address editior comments second round

mikejohnson51 · Apr 13, 2024 · 361dd39 · 361dd39
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diff --git a/paper/paper.bib b/paper/paper.bib
@@ -1,5 +1,5 @@
 @manual{r-project,
-	title        = {{R}: A Language and Environment for Statistical Computing},
+	title        = {{R: A Language and Environment for Statistical Computing}},
 	author       = {{R Core Team}},
 	year         = 2023,
 	address      = {Vienna, Austria},
@@ -8,7 +8,7 @@ @manual{r-project
 }
 
 @book{leopold1953hydraulic,
-  title={The hydraulic geometry of stream channels and some physiographic implications},
+  title={{The hydraulic geometry of stream channels and some physiographic implications}},
   author={Leopold, Luna Bergere and Maddock, Thomas},
   volume={252},
   year={1953},
@@ -17,7 +17,7 @@ @book{leopold1953hydraulic
 }
 
 @article{johnson2022knowledge,
-  title={Knowledge graphs to support real-time flood impact evaluation},
+  title={{Knowledge graphs to support real-time flood impact evaluation}},
   author={Johnson, JM and Narock, Tom and Singh-Mohudpur, Justin and Fils, Doug and Clarke, Keith and Saksena, Siddharth and Shepherd, Adam and Arumugam, Sankar and Yeghiazarian, Lilit},
   journal={AI Magazine},
   volume={43},
@@ -28,23 +28,33 @@ @article{johnson2022knowledge
 }
 
 @manual{referencefabric,
-	title        = {National Hydrologic Geospatial Fabric Reference and Derived Hydrofabrics},
+	title        = {{National Hydrologic Geospatial Fabric Reference and Derived Hydrofabrics}},
 	author       = {Bock, A.R. and Blodgett, D.L. and Johnson, JM and Santiago, M. and Wieczorek, M.E.},
 	year         = 2022,
 	url          = {https://www.sciencebase.gov/catalog/item/60be0e53d34e86b93891012b},
 	organization = {U.S. Geological Survey software release}
 }
 
+@misc{nextgenhf,
+  title={National Hydrologic Geospatial Fabric (Hydrofabric) for the Next Generation (NextGen) Hydrologic Modeling Framework},
+  author={Johnson, JM},
+  year={2022},
+  url={https://www.hydroshare.org/resource/129787b468aa4d55ace7b124ed27dbde/},
+  DOI={129787b468aa4d55ace7b124ed27dbde},
+  organizatio={https://www.hydroshare.org/resource/129787b468aa4d55ace7b124ed27dbde/}
+
+}
+
 @manual{mco,
-    title = {mco: Multiple Criteria Optimization Algorithms and Related Functions},
+    title = {{mco: Multiple Criteria Optimization Algorithms and Related Functions}},
     author = {Olaf Mersmann},
     year = {2020},
     note = {R package version 1.15.6},
     url = {https://CRAN.R-project.org/package=mco},
 }
 
 @article{dingman2018field,
-  title={Field verification of analytical at-a-station hydraulic-geometry relations},
+  title={{Field verification of analytical at-a-station hydraulic-geometry relations}},
   author={Dingman, Lawerence S. and Afshari, Shahab},
   journal={Journal of Hydrology},
   volume={564},
@@ -68,7 +78,7 @@ @dataset{enzminger_thomas_l_2023_7868764
 
 @dataset{afshari_shahab_2019_2558565,
   author       = {Afshari, Shahab},
-  title        = {USGS Table AHG Parameters And Supplementary Data},
+  title        = {{USGS Table AHG Parameters And Supplementary Data}},
   month        = feb,
   year         = 2019,
   publisher    = {Zenodo},
@@ -78,7 +88,7 @@ @dataset{afshari_shahab_2019_2558565
 }
 
