate_Candidate']) as cursor:
         for sample_id, duplicate_flag in cursor:
             duplicate_count = linked_multiple_lake_counts[sample_id]
             if duplicate_count > 1:
@@ -349,20 +320,8 @@ def georeference_lakes(lake_points_fc, out_fc, lake_id_field,
                 duplicate_flag = "N"
             cursor.updateRow((sample_id, duplicate_flag))
 
-    # clean up
+    # Cleanup
     DM.AddField(out_fc, 'Note', 'TEXT', field_length=140)
     DM.Delete('in_memory')
-    arcpy.AddMessage('Completed.')
-
-
-
-
-
-
-
-
-
-
-
-
 
+    return out_fc
\ No newline at end of file
diff --git a/lagosGIS/lake_density.py b/lagosGIS/lake_density.py
index 6dc29f1..2aab406 100644
--- a/lagosGIS/lake_density.py
+++ b/lagosGIS/lake_density.py
@@ -9,14 +9,25 @@
 import polygon_density_in_zones
 import lagosGIS
 
-# Since the ws & nws layers were left with the jagged "rasterization" lines, they sometimes overlap lakes outside
-# their area with small slivers. This function pre-processes the watersheds layer to erase those small sliver overlaps
-# so that the lake count is more accurate.
-# This tool is pretty slow.
 
 def trim_watershed_slivers(watersheds_fc, lakes_fc, output_fc):
+    """
+    Align watershed and lake layers by trimming overlapping slivers from watersheds layer in order to refine the
+    lake count. These overlaps are present because the geometry for these features follows the 10m raster cells used
+    to delinate the watersheds, whereas the lakes do not.
+
+    This tool is pretty slow.
+    :param watersheds_fc: The ws/nws polygon feature class
+    :param lakes_fc: The lakes feature class to be counted
+    :param output_fc: An output feature class to save the modified ws/nws features. Use this output in calc_all, below.
+    :return: Output feature class location
+    """
+
+    # Delineate overlapping regions
     arcpy.Intersect_analysis([watersheds_fc, lakes_fc], output_fc)
-    # want to drop any intersections < 10% of area of the lake, as long as it overlaps shed by 10%+, will count
+
+    # Trim the overlapping regions from the watersheds shape
+    # Want to drop any intersections < 10% of area of the lake, as long as it overlaps shed by 10%+, will count
     arcpy.Select_analysis(output_fc, 'in_memory/slivers', 'Shape_Area < (.1 * lake_waterarea_ha) * 10000')
     arcpy.Delete_management(output_fc) # used this as a temp fc so we could have Shape_Area calculated
     arcpy.Erase_analysis(watersheds_fc, 'in_memory/slivers', output_fc)
@@ -24,13 +35,20 @@ def trim_watershed_slivers(watersheds_fc, lakes_fc, output_fc):
 
 
 def calc_all(zones_fc, zone_field, lakes_fc, output_table):
-
-    # make sure we're only using the right types of lakes, our feature
-    # class excludes everything else but this is a guarantee this will
-    # get checked at some point
+    """
+    Convenience function that runs Polygon Density in Zones for all LAGOS-US lake count metrics.
+
+    :param zones_fc: Zones feature class
+    :param zone_field: Unique identifier for each zone
+    :param lakes_fc: Lakes feature class to be counted (LAGOS-US lake population feature class)
+    :param output_table: Output table to save the results
+    :return: None
+    """
+
+    # Ensure the lakes_fc meets our expectations for LAGOS processing: Albers USGS, contains hectares field, filtered
+    # for the appropriate Fcodes. If not, make it so.
     arcpy.env.workspace = 'in_memory'
     arcpy.env.outputCoordinateSystem = arcpy.SpatialReference(102039)
-
     temp_lakes = 'temp_lakes'
     arcpy.CopyFeatures_management(lakes_fc, temp_lakes)
 
@@ -39,24 +57,22 @@ def calc_all(zones_fc, zone_field, lakes_fc, output_table):
         arcpy.AddField_management(temp_lakes, 'lake_waterarea_ha', 'DOUBLE')
         arcpy.CalculateField_management(temp_lakes, 'lake_waterarea_ha', '!shape.area@hectares!', 'PYTHON')
 
-    # this bit enforces the correct lake type/size restriction just in case
-    # geodata doesn't have this filtered already
     need_selection = False
     fcodes = lagosGIS.LAGOS_FCODE_LIST
-
     with arcpy.da.SearchCursor(temp_lakes, ["FCode"]) as cursor:
             for row in cursor:
                 if row[0] not in fcodes:
                     need_selection = True
-
     if need_selection:
         whereClause = '''"FCode" IN %s''' % (fcodes,)
         arcpy.Select_analysis(temp_lakes, "lakes_lagos", whereClause)
         temp_lakes = os.path.join(arcpy.env.workspace, "lakes_lagos")
 
+    # Use trimming function above if the spatial divisions provided is a watersheds layer
     if 'ws' in zones_fc:
         zones_fc = trim_watershed_slivers(zones_fc, lakes_fc, 'sliverless_sheds')
 
+    # Enumerate filtering queries and metric (table) names so that they are complete and aligned
     selections = [
             # all lake selections
             "",
@@ -159,6 +175,7 @@ def calc_all(zones_fc, zone_field, lakes_fc, output_table):
                'lakes10ha_terminallkperm'
                 ]
 
+    # Run Polygon Density in Zones for all select query & metric pairings and save to temporary tables
     for sel, temp_table in zip(selections, temp_tables):
         arcpy.AddMessage("Creating temporary table called {0} for lakes where {1}".format(temp_table, sel))
         polygon_density_in_zones.calc(zones_fc, zone_field, temp_lakes, temp_table, sel)
@@ -166,12 +183,12 @@ def calc_all(zones_fc, zone_field, lakes_fc, output_table):
         for f in new_fields:
             arcpy.AlterField_management(temp_table, f, f.replace('Poly', temp_table))
 
-    # join em up and copy to final
+    # Join up tables and copy to final output table
     temp_tables.remove('lakes1ha_all')
     for t in temp_tables:
         try:
             arcpy.JoinField_management('lakes1ha_all', zone_field, t, zone_field)
-        #sometimes there's no table if it was an empty selection
+        # sometimes there's no table if it was an empty selection
         except:
             empty_fields = [f.replace('Poly', t) for f in new_fields]
             for ef in empty_fields:
@@ -179,13 +196,13 @@ def calc_all(zones_fc, zone_field, lakes_fc, output_table):
                 arcpy.CalculateField_management('lakes1ha_all', ef, '0', 'PYTHON')
             continue
 
-    # remove all the extra zoneID fields, which have underscore in name
+    # Remove all the extra zoneID fields, which have underscore in name
     drop_fields = [f.name for f in arcpy.ListFields('lakes1ha_all') if 'zoneid_' in f.name or 'AREA' in f.name]
     for f in drop_fields:
         arcpy.DeleteField_management('lakes1ha_all', f)
     arcpy.CopyRows_management('lakes1ha_all', output_table)
 
-    # clean up
+    # Clean up
     arcpy.Delete_management('in_memory')
 
 
@@ -196,5 +213,6 @@ def main():
     output_table = arcpy.GetParameterAsText(3)
     calc_all(zones_fc, zone_field, lakes_fc, output_table)
 
+
 if __name__ == '__main__':
     main()
diff --git a/lagosGIS/line_density_in_zones.py b/lagosGIS/line_density_in_zones.py
index 99cd15d..329a21b 100644
--- a/lagosGIS/line_density_in_zones.py
+++ b/lagosGIS/line_density_in_zones.py
@@ -11,15 +11,30 @@
 
 
 def calc(zones_fc, zone_field, lines_fc, out_table, where_clause='', rename_label=''):
+    """
+    Calculates areal density of line features such as streams and roads.
+    :param zones_fc: Zones feature class
+    :param zone_field: Unique identifier for each zone
+    :param lines_fc: The polyline feature class to be summarized for each zone
+    :param out_table: Output table to save the result
+    :param where_clause: (Optional) Query (SQL where clause) to filter polyline feature class before summary
+    :param rename_label: (Optional) Text string to use as prefix for all output columns
+    :return: None
+    """
+
+    # Setup: enforce coordinates, make names, filter lines if elected
     arcpy.env.workspace = 'in_memory'
     arcpy.env.outputCoordinatesystem = arcpy.SpatialReference(102039)
+
     if rename_label:
-        out_density_field = '{}_mperha'.format(rename_label)
+        density_field_name = '{}_mperha'.format(rename_label)
     else:
-        out_density_field = '{}_mperha'.format(os.path.basename(lines_fc))
+        density_field_name = '{}_mperha'.format(os.path.basename(lines_fc))
 
     if where_clause:
         lines_prep = arcpy.Select_analysis(lines_fc, 'lines_prep', where_clause)
+    elif arcpy.Describe(lines_fc).spatialReference.factoryCode not in (102039, 5070):
+        lines_prep = arcpy.CopyFeatures_management(lines_fc, 'lines_prep')
     else:
         lines_prep = lines_fc
 
