fix paper.md grammer mistakes and update paper.bib to capitalize refe…

…rences correctly
SatelliteShorelines · Jun 28, 2024 · 34c1cd2 · 34c1cd2
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diff --git a/paper/paper.bib b/paper/paper.bib
@@ -1,6 +1,5 @@
-
 @article{vos2019coastsat,
-  title={CoastSat: A Google Earth Engine-enabled Python toolkit to extract shorelines from publicly available satellite imagery},
+  title={{CoastSat}: {A} {Google Earth Engine}-enabled {Python} toolkit to extract shorelines from publicly available satellite imagery},
   author={Vos, K. and Splinter, K. D. and Harley, M. D. and Simmons, J. A. and Turner, I. L.},
   journal={Environmental Modelling \& Software},
   volume={122},
@@ -12,7 +11,7 @@ @article{vos2019coastsat
 }
 
 @article{luijendijk2018state,
-  title={The State of the World's Beaches},
+  title={The {State} of the {World}'s {Beaches}},
   author={Luijendijk, Arjen and Hagenaars, Gerben and Ranasinghe, Roshanka and Baart, Fedor and Donchyts, Gennadii and Aarninkhof, Stefan},
   journal={Scientific Reports},
   volume={8},
@@ -25,7 +24,7 @@ @article{luijendijk2018state
 }
 
 @article{pardopascual20121,
-title = {Automatic extraction of shorelines from Landsat TM and ETM+ multi-temporal images with subpixel precision},
+title = {Automatic extraction of shorelines from {Landsat TM} and {ETM+} multi-temporal images with subpixel precision},
 journal = {Remote Sensing of Environment},
 volume = {123},
 pages = {1-11},
@@ -45,17 +44,12 @@ @article{sayreEtAl2019
 year = {2019},
 publisher = {Taylor \& Francis},
 doi = {10.1080/1755876X.2018.1529714},
-URL = {
-        https://doi.org/10.1080/1755876X.2018.1529714
-},
-eprint = {
-        https://doi.org/10.1080/1755876X.2018.1529714
-}
+URL = {https://doi.org/10.1080/1755876X.2018.1529714},
+eprint = {https://doi.org/10.1080/1755876X.2018.1529714}
 }
 
-
 @article{mclean202350,
-  title={50 Years of Beach--Foredune Change on the Southeastern Coast of Australia: Bengello Beach, Moruya, NSW, 1972--2022},
+  title={50 Years of {Beach--Foredune} Change on the {Southeastern Coast of Australia}: {Bengello Beach, Moruya, NSW, 1972--2022}},
   author={McLean, R. and Thom, B. and Shen, J. and Oliver, T.},
   journal={Geomorphology},
   volume={439},
@@ -66,7 +60,6 @@ @article{mclean202350
   publisher={Elsevier}
 }
 
-
 @article{vos2023benchmarking,
   title={Benchmarking satellite-derived shoreline mapping algorithms},
   author={Vos, K. and Splinter, K.D. and Palomar-V{\'a}zquez, J. and Pardo-Pascual, J. E. and Almonacid-Caballer, J. and Cabezas-Rabad{\'a}n, C. and Kras, E. C. and Luijendijk, A. P. and Calkoen, F. and Almeida, L. P. and others},
@@ -81,7 +74,7 @@ @article{vos2023benchmarking
 }
 
 @article{turner2021satellite,
-  title={Satellite optical imagery in Coastal Engineering},
+  title={Satellite optical imagery in {Coastal Engineering}},
   author={Turner, I. L. and Harley, M. D. and Almar, R. and Bergsma, E. W. J.},
   journal={Coastal Engineering},
   volume={167},
@@ -93,7 +86,7 @@ @article{turner2021satellite
 }
 