 @article{zheng2018river,
-  title={River channel geometry and rating curve estimation using height above the nearest drainage},
+  title={{River channel geometry and rating curve estimation using height above the nearest drainage}},
   author={Zheng, Xing and Tarboton, David G and Maidment, David R and Liu, Yan Y and Passalacqua, Paola},
   journal={JAWRA Journal of the American Water Resources Association},
   volume={54},
@@ -96,15 +106,15 @@ @article{maidment2014national
 	keywords = {flooding, surface water hydrology, data management, geospatial analysis, simulation, decision support system, National Hydrography Dataset (NHD), NHDPlus},
 	number = {2},
 	pages = {245-257},
-	title = {Conceptual Framework for the National Flood Interoperability Experiment},
+	title = {{Conceptual Framework for the National Flood Interoperability Experiment}},
 	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1752-1688.12474},
 	volume = {53},
 	year = {2017},
   DOI = {10.1111/1752-1688.12474}
 }
 
 @article{johnson2019integrated,
-  title={An integrated evaluation of the national water model (NWM)--Height above nearest drainage (HAND) flood mapping methodology},
+  title={{An integrated evaluation of the National Water Model (NWM)--Height Above Nearest Drainage (HAND) flood mapping methodology}},
   author={Johnson, JM and Munasinghe, Dinuke and Eyelade, Damilola and Cohen, Sagy},
   journal={Natural Hazards and Earth System Sciences},
   volume={19},
@@ -116,15 +126,15 @@ @article{johnson2019integrated
 }
 
 @manual{fim,
-  title={Inundation Mapping},
+  title={{Inundation Mapping}},
   author={NOAA,  Office of Water Prediction},
   journal={GitHub},
   url={https://github.com/NOAA-OWP/inundation-mapping},
   year={2023}
 }
 
 @article{blackburn2017development,
-  title={Development of regional curves for hydrologic landscape regions (HLR) in the contiguous United States},
+  title={{Development of regional curves for hydrologic landscape regions (HLR) in the contiguous United States}},
   author={Blackburn-Lynch, Whitney and Agouridis, Carmen T and Barton, Christopher D},
   journal={JAWRA Journal of the American Water Resources Association},
   volume={53},
@@ -136,15 +146,15 @@ @article{blackburn2017development
 }
 
 @article{wrfhydro,
-  title={The WRF-Hydro® modeling system technical description, (Version 5.2.0)},
+  title={{The WRF-Hydro® modeling system technical description, (Version 5.2.0)}},
   author={Gochis, D.J. and M. Barlage, R. and Cabell, M. Casali and A. Dugger and K. FitzGerald, M. McAllister, J. McCreight and A. RafieeiNasab and L. Read, K. Sampson and D. Yates and Y. Zhang},
   journal={NCAR Technical Note},
   url={https://ral.ucar.edu/sites/default/files/public/projects/wrf-hydro/technical-description-user-guide/wrf-hydrov5.2technicaldescription.pdf},
   year={2020}
 }
 
 @article{preprint,
-  title={Determining Feature Based Hydraulic Geometry and Rating Curves using a Physically Based, Computationally Efficient Framework},
+  title={{Determining Feature Based Hydraulic Geometry and Rating Curves using a Physically Based, Computationally Efficient Framework}},
   author={Johnson, JM and Coll, J. and Clarke, K.C., Afshari and S., Saksena, S and Yeghiazarian, L.},
   journal={Preprints},
   url={https://doi.org/10.20944/preprints202212.0390.v1},
@@ -153,7 +163,7 @@ @article{preprint
 }
 
 @manual{cfim,
-  title={Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS - Version 0.2.1. (20200601)},
+  title={{Height Above Nearest Drainage (HAND) and Hydraulic Property Table for CONUS - Version 0.2.1. (20200601)}},
   author={Liu, Yan Y., Tarboton, David G., and Maidment, David R.},
   journal={Oak Ridge Leadership Computing Facility.},
   url={https://cfim.ornl.gov/data/},
@@ -162,7 +172,7 @@ @manual{cfim
 
 @article{hess-26-6121-2022,
   AUTHOR = {Heldmyer, A. and Livneh, B. and McCreight, J. and Read, L. and Kasprzyk, J. and Minear, T.},
-  TITLE = {Evaluation of a new observationally based channel parameterization for the National Water Model},
+  TITLE = {{Evaluation of a new observationally based channel parameterization for the National Water Model}},
   JOURNAL = {Hydrology and Earth System Sciences},
   VOLUME = {26},
   YEAR = {2022},
@@ -173,7 +183,7 @@ @article{hess-26-6121-2022
 }
 