@@ -33,46 +48,51 @@ def calc(zones_fc, zone_field, lines_fc, out_table, where_clause='', rename_labe
             row[0] = row[1]
             cursor.updateRow(row)
 
-    # calc total length grouped by zone (numerator)
-    print("Statistics {}".format(dt.now().strftime("%Y-%m-%d %H:%M:%S")))
-    lines_stat = arcpy.Statistics_analysis(lines_identity, 'lines_stat', 'length_m SUM', zone_field)
-    print("One in One out {}".format(dt.now().strftime("%Y-%m-%d %H:%M:%S")))
-    lines_stat_full = lagosGIS.one_in_one_out(lines_stat, zones_fc, zone_field, 'lines_stat_full')
-
-    # get area of zones for density calc (denominator)
-    print("Zones Area {}".format(dt.now().strftime("%Y-%m-%d %H:%M:%S")))
-    zones_area = {}
-    with arcpy.da.SearchCursor(zones_fc, [zone_field, 'SHAPE@']) as cursor:
-        for row in cursor:
-            zones_area[row[0]] = row[1].getArea(units='HECTARES')
-
-    # calc the density by dividing
-    print("Calc Density {}".format(dt.now().strftime("%Y-%m-%d %H:%M:%S")))
-    arcpy.AddField_management(lines_stat_full, out_density_field, 'DOUBLE')
-    with arcpy.da.UpdateCursor(lines_stat_full, [zone_field, out_density_field, 'SUM_length_m']) as cursor:
-        for row in cursor:
-            zid, mperha, msum = row
-            if msum is None:
-                msum = 0 # replace NULL values with 0 which is physically accurate here
-            if zid:
-                mperha = msum/zones_area[zid]
-                row = (zid, mperha, msum)
-                cursor.updateRow(row)
-            # this branch deletes ONE row that has no zone id--total length of lines not in zones
-            else:
-                cursor.deleteRow()
-
-    # delete extra field and ensure all input zones have output row
-    print("Cleanup {}".format(dt.now().strftime("%Y-%m-%d %H:%M:%S")))
-    arcpy.DeleteField_management(lines_stat_full, 'SUM_length_m')
-    arcpy.DeleteField_management(lines_stat_full, 'FREQUENCY')
-
-    arcpy.CopyRows_management(lines_stat_full, out_table)
-
-    # cleanup
-    for item in ['lines_prep', lines_identity, lines_stat, lines_stat_full]:
+    def summarize_cracked(cracked_lines, density_field_name):
+        # Calculate total length grouped by zone (numerator)
+        lines_stat = arcpy.Statistics_analysis(cracked_lines, 'lines_stat', 'length_m SUM', zone_field)
+        lines_stat_full = lagosGIS.one_in_one_out(lines_stat, zones_fc, zone_field, 'lines_stat_full')
+
+        # Get area of zones for density calc (denominator)
+        zones_area = {}
+        with arcpy.da.SearchCursor(zones_fc, [zone_field, 'SHAPE@']) as cursor:
+            for row in cursor:
+                zones_area[row[0]] = row[1].getArea(units='HECTARES')
+
+        # Calculate the density by dividing numerator by denominator
+        arcpy.AddField_management(lines_stat_full, density_field_name, 'DOUBLE')
+        with arcpy.da.UpdateCursor(lines_stat_full, [zone_field, density_field_name, 'SUM_length_m']) as cursor:
+            for row in cursor:
+                zid, mperha, msum = row
+                if msum is None:
+                    msum = 0  # replace NULL values with 0 which is physically accurate here
+                if zid:
+                    mperha = msum/zones_area[zid]
+                    row = (zid, mperha, msum)
+                    cursor.updateRow(row)
+                # this branch deletes ONE row that has no zone id--total length of lines not in zones
+                else:
+                    cursor.deleteRow()
+
+        # Delete extra fields
+        arcpy.DeleteField_management(lines_stat_full, 'SUM_length_m')
+        arcpy.DeleteField_management(lines_stat_full, 'FREQUENCY')
+
+        # Copy output to an in_memory fc with same name as output field so we can delete lines_stat_full
+        summarized = arcpy.CopyRows_management(lines_stat_full, density_field_name)
+
+        # Cleanup
+        for item in [lines_stat, lines_stat_full]:
+            arcpy.Delete_management(item)
+        return summarized
+
+    # Run summary, copy to output, clean up
+    summary = summarize_cracked(lines_identity, density_field_name)
+    arcpy.CopyRows_management(summary, out_table)
+    for item in ['lines_prep', lines_identity]:
         arcpy.Delete_management(item)
 
+
 def main():
     # Parameters
     zones_fc = arcpy.GetParameterAsText(0)
@@ -84,7 +104,6 @@ def main():
     calc(zones_fc, zone_field, lines_fc, out_table, where_clause, rename_label)
 
 
-
 if __name__ == '__main__':
     main()
 
diff --git a/lagosGIS/mosaic_dem_and_tri.py b/lagosGIS/mosaic_dem_and_tri.py
index 3e316a4..08c7057 100644
--- a/lagosGIS/mosaic_dem_and_tri.py
+++ b/lagosGIS/mosaic_dem_and_tri.py
@@ -3,12 +3,15 @@
 # version: 2.0
 # LAGOS module(s): GEO
 # tool type: code journal, modify paths by hand
+# purpose: Automate the steps to calculate TRI and convert terrain rasters to 30m in a way that conserves disk space
+# while the processing is in progress
 
 import os
 import subprocess
 import zipfile
 import arcpy
 
+# Locate files and specify raster processing environments
 GDALDEM = r'C:\cygwin64\bin\gdaldem.exe' # version GDAL 3.3.0, released 2021/04/26
 
 zip_dir = 'F:/Continental_Limnology/Data_Downloaded/3DEP_National_Elevation_Dataset/Zipped'
@@ -17,52 +20,44 @@
 arcpy.env.outputCoordinateSystem = arcpy.SpatialReference(5070)
 
 
-zip_files = [os.path.join(zip_dir, f) for f in os.listdir(zip_dir)]
-# for each file
-
 def process_file(file):
+    """
+    Demonstrates the steps used to calculate terrain roughness index (TRI) using GDAL and the re-sampling and
+    re-projection of the terrain rasters to the common 30m raster grid.
+    :param file: DEM raster file from NED
+    :return: None
+    """
     print(file)
 
-    # unzip
+    # Unzip
     zf = zipfile.ZipFile(file)
     out_dir = os.path.splitext(file)[0]
     zf.extractall(out_dir)
     img_file = [os.path.join(out_dir,f) for f in os.listdir(out_dir) if f.endswith('.img')][0]
 
-    # calc TRI
+    # Calculate TRI
     tri_file = '{}_TRI.tif'.format(os.path.splitext(img_file)[0])
     tri_call = '{} TRI {} {} -alg Riley'.format(GDALDEM, img_file, tri_file)
     subprocess.call(tri_call)
 
-    # warp orig to 30/30 with env settings above
+    # Resample original both terrain files to 30m with cells matching common_grid.tif
     img_30 = '{}_30.tif'.format(os.path.splitext(img_file)[0])
     arcpy.Resample_management(img_file, img_30, cell_size=30, resampling_type='BILINEAR')
-
-    # warp TRI to 30/30 with env settings above
     tri_30 = '{}_30.tif'.format(os.path.splitext(tri_file)[0])
     arcpy.Resample_management(tri_file, tri_30, cell_size=30, resampling_type='BILINEAR')
 
-    # delete unzipped files
+    # Delete unzipped files upon completion
     all_files = os.listdir(out_dir)
     arcpy.env.workspace = out_dir
     for f in all_files:
         if os.path.basename(img_30) not in f and os.path.basename(tri_30) not in f:
             arcpy.Delete_management(f)
 
+
+# Run all the files through
+zip_files = [os.path.join(zip_dir, f) for f in os.listdir(zip_dir)]
 counter = 0
 for f in zip_files:
     counter += 1
     print(counter)
     process_file(f)
-
-os.mkdir(os.path.join(zip_dir, 'tri'))
-os.mkdir(os.path.join(zip_dir, 'elevation'))
-for root, dirs, files in os.walk(zip_dir):
-    for file in files:
-        if '_TRI_30.tif' in file:
-            os.rename(os.path.join(root, file), os.path.join(zip_dir, 'tri', file))
-        elif '_30.tif' in file:
-            os.rename(os.path.join(root, file), os.path.join(zip_dir, 'elevation', file))
-
-
-
diff --git a/lagosGIS/point_attribution_of_raster_data.py b/lagosGIS/point_attribution_of_raster_data.py
index 13bccf0..41266bf 100644
--- a/lagosGIS/point_attribution_of_raster_data.py
+++ b/lagosGIS/point_attribution_of_raster_data.py
@@ -9,12 +9,25 @@
 
 
 def attribution(zone_points, zone_field, in_value_raster, out_table, rename_tag='', units=''):
+    """
+    Extracts the raster value at a point representing a zone when the zone is much smaller than the raster cell size.
+    :param zone_points: Point feature class representing the zones or lakes
+    :param zone_field: Unique identifier for each zone
+    :param in_value_raster: The raster dataset to be summarized
+    :param out_table: Output table to save the result
+    :param rename_tag: (Optional) Text string containing prefix to append to all output columns
+    :param units: (Optional) Text string containing units to append as a suffix to all output columns
+    :return:
+    """
+
     arcpy.env.workspace = 'in_memory'
     arcpy.CheckOutExtension("Spatial")
 
