Merge branch 'develop'

Author: nicolejeansmith

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).