 @article{vos2023pacific,
-  title={Pacific shoreline erosion and accretion patterns controlled by El Ni{\~n}o/Southern Oscillation},
+  title={Pacific shoreline erosion and accretion patterns controlled by {El Ni{\~n}o/Southern Oscillation}},
   author={Vos, K. and Harley, M. D. and Turner, I. L. and Splinter, K. D.},
   journal={Nature Geoscience},
   volume={16},
@@ -117,9 +110,8 @@ @article{castelle2021satellite
   url={https://doi.org/10.1016/j.geomorph.2021.107707}
 }
 
-
 @article{warrick2023large,
-  title={A Large Sediment Accretion Wave Along a {N}orthern {C}alifornia Littoral Cell},
+  title={A {Large Sediment Accretion Wave} Along a {Northern California Littoral Cell}},
   author={Warrick, J. A. and Vos, K. and Buscombe, D. and Ritchie, A. C. and Curtis, J. A.},
   journal={Journal of Geophysical Research: Earth Surface},
   pages={e2023JF007135},
@@ -129,7 +121,6 @@ @article{warrick2023large
   url={https://doi.org/10.1029/2023JF007135}
 }
 
-
 @article{vitousek2023future,
   title={The future of coastal monitoring through satellite remote sensing},
   author={Vitousek, S. and Buscombe, D. and Vos, K. and Barnard, P. L. and Ritchie, A. C. and Warrick, J. A.},
@@ -165,7 +156,6 @@ @article{vandenhove2024secular
   url={https://doi.org/10.1016/j.geomorph.2023.108972}
 }
 
-
 @article{castelle2022primary,
   title={Primary drivers of multidecadal spatial and temporal patterns of shoreline change derived from optical satellite imagery},
   author={Castelle, B. and Ritz, A. and Marieu, V. and Lerma, A. N. and Vandenhove, M.},
@@ -180,15 +170,15 @@ @article{castelle2022primary
 
 @misc{tyler_sutterley_2024,
   author       = {Tyler Sutterley},
-  title        = {tsutterley/pyTMD: v2.1.1},
+  title        = {tsutterley/{pyTMD}: v2.1.1},
   year         = 2024,
   publisher    = {Zenodo},
   doi          = {10.5281/zenodo.10929240},
   url          = {https://doi.org/10.5281/zenodo.10929240},
 }
 
 @article{lyard2021fes2014,
-  title={{FES2014} global ocean tide atlas: {D}esign and performance},
+  title={{FES2014} global ocean tide atlas: {Design} and performance},
   author={Lyard, F. H. and Allain, D. J. and Cancet, M. and Carrere, L. and Picot, N.},
   journal={Ocean Science},
   volume={17},
@@ -201,7 +191,7 @@ @article{lyard2021fes2014
 }
 
 @article{doherty2022python,
-  title={A Python toolkit to monitor sandy shoreline change using high-resolution PlanetScope cubesats},
+  title={A {Python} toolkit to monitor sandy shoreline change using high-resolution {PlanetScope} cubesats},
   author={Doherty, Y. and Harley, M. D. and Vos, K. and Splinter, K. D.},
   journal={Environmental Modelling \& Software},
   volume={157},
@@ -213,7 +203,7 @@ @article{doherty2022python
 }
 
 @article{scheffler2017arosics,
-  title={AROSICS: An automated and robust open-source image co-registration software for multi-sensor satellite data},
+  title={{AROSICS}: {An} automated and robust open-source image co-registration software for multi-sensor satellite data},
   author={Scheffler, D. and Hollstein, A. and Diedrich, H. and Segl, K. and Hostert, P.},
   journal={Remote Sensing},
   volume={9},
@@ -225,36 +215,30 @@ @article{scheffler2017arosics
   url={https://doi.org/10.3390/rs9070676}
 }
 
-
 @dataset{buscombe_2023_8187949,
-  author       = {Buscombe, D. and
-                  Fitzpatrick, S.},
-  title        = {{CoastSeg: Beach transects and beachface slope 
-                   database v1.0}},
+  author       = {Buscombe, D. and Fitzpatrick, S.},
+  title        = {{CoastSeg}: {Beach transects and beachface slope database} v1.0},
   month        = jul,
   year         = 2023,
   publisher    = {Zenodo},
   version      = {v1.0},
   doi          = {10.5281/zenodo.8187949},
-  url          = {\url{https://doi.org/10.5281/zenodo.8187949}}
+  url          = {https://doi.org/10.5281/zenodo.8187949}
 }
 