+    # Extract values to points
     points = lagosGIS.select_fields(zone_points, 'points', [zone_field])
     point_stats = arcpy.sa.ExtractValuesToPoints(points, in_value_raster, 'point_stats', 'INTERPOLATE')
 
+    # Convert NoData numeric codes to missing values in output table
     nodata = arcpy.Describe(in_value_raster).noDataValue
     if nodata:
         with arcpy.da.UpdateCursor(point_stats, 'RASTERVALU') as cursor:
@@ -23,12 +36,14 @@ def attribution(zone_points, zone_field, in_value_raster, out_table, rename_tag=
                     row[0] = None
                 cursor.updateRow(row)
 
+    # Rename fields, if elected
     if rename_tag:
         new_field_name = '{}_{}'.format(rename_tag, units)
         lagosGIS.rename_field(point_stats, 'RASTERVALU', new_field_name, deleteOld=True)
     arcpy.CopyRows_management(point_stats, out_table)
     return out_table
 
+
 def main():
     zone_points = arcpy.GetParameterAsText(0)
     zone_field = arcpy.GetParameterAsText(1)
@@ -38,5 +53,6 @@ def main():
     units = arcpy.GetParameterAsText(5)
     attribution(zone_points, zone_field, in_value_raster, out_table, rename_tag, units)
 
+
 if __name__ == '__main__':
     main()
\ No newline at end of file
diff --git a/lagosGIS/point_density_in_zones.py b/lagosGIS/point_density_in_zones.py
index 58b644e..a8db7ab 100644
--- a/lagosGIS/point_density_in_zones.py
+++ b/lagosGIS/point_density_in_zones.py
@@ -7,27 +7,44 @@
 import os
 import arcpy
 
-def calc(zone_fc, zone_field, points_fc, output_table, interest_selection_expr ='', rename_label =''):
+
+def calc(zone_fc, zone_field, points_fc, output_table, where_clause='', rename_label=''):
+    """
+    Calculates count and areal density of point features such as dams, pollution sources, and mining locations.
+    :param zone_fc: Zones polygon feature class
+    :param zone_field: Unique identifier for each zone
+    :param points_fc: Points feature class to be summarized
+    :param output_table: Output table to save the result
+    :param where_clause: (Optional) Query (SQL where clause) for filtering points before summary
+    :param rename_label: (Optional) Text string containing prefix to append to all output columns
+    :return: None
+    """
+
+    # Set up and filter if elected
     arcpy.env.workspace = 'in_memory'
-    if interest_selection_expr:
-        arcpy.MakeFeatureLayer_management(points_fc, "selected_points", interest_selection_expr)
+    if where_clause:
+        arcpy.MakeFeatureLayer_management(points_fc, "selected_points", where_clause)
     else:
         arcpy.MakeFeatureLayer_management(points_fc, "selected_points")
 
+    # Do the spatial join to assign points to zones
     arcpy.SpatialJoin_analysis(zone_fc, "selected_points", 'temp_fc',
                             'JOIN_ONE_TO_ONE', 'KEEP_ALL',
                             match_option= 'INTERSECT')
 
+    # Establish names for output
     field_names = ['n', 'npersqkm']
     if rename_label:
         field_names = ['{}_{}'.format(rename_label, fn) for fn in field_names]
     field_types = ['LONG', 'DOUBLE']
     calc_expressions = ['!Join_Count!', '!Join_Count!/!shape.area@squarekilometers!']
 
+    # Add and calculate the new fields
     for fname, ftype, expr in zip(field_names, field_types, calc_expressions):
         arcpy.AddField_management('temp_fc', fname, ftype)
         arcpy.CalculateField_management('temp_fc', fname, expr, 'PYTHON')
 
+    # Select fields for output and clean up
     arcpy.CopyRows_management('temp_fc', output_table)
     keep_fields = [zone_field] + field_names
     out_fields = [f.name for f in arcpy.ListFields(output_table)]
@@ -40,6 +57,7 @@ def calc(zone_fc, zone_field, points_fc, output_table, interest_selection_expr =
     arcpy.Delete_management('selected_points')
     arcpy.Delete_management('temp_fc')
 
+
 def main():
     zone_fc = arcpy.GetParameterAsText(0)
     zone_field = arcpy.GetParameterAsText(1)
@@ -48,13 +66,6 @@ def main():
     interest_selection_expr = arcpy.GetParameterAsText(3)
     calc(zone_fc, zone_field, points_fc, output_table, interest_selection_expr)
 
-def test():
-    test_gdb = '../TestData_0411.gdb'
-    zone_fc = os.path.join(test_gdb, 'HU12')
-    zone_field = 'ZoneID'
-    points_fc = os.path.join(test_gdb, 'Dams')
-    output_table = 'C:/GISData/Scratch/Scratch.gdb/test_points_tool'
-    calc(zone_fc, zone_field, points_fc, output_table, '')
 
 if __name__ == '__main__':
     main()
diff --git a/lagosGIS/polygon_density_in_zones.py b/lagosGIS/polygon_density_in_zones.py
index cf364c4..0dc73e2 100644
--- a/lagosGIS/polygon_density_in_zones.py
+++ b/lagosGIS/polygon_density_in_zones.py
@@ -11,39 +11,43 @@
 import lagosGIS
 
 
-def calc(zone_fc, zone_field, polygons_of_interest, output_table, interest_selection_expr):
+def calc(zone_fc, zone_field, polygons_of_interest, output_table, where_clause=''):
+    """
+    Calculates total area and percent of zonal polygon occupied by polygons of interest for polygon features such as
+    lakes.
+    :param zone_fc: Zones polygon feature class
+    :param zone_field: Unique identifier for each zone
+    :param polygons_of_interest: Polygon feature class to be summarized
+    :param output_table: Output table to save the result
+    :param where_clause: (Optional) Query (SQL where clause) to filter the polygons of interest before summary
+    :return: None
+    """
+
+    # Setup
     old_workspace = arcpy.env.workspace
     arcpy.env.workspace = 'in_memory'
-    arcpy.SetLogHistory(False)
     arcpy.env.outputCoordinateSystem = arcpy.SpatialReference(102039)
     selected_polys = 'selected_polys'
-    # fixes some stupid ArcGIS thing with the interactive Python window
     if arcpy.Exists(selected_polys):
         arcpy.env.overwriteOutput = True
 
-    if interest_selection_expr:
-        arcpy.Select_analysis(polygons_of_interest, selected_polys, interest_selection_expr)
+    if where_clause:
+        arcpy.Select_analysis(polygons_of_interest, selected_polys, where_clause)
     else:
         arcpy.CopyFeatures_management(polygons_of_interest, selected_polys)
 
-    # use tabulate intersection for the areas overlapping
+    # Calculate area and percentage of polygons of interest that overlap zones
     arcpy.AddMessage('Tabulating intersection between zones and polygons...')
     tab_table = arcpy.TabulateIntersection_analysis(zone_fc, zone_field, selected_polys,
                                         'tabulate_intersection_table')
 
-    # area was calculated in map units which was m2 so convert to hectares
+    # Convert area to hectares from m2 and rename percentage
     arcpy.AddField_management(tab_table, 'Poly_ha', 'DOUBLE')
     arcpy.CalculateField_management(tab_table, 'Poly_ha', '!AREA!/10000', 'PYTHON')
-
-
-    # just change the name of the percent field
     arcpy.AlterField_management(tab_table, 'PERCENTAGE', 'Poly_pct')
     arcpy.CalculateField_management(tab_table, 'Poly_pct', 'min(!Poly_pct!, 100)', 'PYTHON') # fix rar val slightly 100+
 
-    # Now just get the count as there is no other area metric anymore
-
-    # stupid bit of code that allows at least a few pre-existing "Join_Count" fields to
-    # not mess up the next bit in which we re-name that output field
+    # Guarantee that a new "Join_Count" field (produced with Spatial Join) is the one to use in upcoming calculations
     join_count_fnames = ['Join_Count', 'Join_Count_1', 'Join_Count_12']
 
     for fname in join_count_fnames:
@@ -53,30 +57,27 @@ def calc(zone_fc, zone_field, polygons_of_interest, output_table, interest_selec
             join_count_field_name = fname
             break
 
-    # and now we proceed with said join
+    # Spatial join to get count of polygons intersecting zone
     spjoin_fc = arcpy.SpatialJoin_analysis(zone_fc, selected_polys, 'spatial_join_output')
     arcpy.AlterField_management(spjoin_fc, join_count_field_name, 'Poly_n')
 