 @article{blodgett2021mainstems,
-  title={Mainstems: A logical data model implementing mainstem and drainage basin feature types based on WaterML2 Part 3: HY Features concepts},
+  title={{Mainstems: A logical data model implementing mainstem and drainage basin feature types based on WaterML2 Part 3: HY Features concepts}},
   author={Blodgett, David and Johnson, JM and Sondheim, Mark and Wieczorek, Michael and Frazier, Nels},
   journal={Environmental Modelling \& Software},
   volume={135},
@@ -184,7 +194,7 @@ @article{blodgett2021mainstems
 }
 
 @article{blodgett2023generating,
-  title={Generating a reference flow network with improved connectivity to support durable data integration and reproducibility in the coterminous US},
+  title={{Generating a reference flow network with improved connectivity to support durable data integration and reproducibility in the coterminous US}},
   author={Blodgett, David and Johnson, JM and Bock, Andy},
   journal={Environmental Modelling \& Software},
   volume={165},
@@ -195,19 +205,18 @@ @article{blodgett2023generating
 }
 
 @article{johnson2023comprehensive,
-  title={Comprehensive analysis of the NOAA National Water Model: A call for heterogeneous formulations and diagnostic model selection},
+  title={{Comprehensive analysis of the NOAA National Water Model: A call for heterogeneous formulations and diagnostic model selection}},
   author={Johnson, JM and Fang, Shiqi and Sankarasubramanian, Arumugam and Rad, Arash Modaresi and Kindl da Cunha, Luciana and Jennings, Keith S and Clarke, Keith C and Mazrooei, Amir and Yeghiazarian, Lilit},
   journal={Journal of Geophysical Research: Atmospheres},
   volume={128},
   number={24},
-  pages={e2023JD038534},
   year={2023},
   publisher={Wiley Online Library},
   DOI={10.1029/2023JD038534}
 }
  
 @article{afshari2017statistical,
-  title={Statistical filtering of river survey and streamflow data for improving At-A-Station hydraulic geometry relations},
+  title={{Statistical filtering of river survey and streamflow data for improving At-A-Station hydraulic geometry relations}},
   author={Afshari, Shahab and Fekete, Balazs M and Dingman, S Lawrence and Devineni, Naresh and Bjerklie, David M and Khanbilvardi, Reza M},
   journal={Journal of Hydrology},
   volume={547},
@@ -218,7 +227,7 @@ @article{afshari2017statistical
 }
 
 @article{bieger2015development,
-  title={Development and evaluation of bankfull hydraulic geometry relationships for the physiographic regions of the United States},
+  title={{Development and evaluation of bankfull hydraulic geometry relationships for the physiographic regions of the United States}},
   author={Bieger, Katrin and Rathjens, Hendrik and Allen, Peter M and Arnold, Jeffrey G},
   journal={JAWRA Journal of the American Water Resources Association},
   volume={51},
@@ -230,7 +239,7 @@ @article{bieger2015development
 }
 
 @article{bieger2016development,
-  title={Development and comparison of multiple regression models to predict bankfull channel dimensions for use in hydrologic models},
+  title={{Development and comparison of multiple regression models to predict bankfull channel dimensions for use in hydrologic models}},
   author={Bieger, Katrin and Rathjens, Hendrik and Arnold, Jeffrey G and Chaubey, Indrajeet and Allen, Peter M},
   journal={JAWRA Journal of the American Water Resources Association},
   volume={52},
@@ -242,7 +251,7 @@ @article{bieger2016development
 }
 
 @article{hrafnkelsson2022generalization,
-  title={Generalization of the power-law rating curve using hydrodynamic theory and Bayesian hierarchical modeling},
+  title={{Generalization of the power-law rating curve using hydrodynamic theory and Bayesian hierarchical modeling}},
   author={Hrafnkelsson, Birgir and Sigurdarson, Helgi and R{\"o}gnvaldsson, S{\"o}lvi and Jansson, Axel {\"O}rn and Vias, Rafael Dan{\'\i}el and Gardarsson, Sigurdur M},
   journal={Environmetrics},
   volume={33},
@@ -254,7 +263,7 @@ @article{hrafnkelsson2022generalization
 }
 