-    # Add the density
+    # Add and calculate density field from count
     arcpy.AddField_management(spjoin_fc, 'Poly_nperha', 'DOUBLE')
     arcpy.CalculateField_management(spjoin_fc, 'Poly_nperha', '!Poly_n!/!shape.area@hectares!', 'PYTHON')
-
     arcpy.JoinField_management(tab_table, zone_field, spjoin_fc, zone_field, ["Poly_n", 'Poly_nperha'])
     final_fields = ['Poly_ha', 'Poly_pct', 'Poly_n', 'Poly_nperha']
 
-    # make output nice
+    # Refine output, one row out for every one row in and null values mean 0 polygons in zone
     arcpy.env.overwriteOutput = False
     lagosGIS.one_in_one_out(tab_table, zone_fc, zone_field, output_table)
 
     lagosGIS.redefine_nulls(output_table, final_fields, [0, 0, 0, 0])
 
-    # clean up
-    # can't delete all of in_memory because this function is meant to be called from another one that uses in_memory
+    # Cleanup
     for item in [selected_polys, tab_table, spjoin_fc]:
         arcpy.Delete_management(item)
     arcpy.env.workspace = old_workspace
 
-    arcpy.SetLogHistory(True)
 
 def main():
     zone_fc = arcpy.GetParameterAsText(0)
@@ -86,5 +87,6 @@ def main():
     output_table = arcpy.GetParameterAsText(4)
     calc(zone_fc, zone_field, polygons_of_interest, output_table, interest_selection_expr)
 
+
 if __name__ == '__main__':
     main()
diff --git a/lagosGIS/preprocess_padus.py b/lagosGIS/preprocess_padus.py
index ae3c47f..ca2e3df 100644
--- a/lagosGIS/preprocess_padus.py
+++ b/lagosGIS/preprocess_padus.py
@@ -20,24 +20,23 @@ def preprocess(padus_combined_fc, output_fc):
     Own_Type -> "agency" variable in LAGOS-US. Rule is FeatClass "Fee" > "Easement" > "Marine" > "Designation"
     GAP_Sts -> "gap" . Highest GAP status preferentially retained.
     IUCN_Cat -> "iucn". Lowest number codes preferentially retained, then "Other", last "Unassigned".
-    :param padus_combined_fc:
-    :param output_fc:
-    :return:
+    :param padus_combined_fc: The PADUS2_0Combined_Marined_Fee_Designation_Easement dataset from the PADUS database
+    :param output_fc: Output feature class to save the result
+    :return: Result object for output feature class
     """
 
-    arcpy.env.workspace = 'in_memory'
-
     # Prep: Select only the fields needed, remove curves (densify) which prevents problems with geometry
     # that prevents DeleteIdentical based on Shape
+    arcpy.env.workspace = 'in_memory'
     padus_fields = ['FeatClass', 'Own_Type', 'GAP_Sts', 'IUCN_Cat']
     padus_select = lagosGIS.select_fields(padus_combined_fc, 'padus_select', padus_fields, convert_to_table=False)
     arcpy.Densify_edit(padus_select, 'OFFSET', max_deviation = '1 Meters')
     arcpy.AddMessage('{} union...'.format(time.ctime()))
 
-    # self-union
+    # Self-union to create new features from overlapping regions between polygons
     union = arcpy.Union_analysis([padus_select, padus_select], 'union', 'ALL', cluster_tolerance='1 Meters')
 
-    # self-union creates duplicates, remove
+    # Remove full duplicates resulting from self-union before further processing
     fid1 = 'FID_padus_select'
     fid2 = 'FID_padus_select_1'
     padus_fields_1 = padus_fields + [f + '_1' for f in padus_fields]
@@ -45,7 +44,7 @@ def preprocess(padus_combined_fc, output_fc):
     arcpy.AddMessage('{} delete identical round 1...'.format(time.ctime()))
     DM.DeleteIdentical(union, padus_fields_1)
 
-    # calculate the new class values based on the overlaid polygons
+    # Setup for new class fields
     new_fields = ['agency', 'gap', 'iucn', 'merge_flag', 'area_m2']
     cursor_fields = sorted(padus_fields_1) + new_fields + ['SHAPE@AREA']
     DM.AddField(union, 'agency', 'TEXT', field_length=5)
@@ -54,6 +53,9 @@ def preprocess(padus_combined_fc, output_fc):
     DM.AddField(union, 'merge_flag', 'TEXT', field_length=1)
     DM.AddField(union, 'area_m2', 'DOUBLE')
 
+    # Establish rules for class priority for each polygon
+    # If polygon was an overlapping region, these rules will select which class value is assigned from the multiple
+    # originals, if they were not the same already
     owner_rule = {'Fee': 1, 'Easement': 2, 'Marine': 3, 'Designation': 4}
     iucn_rule = {'Ia': 1,
                  'Ib': 2,
@@ -65,25 +67,28 @@ def preprocess(padus_combined_fc, output_fc):
                  'Other Conservation Area': 8,
                  'Unassigned': 9}
 
+    # Calculate the new class values according to the rules above
     with arcpy.da.UpdateCursor(union, cursor_fields) as cursor:
         for row in cursor:
             id1, id2, fc1, fc2, gap1, gap2, iucn1, iucn2, own1, own2, agency, gap, iucn, flag, areacalc, areashp = row
             flag = 'N'
-            # take fee first, designation last to pull owner type from
+            # Take Fee feature class type first, Designation fc type last. Pull owner value from that feature class type
             if owner_rule[fc1] < owner_rule[fc2]:
                 agency = own1
             else:
                 agency = own2
 
-            # most protected gap
+            # Take most protected GAP value
             gap = min([gap1, gap2])
 
-            # numbered iucn over other or unassigned; use numbers as priority order
+            # Take numbered IUCN over "other" or "unassigned"; use numbers as priority order
             if iucn_rule[iucn1] < iucn_rule[iucn2]:
                 iucn = iucn1
             else:
                 iucn = iucn2
 
+            # Set merge flag to 'Y' if any output field contains a value that had to be resolved among multiple
+            # original polygons
             if fc1 <> fc2 or own1 <> own2 or gap1 <> gap2 or iucn1 <> iucn2:
                 flag = 'Y'
 
@@ -92,15 +97,14 @@ def preprocess(padus_combined_fc, output_fc):
             row = (id1, id2, fc1, fc2, gap1, gap2, iucn1, iucn2, own1, own2, agency, gap, iucn, flag, areacalc, areashp)
             cursor.updateRow(row)
 
-
-    # Prep for DeleteIdentical: Dispose of small polygons (they cause trouble, don't effect
+    # Prep for DeleteIdentical: Dispose of polygons under 4 sq. m (they cause trouble, don't effect
     # stats enough to bother) and repair geometry on the rest.
     large_enough = arcpy.Select_analysis(union, 'large_enough', 'area_m2 > 4')
     arcpy.AddMessage('{} repair...'.format(time.ctime()))
     DM.RepairGeometry(large_enough)
 
-    # Sort so that merged polygons are retained in DeleteIdentical, and delete identical shapes to end
-    # up with just the merged polygons and non-overlapping polygons
+    # Sort so that merged polygons are highest/retained in DeleteIdentical
+    # Delete identical shapes to end up with just the merged polygons and polygons from non-overlapping regions
     arcpy.AddMessage('{} sort...'.format(time.ctime()))
     sorted_fc = DM.Sort(large_enough, 'sorted_fc', [['merge_flag', 'DESCENDING']])
 
@@ -109,16 +113,18 @@ def preprocess(padus_combined_fc, output_fc):
     output_fields = [fid1, fid2] + new_fields
     output_fc = lagosGIS.select_fields(sorted_fc, output_fc, output_fields)
 
-    # cleanup
+    # Clean up
     for item in [padus_select, union, sorted_fc, large_enough]:
         DM.Delete(item)
     return output_fc
 
+
 def main():
     padus_combined_fc = arcpy.GetParameterAsText(0)
     output_fc = arcpy.GetParameterAsText(1)
     preprocess(padus_combined_fc, output_fc)
 
+
 if __name__ == '__main__':
     main()
 
diff --git a/lagosGIS/rasterize_zones.py b/lagosGIS/rasterize_zones.py
index ebefc89..0a6f928 100644
--- a/lagosGIS/rasterize_zones.py
+++ b/lagosGIS/rasterize_zones.py
@@ -4,8 +4,7 @@
 # LAGOS module(s): GEO
 # tool type: re-usable (ArcGIS Toolbox)
 
-# Converts multiple polygon feature classes to "zone" rasters using a common grid
-import math
+
 import os
 import arcpy
 from arcpy import env
@@ -14,27 +13,41 @@
 SNAP_RASTER = '../common_grid.tif'
 CELL_SIZE = 90
 
+
 def rasterize(polygon_fc_list, output_workspace):
+    """
+    Converts zone polygons in a spatial division dataset to a classed raster dataset with one class per unique zone
+    polygon using a common standard for cell size and cell centers.
+    :param polygon_fc_list: List of one or more polygon feature classes representing zones (spatial divisions)
+    :param output_workspace: Output file geodatabase to save the output Raster datasets to
+    :return: None
+    """
 
     for polygon_fc in polygon_fc_list:
+        # Choose 30m for spatial divisions with smaller average feature size (hu12, buff100, buff500, nws)
+        # Choose 90m for spatial divisions larger than about the average County size
+        # 90m is enough to get mean raster stats for zone with necessary precision
         if 'hu12' in polygon_fc or 'buff' in polygon_fc or ('ws' in polygon_fc and 'nws' not in polygon_fc):
             cell_size = 30
         else:
             cell_size = CELL_SIZE
 
+        # Set up raster processing environments to control output and make names
         env.extent = polygon_fc
         env.snapRaster = SNAP_RASTER
         short_name = os.path.splitext(os.path.basename(polygon_fc))[0]
         arcpy.AddMessage("Converting {}...".format(short_name))
         output_raster = os.path.join(output_workspace, short_name + '_raster')
         zoneid_field = arcpy.ListFields(polygon_fc, '*zoneid')[0].name
+
+        # Convert the polygons to raster and build pyramids with first level missing to save space
         output_raster = arcpy.PolygonToRaster_conversion(polygon_fc,
-                                         zoneid_field,
-                                         output_raster,
-                                         'CELL_CENTER',
-                                         cellsize = cell_size)
-        arcpy.BuildPyramids_management(output_raster, SKIP_FIRST = True)
-    arcpy.AddMessage("Completed.")
+                                                         zoneid_field,
+                                                         output_raster,
+                                                         'CELL_CENTER',
+                                                         cellsize = cell_size)
+        arcpy.BuildPyramids_management(output_raster, SKIP_FIRST=True)
+
 
 def main():
     polygon_fc_input = arcpy.GetParameterAsText(0)
@@ -42,5 +55,6 @@ def main():
     output_workspace = arcpy.GetParameterAsText(1)
     rasterize(polygon_fc_list, output_workspace)
 
+
 if __name__ == '__main__':
     main()
diff --git a/lagosGIS/read_job_control.py b/lagosGIS/read_job_control.py
index d49a41a..243f65b 100644
--- a/lagosGIS/read_job_control.py
+++ b/lagosGIS/read_job_control.py
@@ -4,64 +4,79 @@
 # LAGOS module(s): GEO
 # tool type: re-usable (NOT in ArcGIS Toolbox)
 
+
 import csv
 import os
 import time
-import warnings
 import arcpy
 import lagosGIS
 
 ARG_NUMBERS = ['Arg1', 'Arg2', 'Arg3', 'Arg4', 'Arg5', 'Arg6', 'Arg7', 'Arg8']
 
-def read_job_control(job_control_csv, start_line = -1, end_line = -1, validate=False, validate_args = []):
+
+def cook_string(input):
+    """
+    This function takes a "raw" string contained inside another string and makes it just a plain string.
+    :param input: A string with contents that include r'[text'.
+    :return: String
+    """
+    if input.startswith('r\'') and input.endswith('\''):
+        result = input[2:-1]
+    else:
+        result = input
+    if result.upper() == 'TRUE':
+        result = True
+    elif result.upper() == 'FALSE':
+        result = False
+    return result
+
+
+def read_job_control(job_control_csv, start_line=-1, end_line=-1, validate=False, validate_args=[]):
     """
-    Reads a job control file with the following CSV format: First column contains function name to run. Columns contain arguments to use, in order.
+    Reads a job control file with the following CSV format: First column contains function name to run. Columns contain
+    arguments to use, in order.
     :param job_control_csv: The path to the job control CSV file
-    :param start_line: The line to start the job from or a list of line numbers to run
-    :param end_line: The line to end the job from
-    :param validate: Validate the inputs only, do not run.
-    :param validate_args: A list of the argument labels to validate. Use ['Arg1', 'Arg2'] etc.
+    :param start_line: (Optional)The line number (row) to start the job from or a list of line numbers to run. Default
+    runs all lines.
+    :param end_line: (Optional) The line to end the job from. Default runs all lines.
+    :param validate: (Optional) Boolean. Whether to validate the inputs only, do not actually execute commands.
+    :param validate_args: (Optional) If validate=True, provide a list of the argument labels to validate. Use
+    ['Arg1', 'Arg2', 'Arg3'] etc.
     :return: None
     """
 
-    # validate inputs
+    # Define valid CSV file header
+    # Line is sequential integer identifying row number
+    # Function is function call without parenthesis i.e. "lagosGIS.lake_density"
+    # Arg1-Arg8 provide the arguments to the function, leave missing after last argument needed
+    # Output repeats output path/location argument (which has variable position)
+    # CSV specifies location for CSV export file
+    csv_header = ['Line', 'Function', 'Arg1', 'Arg2', 'Arg3', 'Arg4', 'Arg5', 'Arg6', 'Arg7', 'Arg8', 'Output', 'CSV']
+
+    # Validate inputs
     if validate and not validate_args:
         raise Exception("Provide validation arguments keyword as a list of 'Arg1', 'Arg2', etc.")
     for arg in validate_args:
         if arg not in ARG_NUMBERS:
             raise Exception("Provide validation arguments keyword as a list of 'Arg1', 'Arg2', etc.")
 
-    def cook_string(input):
-        """
-        This function takes a "raw" string contained inside another string and makes it just a plain string.
-        :param input: A string with contents that include r'[text'.
-        :return: String
-        """
-        if input.startswith('r\'') and input.endswith('\''):
-            result = input[2:-1]
-        else:
-            result = input
-        if result.upper() == 'TRUE':
-            result = True
-        elif result.upper() == 'FALSE':
-            result = False
-        return result
-
-
+    # Read CSV and filter for line numbers requested in this batch run
     with open(job_control_csv) as csv_file:
         reader = csv.DictReader(csv_file)
         lines = [line for line in reader]
+        if not lines[0].keys().sort() == csv_header.sort():
+            raise Exception("""CSV file is not in the required format. Please provide a file with the header as follows:
+                            \n{}""".format(csv_header))
         if isinstance(start_line, int) and \
                 (start_line > 0 or end_line > 0):
             lines = lines[start_line-1:end_line]
         elif isinstance(start_line, list):
             lines = [line for line in lines if int(line['Line']) in start_line]
 
+    # Read the table and compose the calls
     calls = []
     outputs = []
     csv_paths = []
-
-    # Read the table and compose the calls
     for line in lines:
         function = cook_string(line['Function'])
         args = []
@@ -80,11 +95,7 @@ def cook_string(input):
         outputs.append(output)
         csv_paths.append(csv_path)
         formatted_args = ','.join(["r'{}'".format(arg) if isinstance(arg, str) else str(arg) for arg in args])
-
-        if "arcpy." in function:
-            call = "{}({})".format(function, formatted_args)
-        else:
-            call = "lagosGIS.{}({})".format(function, formatted_args)
+        call = "{}({})".format(function, formatted_args)
         calls.append(call)
 
         # validate (optional)
@@ -106,7 +117,6 @@ def cook_string(input):
                 try:
                     eval(call)
                     out_folder = os.path.dirname(csv_path)
-                    out_basename = os.path.splitext(os.path.basename(csv_path))[0]
                     lagosGIS.export_to_csv(output, out_folder, rename_fields=False)
                 except Exception as e:
                     exceptions.append(e.message)
@@ -114,9 +124,10 @@ def cook_string(input):
             else:
                 print("{} already exists.".format(output))
 
-
             # Keep in_memory workspace from carrying over to the next call
             arcpy.Delete_management('in_memory')
+
+        # Finish
         print("ALL EXCEPTION MESSAGES FROM THIS RUN:----------------")
         for emsg in exceptions:
             print(emsg)
diff --git a/lagosGIS/lake_processing.py b/lagosGIS/run_tools/lake_processing.py
similarity index 100%
rename from lagosGIS/lake_processing.py
rename to lagosGIS/run_tools/lake_processing.py
diff --git a/lagosGIS/spatial_divisions_processing.py b/lagosGIS/spatial_divisions_processing.py
index 0e55a95..716fd78 100644
--- a/lagosGIS/spatial_divisions_processing.py
+++ b/lagosGIS/spatial_divisions_processing.py
@@ -10,7 +10,13 @@
 
 
 def add_lat_lon(fc, zone_name=''):
-    """Add fields for lat and long, per LAGOS naming standard. Only works when fc path is short (use env.workspace.)"""
+    """
+    Add latitude and longitude (centroid) fields, per LAGOS naming standard. Only works when fc path is short
+    (use env.workspace.)
+    :param fc: Zone feature class
+    :param zone_name: (Optional) Zone shortname to use as prefix for lat and lon fields
+    :return: None
+    """
     if not zone_name:
         zone_name = fc
     lat = '{}_lat_decdeg'.format(zone_name)
@@ -19,7 +25,7 @@ def add_lat_lon(fc, zone_name=''):
         DM.AddField(fc, lat, 'DOUBLE')
     if not arcpy.ListFields(fc, lon):
         DM.AddField(fc, lon, 'DOUBLE')
-    orig_crs = arcpy.SpatialReference(5070)
+    orig_crs = arcpy.SpatialReference(5070) # Albers USGS
     new_crs = arcpy.SpatialReference(4326)  # NAD83
 
     with arcpy.da.UpdateCursor(fc, [lat, lon, 'SHAPE@']) as u_cursor:
@@ -31,23 +37,33 @@ def add_lat_lon(fc, zone_name=''):
             u_cursor.updateRow(row)
 