 @article{owpsi2017,
-  title={National Water Center Innovators Program Summer Institute Report 2017},
+  title={{National Water Center Innovators Program Summer Institute Report 2017}},
   author={Johnson, JM and Coll, JM and Maidment, DR and Cohen, S and Nelson, J and Ogden, F and Praskievicz, S and Clark, EP},
   journal={Consortium of Universities for the Advancement of Hydrologic Science, Inc., Technical Report},
   number={14},
@@ -263,7 +272,7 @@ @article{owpsi2017
 }
 
 @article{cosgrove2023,
-  title={NOAA's National Water Model: Advancing operational hydrology through continental-scale modeling},
+  title={{NOAA's National Water Model: Advancing operational hydrology through continental-scale modeling}},
   author={Cosgrove, Brian and Gochis, David and Flowers, Trey and Dugger, Aubrey and Ogden, Fred and Graziano, Tom and Clark, Ed and Cabell, Ryan and Casiday, Nick and Cui, Zhengtao and others},
   journal={JAWRA Journal of the American Water Resources Association},
   year={2024},
@@ -272,7 +281,7 @@ @article{cosgrove2023
 }
 
 @article{archfield2015,
-  title={Accelerating advances in continental domain hydrologic modeling},
+  title={{Accelerating advances in continental domain hydrologic modeling}},
   author={Archfield, Stacey A and Clark, Martyn and Arheimer, Berit and Hay, Lauren E and McMillan, Hilary and Kiang, Julie E and Seibert, Jan and Hakala, Kirsti and Bock, Andrew and Wagener, Thorsten and others},
   journal={Water Resources Research},
   volume={51},
@@ -281,4 +290,15 @@ @article{archfield2015
   year={2015},
   publisher={Wiley Online Library},
   DOI={10.1002/2015WR017498}
+}
+
+@article{fang2024,
+  title={{Improved National-Scale Above-Normal Flow Prediction for Gauged and Ungauged Basins Using a Spatio-Temporal Hierarchical Model}},
+  author={Fang, Shiqi and Johnson, JM and Yeghiazarian, Lilit and Sankarasubramanian, A},
+  journal={Water Resources Research},
+  volume={60},
+  number={1},
+  year={2024},
+  DOO={10.1029/2023WR034557},
+  publisher={Wiley Online Library}
 }
diff --git a/paper/paper.md b/paper/paper.md
@@ -51,9 +51,9 @@ Real-world data often fails to meet these conditions precisely, so an allowance
 
 Hydrologic models that simulate streamflow are critical for forecasting water availability, drought, and flood inundation. A key aspect of these models is estimating the size and shape of channels, often achieved through hydraulic geometry relationships.
 
-While extensively studied at local scales, these relationships remain unquantified for the majority of stream reaches globally, including in the United States. As a result, large-scale models often rely on incomplete approximations, leading to less accurate streamflow estimates [@hess-26-6121-2022; @johnson2023comprehensive] and flood forecasting [@zheng2018river; @maidment2014national; @johnson2019integrated; @fim]. For instance, the National Oceanic and Atmospheric Administration National Water Model [@cosgrove2023] uses trapezoidal geometries [@wrfhydro] that are in part derived from hydraulic geometry relationships and drainage area assumptions found in @bieger2015development; @bieger2016development; @blackburn2017development. Although these approximations are recognized as overly simplistic, advancing them requires integrating diverse observation systems and refining them into parameterized, mass-conserving relationships.
+While extensively studied at local scales, these relationships remain unquantified for the majority of stream reaches globally, including in the United States. As a result, large-scale models often rely on incomplete approximations, leading to less accurate streamflow estimates [@hess-26-6121-2022; @johnson2023comprehensive; @fang2024] and flood forecasts [@zheng2018river; @maidment2014national; @johnson2019integrated; @fim]. For instance, the National Oceanic and Atmospheric Administration National Water Model [@cosgrove2023] uses trapezoidal geometries [@wrfhydro] that are in part derived from hydraulic geometry relationships and drainage area assumptions found in @bieger2015development; @bieger2016development; @blackburn2017development. Although these approximations are recognized as overly simplistic, advancing them requires integrating diverse observation systems and refining them into parameterized, mass-conserving relationships.
 