 
-def find_states(fc, state_fc, zone_name=''):
-    """Populate *_states field. States fc must have field 'states' with length 255 and state abbreviations within."""
+def find_states(zones_fc, state_fc, zone_name=''):
+    """
+    Populate *_states field in input zones feature class (modifies original. States fc must have field 'states' with
+    length 255 and state abbreviations within.
+    :param zones_fc: Zones polygon feature class
+    :param state_fc: Polygon feature class containing U.S. geometry and field "states" with length 255 and state
+    abbreviations within
+    :param zone_name: (Optional) If the feature class is not named with the LAGOS-US zone shortname, provide a zone
+    prefix to add to output "*_states" field
+    :return: None
+    """
+
+    # Setup names
     if zone_name:
         zone_name = zone_name
     else:
-        zone_name = os.path.basename(fc)
+        zone_name = os.path.basename(zones_fc)
     states_field = '{}_states'.format(zone_name)
-    if arcpy.ListFields(fc, states_field):
-        DM.DeleteField(fc, states_field)
-
+    if arcpy.ListFields(zones_fc, states_field):
+        DM.DeleteField(zones_fc, states_field)
 
-    # make a field mapping that gathers all the intersecting states into one new value
-    field_list = [f.name for f in arcpy.ListFields(fc) if f.type <> 'OID' and f.type <> 'Geometry']
+    # Make a field mapping that gathers all the intersecting states into one new value separated by space
+    field_list = [f.name for f in arcpy.ListFields(zones_fc) if f.type <> 'OID' and f.type <> 'Geometry']
     field_mapping = arcpy.FieldMappings()
     for f in field_list:
         map = arcpy.FieldMap()
-        map.addInputField(fc, f)
+        map.addInputField(zones_fc, f)
         field_mapping.addFieldMap(map)
     map_states = arcpy.FieldMap()
     map_states.addInputField(state_fc, 'states')
@@ -55,15 +71,25 @@ def find_states(fc, state_fc, zone_name=''):
     map_states.joinDelimiter = ' '
     field_mapping.addFieldMap(map_states)
 
-    # perform join and use output to replace original fc
-    spjoin = AN.SpatialJoin(fc, state_fc, 'in_memory/spjoin_intersect', 'JOIN_ONE_TO_ONE',
+    # Perform join and use output to replace original fc
+    spjoin = AN.SpatialJoin(zones_fc, state_fc, 'in_memory/spjoin_intersect', 'JOIN_ONE_TO_ONE',
                             field_mapping=field_mapping, match_option='INTERSECT')
     DM.AlterField(spjoin, 'states', new_field_name=states_field, clear_field_alias=True)
-    DM.Delete(fc)
-    DM.CopyFeatures(spjoin, fc)
+    DM.Delete(zones_fc)
+    DM.CopyFeatures(spjoin, zones_fc)
     DM.Delete(spjoin)
 
+
 def inusa_pct(zone_fc, zoneid, states_fc, zone_name=''):
+    """
+    Calculates percentage of zone that is within the U.S. boundaries. Modifies original zones feature class input.
+    :param zone_fc: Zones feature class
+    :param zoneid: Unique identifier for each zone
+    :param states_fc: Polygon feature class containing U.S. states
+    :param zone_name: (Optional) If the feature class is not named with the LAGOS-US zone shortname, provide a zone
+    prefix to add to output "*_states" field
+    :return: None
+    """
     DM.AddField(zone_fc, '{}_inusa_pct'.format(zone_name), 'DOUBLE')
     # percent in USA
     arcpy.AddMessage('Tabulating intersection...')
diff --git a/lagosGIS/stream_density.py b/lagosGIS/stream_density.py
index bd6a267..f4cd24d 100644
--- a/lagosGIS/stream_density.py
+++ b/lagosGIS/stream_density.py
@@ -10,6 +10,18 @@
 
 
 def calc_all(zones_fc, zone_field, lines_fc, out_table, zone_prefix=''):
+    """
+    Convenience function that runs a modified version of Line Density in Zones for all LAGOS-US stream metrics.
+    :param zones_fc: Zones polygon feature class
+    :param zone_field: Unique identifier for each zone
+    :param lines_fc: LAGOS-US streams polyline feature class (derived from NHDPllus HR) containing all streams to be
+    summarized
+    :param out_table: Output table to save the result
+    :param zone_prefix: (Optional) Text string containing zone shortname to prefix all output column names
+    :return: None
+    """
+
+    # Set up
     arcpy.env.workspace = 'in_memory'
     arcpy.env.outputCoordinateSystem = arcpy.SpatialReference(102039)
     if zone_prefix:
@@ -27,10 +39,11 @@ def calc_all(zones_fc, zone_field, lines_fc, out_table, zone_prefix=''):
 
     intermit_fcodes = ['46003', '46007']
 
-    # Keep only necessary columns from zones
+    # Select only necessary columns from zones for speed
     zones_only = lagosGIS.select_fields(zones_fc, 'in_memory/zones_only', [zone_field], convert_to_table=False)
 
-    # Perform identity analysis to join fields and crack lines at polygon boundaries
+    # ---EMULATES line_density_in_zones.py, BUT RE-USES IDENTITY RESULT FOR ALL CALCULATIONS---------------------------
+    # Perform identity analysis to crack lines at polygon boundaries
     arcpy.AddMessage("Cracking lines...")
     lines_identity = arcpy.Identity_analysis(lines_fc, zones_only, 'lines_identity', cluster_tolerance='1 meters')
     arcpy.AddField_management(lines_identity, 'length_m', 'DOUBLE')
@@ -39,11 +52,11 @@ def calc_all(zones_fc, zone_field, lines_fc, out_table, zone_prefix=''):
             row[0] = row[1]
             cursor.updateRow(row)
 
-    # make permanent-only layer
+    # make Permanent-only layer
     perm_query = 'FCode NOT IN ({})'.format(','.join(intermit_fcodes))
     lines_identity_perm = arcpy.Select_analysis(lines_identity, 'lines_identity_perm', perm_query)
 
-    # make strahler grouped layers
+    # make Strahler grouped layers
     rivers_query = 'StreamOrder >= 7'
     midreaches_query = 'StreamOrder > 3 AND StreamOrder <= 6'
     headwaters_query = 'StreamOrder <= 3 OR StreamOrder IS NULL'
@@ -51,8 +64,6 @@ def calc_all(zones_fc, zone_field, lines_fc, out_table, zone_prefix=''):
     lines_identity_midreaches = arcpy.Select_analysis(lines_identity, 'lines_identity_midreaches', midreaches_query)
     lines_identity_headwaters = arcpy.Select_analysis(lines_identity, 'lines_identity_headwaters', headwaters_query)
 
-
-
     def summarize_cracked(cracked_lines, density_field_name):
         # calc total length grouped by zone (numerator)
         lines_stat = arcpy.Statistics_analysis(cracked_lines, 'lines_stat', 'length_m SUM', zone_field)
@@ -70,7 +81,7 @@ def summarize_cracked(cracked_lines, density_field_name):
             for row in cursor:
                 zid, mperha, msum = row
                 if msum is None:
-                    msum = 0 # replace NULL values with 0 which is physically accurate here
+                    msum = 0  # replace NULL values with 0 which is physically accurate here
                 if zid:
                     mperha = msum/zones_area[zid]
                     row = (zid, mperha, msum)
@@ -79,7 +90,7 @@ def summarize_cracked(cracked_lines, density_field_name):
                 else:
                     cursor.deleteRow()
 
-        # delete extra field and ensure all input zones have output row
+        # Delete extra fields
         arcpy.DeleteField_management(lines_stat_full, 'SUM_length_m')
         arcpy.DeleteField_management(lines_stat_full, 'FREQUENCY')
 
@@ -91,14 +102,14 @@ def summarize_cracked(cracked_lines, density_field_name):
 
         return summarized
 
-    # run summaries
+    # Run summaries for each subgroup
     streams_summary = summarize_cracked(lines_identity, streams_density_field)
     perm_summary = summarize_cracked(lines_identity_perm, perm_density_field)
     rivers_summary = summarize_cracked(lines_identity_rivers, rivers_density_field)
     midreaches_summary = summarize_cracked(lines_identity_midreaches, midreaches_density_field)
     headwaters_summary = summarize_cracked(lines_identity_headwaters, headwaters_density_field)
 
-    # put all tables together
+    # Put all tables together--cursor goes faster than join
     arcpy.AddField_management(streams_summary, perm_density_field, 'DOUBLE')
     arcpy.AddField_management(streams_summary, rivers_density_field, 'DOUBLE')
     arcpy.AddField_management(streams_summary, midreaches_density_field, 'DOUBLE')
@@ -128,6 +139,7 @@ def summarize_cracked(cracked_lines, density_field_name):
                  midreaches_summary, headwaters_summary]:
         arcpy.Delete_management(item)
 
+
 def main():
     # Parameters
     zones_fc = arcpy.GetParameterAsText(0)
diff --git a/lagosGIS/summarize_raster_for_all_zones.py b/lagosGIS/summarize_raster_for_all_zones.py
deleted file mode 100644
index 86071a4..0000000
--- a/lagosGIS/summarize_raster_for_all_zones.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# filename: summarize_raster_for_all_zones.py
-# author: Nicole J Smith
-# version: 2.0
-# LAGOS module(s): GEO
-# tool type: re-usable (ArcGIS Toolbox)
-# status: To be implemented
-
-import os
-import arcpy
-import zonal_summary_of_raster_data
-
-def summarize(lagos_zone_rasters_list, raster_to_summarize, variable_basename = '', is_thematic=False):
-    """
-    This is the "magic button" function that calculates statistics at multiple scales for a value raster of interest.
-    This wrapper function also serves to do some name management in conformance with the design of the LAGOS database
-    creation workflow.
-    :param lagos_zone_rasters_list:
-    :param raster:
-    :param variable_basename:
-    :param is_thematic:
-    :return:
-    """
-    # manage the call
-
-    # manage the renaming process
-
-def main():
-    lagos_zone_raster_list_input = arcpy.GetParameterAsText(0)
-    lagos_zone_raster_list = lagos_zone_raster_list_input.split(";")
-    raster_to_summarize = arcpy.GetParameterAsText(1)
-    variable_basename = arcpy.GetParameterAsText(2)
-    is_thematic = arcpy.GetParameter(3) # boolean
-    summarize(lagos_zone_raster_list, raster_to_summarize, variable_basename, is_thematic)
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file
diff --git a/lagosGIS/zonal_summary_of_classed_polygons.py b/lagosGIS/zonal_summary_of_classed_polygons.py
index e402614..0b8349c 100644
--- a/lagosGIS/zonal_summary_of_classed_polygons.py
+++ b/lagosGIS/zonal_summary_of_classed_polygons.py
@@ -11,8 +11,26 @@
 
 
 def summarize(zone_fc, zone_field, class_fc, out_table, class_field, rename_tag=''):
+    """
+    Calculates percentage of zonal area occupied by classed polygon data such as land ownership and conservation data.
+    :param zone_fc: Zones polygon feature class
+    :param zone_field: Unique identifier for each zone
+    :param class_fc: Polygon feature class containing classed data to be summarized
+    :param out_table: Output table to save the result
+    :param class_field: Field name containing the class values to summarize individually
+    :param rename_tag: (Optional) Text string containing variable name to insert into all output column names
+    :return: None
+    """
 
     def rename_to_standard(table, numeric=False):
+        """
+        Rename columns in the table according to the LAGOS-US variable taxonomy using name mappings stored in a
+        CSV file in this module.
+        :param table: Table dataset for which to rename columns
+        :param numeric: (Optional) Default False. Whether the class field uses has numeric value type. Output column
+        names will be preceded by the class field name if this parameter is True.
+        :return: Table dataset location
+        """
         # look up the values based on the rename tag
         this_files_dir = os.path.dirname(os.path.abspath(__file__))
         os.chdir(this_files_dir)
@@ -37,10 +55,11 @@ def rename_to_standard(table, numeric=False):
                     lagosGIS.rename_field(table, old_fname, new_fname, deleteOld=True)
         return table
 
-
+    # Tabulate intersection between zones and polygons using class groupings
     arcpy.env.workspace = 'in_memory'
     tab = arcpy.TabulateIntersection_analysis(zone_fc, zone_field, class_fc, 'tab', class_field, xy_tolerance='0.001 Meters')
-    # guard against all numeric values--can't pivot when that is the case
+
+    # Guard against all numeric values--can't pivot when that is the case
     vals = [r[0] for r in arcpy.da.SearchCursor(tab, class_field)]
     all_numeric = all([str.isdigit(str(v)) for v in vals])
     if all_numeric:
@@ -49,11 +68,11 @@ def rename_to_standard(table, numeric=False):
                 row[0] = '{}{}'.format(class_field, row[0])
                 cursor.updateRow(row)
     pivot = arcpy.PivotTable_management(tab, zone_field, class_field, "PERCENTAGE", 'pivot')
+
+    # Rename variables to fit LAGOS naming standard
     renamed = rename_to_standard(pivot, all_numeric)
 
-    # make sure all input zones have an output row, and where there was no data, consider this a 0 value, assuming
-    # the vector data was comprehensive.
-    # also replace values over 100% with 100. Getting a few of these (like 100.0000003) even with a good tolerance.
+    # Refine output table to ensure output row for every input row and enforce maximum value of 100%
     all_zones = lagosGIS.one_in_one_out(renamed, zone_fc, zone_field, 'all_zones')
     new_fields = [f.name for f in arcpy.ListFields(all_zones) if f.name <> zone_field and f.type not in ('OID', 'Geometry')]
     with arcpy.da.UpdateCursor(all_zones, new_fields) as cursor:
@@ -65,6 +84,7 @@ def rename_to_standard(table, numeric=False):
     for item in [tab, pivot, renamed]:
         arcpy.Delete_management(item)
 
+
 def main():
     zone_fc = arcpy.GetParameterAsText(0)
     zone_field = arcpy.GetParameterAsText(1)
@@ -74,5 +94,6 @@ def main():
     rename_tag = arcpy.GetParameterAsText(5)
     summarize(zone_fc, zone_field, class_fc, output_table, class_field, rename_tag)
 
+
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()
diff --git a/lagosGIS/zonal_summary_of_raster_data.py b/lagosGIS/zonal_summary_of_raster_data.py
index 5dfc44e..90d3f95 100644
--- a/lagosGIS/zonal_summary_of_raster_data.py
+++ b/lagosGIS/zonal_summary_of_raster_data.py
@@ -16,13 +16,42 @@
 
 def calc(zone_fc, zone_field, in_value_raster, out_table, is_thematic, unflat_table='',
          rename_tag='', units=''):
+    """
+    Calculates the mean raster value in each zone or summarizes categorical raster data as a percent of each zone
+    depending on the input raster type.
+    :param zone_fc: Zones polygon feature class
+    :param zone_field: Unique identifier for each zone
+    :param in_value_raster: Raster dataset for which to summarize all values for each zone
+    :param out_table: Output table to save the result
+    :param is_thematic: Boolean. Whether the raster dataset to be summarized is thematic/categorical data (True), or
+    continuous/numerical data (False).
+    :param unflat_table: (Optional) If the zones provided are derived from zones that originally overlapped, provide
+    the location of the overlapping vs. non-overlapping identifier mapping table.
+    :param rename_tag: (Optional) A variable name to include in all output columns
+    :param units: (Optional) A units suffix to append to all output columns
+    :return: Out_table location
+    """
+
     orig_env = env.workspace
     env.workspace = 'in_memory'
     arcpy.SetLogHistory(False)
     arcpy.CheckOutExtension("Spatial")
-    
+
+    # ---DEFINE FUNCTIONS-----------------------------------------------------------------------------------------
     def stats_area_table(zone_fc=zone_fc, zone_field=zone_field, in_value_raster=in_value_raster,
                          out_table=out_table, is_thematic=is_thematic):
+        """
+        Runs Zonal Statistics as Table for continuous data or Tabulate Area for thematic/categorical data and refines
+        the output to prepare the table for being included in LAGOS-US.
+        :param zone_fc: Zones feature class
+        :param zone_field: Unique identifier for each zone
+        :param in_value_raster: Raster dataset for which to summarize all values for each zone
+        :param out_table: Output table to save the result
+        :param is_thematic: Boolean. Whether the raster dataset to be summarized is thematic/categorical data (True), or
+    continuous/numerical data (False).
+        :return:
+        """
+
         def refine_zonal_output(t):
             """Makes a nicer output for this tool. Rename some fields, drop unwanted
                 ones, calculate percentages using raster AREA before deleting that
@@ -61,6 +90,7 @@ def refine_zonal_output(t):
                 except:
                     continue
 
+        # SETUP---------------------------------------------------------------------------------------------------
         # Set up environments for alignment between zone raster and theme raster
         if isinstance(zone_fc, arcpy.Result):
             zone_fc = zone_fc.getOutput(0)
@@ -71,6 +101,7 @@ def refine_zonal_output(t):
         env.cellSize = common_grid
         env.extent = zone_fc
 