-Several efforts have aimed to address this challenge in the United States, primarily relying on traditional Ordinary Least Squares (OLS) fitting methods and data preprocessing [@enzminger_thomas_l_2023_7868764; @afshari_shahab_2019_2558565; @afshari2017statistical]. However, these efforts are limited by the lack of shared software and source data, hindering the evolution, and interoproabilty, of their products.
+Several efforts have aimed to address this challenge in the United States, primarily relying on traditional OLS fitting methods and data preprocessing [@enzminger_thomas_l_2023_7868764; @afshari_shahab_2019_2558565; @afshari2017statistical]. However, these efforts are limited by the lack of shared software and source data, hindering the evolution, and interoproabilty, of their products.
 
 ### Software
 
@@ -69,12 +69,12 @@ Towards this, `AHGestimation` is an R package [@r-project] providing three capab
 
 The package documentation includes several examples on the theory, design, and application of these tools.
 
-The first stable version of `AHGestimation` was made available in 2019 and was applied to an aggregated dataset of USGS manual field measurements. Since then, it has been actively developed to better understand and quantify these fundamental relationships in the face of noisy, large, and disparate data sources. Applications of the software have been used to (1) demonstrate how improved flood forecasts could be delivered from the NOAA/NWS National Water Model [@johnson2022knowledge] (2) help the NOAA/NWS Office of Water Prediction develop continental scale channel size and shape estimates to improve flood prediction and hydraulic routing and to (3) bolster the co-agency sponsored National Hydrologic Geospatial Fabric [@referencefabric; @blodgett2021mainstems; @blodgett2023generating].
+The first stable version of `AHGestimation` was made available in 2019 and was applied to an aggregated dataset of USGS manual field measurements. Since then, it has been actively developed to better understand and quantify these fundamental relationships in the face of noisy, large, and disparate data sources. Applications of the software have been used to (1) demonstrate how improved flood forecasts could be delivered from the NOAA/NWS National Water Model [@johnson2022knowledge], (2) help the NOAA/NWS Office of Water Prediction develop continental scale channel size and shape estimates to improve flood prediction and hydraulic routing, and (3) bolster the co-agency USGS/NOAA National Hydrologic Geospatial Fabric and Next Generation Water Resource Modeling Framework Hydrofabric efforts [@referencefabric; @blodgett2021mainstems; @blodgett2023generating; @nextgenhf].
 
 # Example of use
 
 `AHGestimation` is available on
-[GitHub](https://hub.com/mikejohnson51/AHGestimation) and can be installed as follows:
+[GitHub](https://github.com/mikejohnson51/AHGestimation) and can be installed as follows:
 
 ``` r
 #install.packages(remotes)
@@ -87,7 +87,7 @@ This example illustrates how the package can be utilized to:
 2. **Fit AHG Parameters**: AHG parameters are estimated using the hybrid modeling approach.
 3. **Estimate and Plot Cross-Section Shape**: The shape of the associated cross-section is estimated and plotted with an area-depth relation.
 
-The script to generate the plot can be found [here](image.R), and the `nwis` data object is exported with the package to provides field measurements taken at [USGS site 01096500 on the Nashua River at East Pepperell in Massachusetts](https://waterdata.usgs.gov/nwis/measurements/?site_no=01096500&agency_cd=USGS). 
+The script to generate the plot found in \autoref{fig:ahg-1} can be found [here](https://github.com/mikejohnson51/AHGestimation/blob/master/paper/image.R), and the `nwis` data object is exported with the package to provides field measurements taken at [USGS site 01096500 on the Nashua River at East Pepperell in Massachusetts](https://waterdata.usgs.gov/nwis/measurements/?site_no=01096500&agency_cd=USGS). 
 
 ``` r 
 nwis

diff --git a/paper/paper.pdf b/paper/paper.pdf