+        # Convert zones to raster if provided as polygon feature class
         zone_desc = arcpy.Describe(zone_fc)
         zone_raster = 'convertraster'
         if zone_desc.dataType not in ['RasterDataset', 'RasterLayer']:
@@ -88,6 +119,8 @@ def refine_zonal_output(t):
         # I tested and there is no need to resample the raster being summarized. It will be resampled correctly
         # internally in the following tool given that the necessary environments are set above (cell size, snap).
         # # in_value_raster = arcpy.Resample_management(in_value_raster, 'in_value_raster_resampled', CELL_SIZE)
+
+        # ---RUN STATS---------------------------------------------------------------------------------------------
         if not is_thematic:
             arcpy.AddMessage("Calculating Zonal Statistics...")
             if 'elevation' in rename_tag:
@@ -98,6 +131,7 @@ def refine_zonal_output(t):
                                                                 'temp_zonal_table', 'DATA', 'MEAN')
 
 
+        # POST-PROCESSING OUTPUT-----------------------------------------------------------------------------------
         if is_thematic:
             # for some reason env.cellSize doesn't work
             # calculate/doit
@@ -192,20 +226,24 @@ def refine_zonal_output(t):
         arcpy.CheckInExtension("Spatial")
 
         return [stats_result, count_diff]
-    
+
     def unflatten(intermediate_table):
+        """
+        Uses a weighted average to reconstitute mean value for original zone when provided a stats table based on
+        the "flattened" zone regions.
+        :param intermediate_table: Output of stats_area_table
+        :return: A list containing two elements 1) the output stats table with the final value calculated for each zone
+        2) The count of rows missing any data
+        """
+
+        # ---SETUP-----------------------------------------------------------------------------------------------
+        # names
         flat_zoneid = zone_field
         unflat_zoneid = zone_field.replace('flat', '')
         zone_type = [f.type for f in arcpy.ListFields(zone_fc, flat_zoneid)][0]
-        # Set up the output table (can't do this until the prior tool is run)
-        # if os.path.dirname(out_table):
-        #     out_path = os.path.dirname(out_table)
-        # else:
-        #     out_path = orig_env
 
+        # create table and get fields to add
         unflat_result = DM.CreateTable('in_memory', os.path.basename(out_table))
-
-        # get the fields to add to the table
         editable_fields = [f for f in arcpy.ListFields(intermediate_table)
                            if f.editable and f.name.lower() != flat_zoneid.lower()]
 
@@ -214,22 +252,25 @@ def unflatten(intermediate_table):
         for f in editable_fields:
             DM.AddField(unflat_result, f.name, f.type, field_length=f.length)
 
-        # map original zone ids to new zone ids
+        # ---FIND ORIGINAL VS FLAT ZONE MAPPING-----------------------------------------------------------------
         original_flat = defaultdict(list)
         with arcpy.da.SearchCursor(unflat_table, [unflat_zoneid, flat_zoneid]) as cursor:
             for row in cursor:
                 if row[1] not in original_flat[row[0]]:
                     original_flat[row[0]].append(row[1])
 
+        # ---DO THE CALCULATION----------------------------------------------------------------------------------
         # Use CELL_COUNT as weight for means to calculate final values for each zone.
         fixed_fields = [unflat_zoneid, 'ORIGINAL_COUNT', 'CELL_COUNT', 'datacoveragepct']
         other_field_names = [f.name for f in editable_fields if f.name not in fixed_fields]
         i_cursor = arcpy.da.InsertCursor(unflat_result, fixed_fields + other_field_names)  # open output table cursor
+        # read component stats
         flat_stats = {r[0]: r[1:] for r in arcpy.da.SearchCursor(
             intermediate_table, [flat_zoneid, 'ORIGINAL_COUNT', 'CELL_COUNT', 'datacoveragepct'] + other_field_names)}
 
         count_diff = 0
         for zid, unflat_ids in original_flat.items():
+            # get values needed to do the math
             valid_unflat_ids = [id for id in unflat_ids if id in flat_stats] # skip flatpolys not rasterized
             area_vec = [flat_stats[id][0] for id in valid_unflat_ids]  # ORIGINAL_COUNT specified in 0 index earlier
             cell_vec = [flat_stats[id][1] for id in valid_unflat_ids]
@@ -268,11 +309,14 @@ def unflatten(intermediate_table):
         return [unflat_result, count_diff]
 
     def rename_to_standard(table):
+        """Construct output variable names from the rename_tag, units, and zone feature class name.
+        Substitutes variable name parts from the mappings in geo_metric_provenance.csv if the variables
+        are to fit the LAGOS-US standard."""
         arcpy.AddMessage("Renaming.")
         # datacoverage just gets tag
         new_datacov_name = '{}_datacoveragepct'.format(rename_tag)
         lagosGIS.rename_field(table, 'datacoveragepct', new_datacov_name, deleteOld=True)
-        # DM.AlterField(out_table, 'datacoveragepct', new_datacov_name, clear_field_alias=True)
+
         if not is_thematic:
             if 'elevation' in rename_tag:
                 new_mean_name = '{}_mean_{}'.format(rename_tag, units).rstrip('_')
@@ -290,7 +334,6 @@ def rename_to_standard(table):
                 new_mean_name = '{}_{}'.format(rename_tag, units).rstrip('_')  # if no units, just rename_tag
                 lagosGIS.rename_field(table, 'MEAN', new_mean_name, deleteOld=True)
 
-            # DM.AlterField(out_table, 'MEAN', new_mean_name, clear_field_alias=True)
         else:
             # look up the values based on the rename tag
             geo_file = os.path.abspath('../geo_metric_provenance.csv')
@@ -311,7 +354,9 @@ def rename_to_standard(table):
                     except:
                         lagosGIS.rename_field(table, old_fname, new_fname, deleteOld=True)
         return table
-    
+
+    # ---RUN ------------------------------------------------------------------------------------------------------
+    # Determine whether user provided "flattened zones" that need re-constitution and run stats
     if unflat_table:
         if not arcpy.Exists(unflat_table):
             raise Exception('Unflat_table must exist.')
@@ -320,22 +365,23 @@ def rename_to_standard(table):
     else:
         named_as_original = stats_area_table(out_table='named_as_original')
 
+    # Rename all fields to match desired output, if elected
     if rename_tag:
         named_as_standard = rename_to_standard(named_as_original[0])
         out_table = DM.CopyRows(named_as_standard, out_table)
     else:
         out_table = DM.CopyRows(named_as_original[0], out_table)
 
+    # Check counts and alert user if there are fewer zones in the output than were in the input
     total_count_diff = named_as_original[1]
-
     if total_count_diff > 0:
         warn_msg = ("WARNING: {0} zones have null zonal statistics. There are 2 possible reasons:\n"
                     "1) Presence of zones that are fully outside the extent of the raster summarized.\n"
                     "2) Zones are too small relative to the raster resolution.".format(total_count_diff))
         arcpy.AddWarning(warn_msg)
 
+    # Clean up
     arcpy.SetLogHistory(True)
-
     return out_table
 
 
@@ -344,13 +390,13 @@ def main():
     zone_field = arcpy.GetParameterAsText(1)
     unflat_table = arcpy.GetParameterAsText(2)
     in_value_raster = arcpy.GetParameterAsText(3)
-    is_thematic = arcpy.GetParameter(4) # boolean
+    is_thematic = arcpy.GetParameter(4)  # boolean
     out_table = arcpy.GetParameterAsText(5)
-    rename_tag = arcpy.GetParameterAsText(6) # optional
-    units = arcpy.GetParameterAsText(7) # optional
-
+    rename_tag = arcpy.GetParameterAsText(6)  # optional
+    units = arcpy.GetParameterAsText(7)  # optional
     calc(zone_fc, zone_field, in_value_raster, out_table, is_thematic, unflat_table,
          rename_tag, units)
 
+
 if __name__ == '__main__':
     main()
\ No newline at end of file
diff --git a/test_lagosGIS.py b/test_lagosGIS.py
index 7a54864..cf25cb2 100644
--- a/test_lagosGIS.py
+++ b/test_lagosGIS.py
@@ -35,7 +35,6 @@
             "zonal_summary_of_raster_data",
             "zonal_summary_of_classed_polygons",
             "point_attribution_of_raster_data",
-            "summarize_raster_for_all_zones",
             "preprocess_padus",
 
             "export_to_csv"]
@@ -76,7 +75,7 @@ def point_density_in_zones(out_table, selection_expression=''):
 
 def line_density_in_zones(out_table, selection_expression=''):
     lines_fc = os.path.join(TEST_DATA_GDB, 'lagos_streams')
-    lagosGIS.point_density_in_zones(hu12, 'hu12_zoneid', lines_fc, out_table, selection_expression)
+    lagosGIS.line_density_in_zones(hu12, 'hu12_zoneid', lines_fc, out_table, selection_expression)
 
 
 def polygon_density_in_zones(out_table, selection_expression=''):
@@ -138,10 +137,6 @@ def point_attribution_of_raster_data(out_table):
                                               'lake_wetdepinorgnitrogen', 'kgperha')
 
 
-def summarize_raster_for_all_zones():
-    pass
-
-
 def preprocess_padus(out_fc):
     padus_original = os.path.join(TEST_DATA_GDB, 'padus_original')
     lagosGIS.preprocess_padus(padus_original, out_fc)