 @dataset{buscombe_2023_7786276,
   author       = {Buscombe, D.},
-  title        = {{CoastSeg: Shoreline data at 30-m spatial 
-                   resolution for 5x5 degree regions of the world, in
-                   geoJSON format.}},
+  title        = {{CoastSeg}: {Shoreline data at 30-m spatial resolution for 5x5 degree regions of the world, in geoJSON format}},
   month        = apr,
   year         = 2023,
   publisher    = {Zenodo},
   version      = {v1.0},
   doi          = {10.5281/zenodo.7786276},
-  url          = {\url{https://doi.org/10.5281/zenodo.7786276}}
+  url          = {https://doi.org/10.5281/zenodo.7786276}
 }
 
-
 @misc{voscoastsat,
-  title={{C}oastsat-package},
+  title={{Coastsat-package}},
   author={Vos, K. and Fitzpatrick, S.},
   publisher={PyPi},
   year={2023},
@@ -263,8 +247,8 @@ @misc{voscoastsat
 }
 
 @misc{CoastSeg,
-  author       = {Fitzpatrick, S. and Buscombe,D. and Lundine, M. and Warrick,J. and Vos, K.},
-  title        = {SatelliteShorelines/CoastSeg: v1.2.9},
+  author       = {Fitzpatrick, S. and Buscombe, D. and Lundine, M. and Warrick, J. and Vos, K.},
+  title        = {SatelliteShorelines/{CoastSeg}: v1.2.9},
   year         = 2024,
   publisher    = {Zenodo},
   doi          = {10.5281/zenodo.12555413},
@@ -273,7 +257,7 @@ @misc{CoastSeg
 }
 
 @misc{krause2021dea,
-  title={{Digital Earth Australia notebooks and tools repository}},
+  title={{Digital Earth Australia} notebooks and tools repository},
   author={Krause, C. and Dunn, B. and Bishop-Taylor, R. and Adams, C. and Burton, C. and Alger, M. and Chua, S. and Phillips, C. and Newey, V. and Kouzoubov, K. and Leith, A. and Ayers, D. and Hicks, A.},
   year={2021},
   publisher={Commonwealth of Australia (Geoscience Australia)},
@@ -282,7 +266,6 @@ @misc{krause2021dea
   doi={10.26186/145234}
 }
 
-
 @article{konstantinou2023satellite,
   title={Satellite-based shoreline detection along high-energy macrotidal coasts and influence of beach state},
   author={Konstantinou, A. and Scott, T. and Masselink, G. and Stokes, K. and Conley, D. and Castelle, B.},
@@ -295,7 +278,7 @@ @article{konstantinou2023satellite
 }
 
 @article{wu2021leafmap,
-  title={Leafmap: {A P}ython package for interactive mapping and geospatial analysis with minimal coding in a {J}upyter environment},
+  title={{Leafmap}: {A P}ython package for interactive mapping and geospatial analysis with minimal coding in a {J}upyter environment},
   author={Wu, Q.},
   journal={Journal of Open Source Software},
   volume={6},
@@ -320,7 +303,7 @@ @article{buscombe2022reproducible
 }
 
 @article{bishop2021mapping,
-  title={Mapping Australia's Dynamic Coastline at Mean Sea Level Using Three Decades of Landsat Imagery},
+  title={Mapping {Australia}'s {Dynamic Coastline} at {Mean Sea Level} Using {Three Decades of Landsat Imagery}},
   author={Bishop-Taylor, R. and Nanson, R. and Sagar, S. and Lymburner, L.},
   journal={Remote Sensing of Environment},
   volume={267},
@@ -344,7 +327,7 @@ @article{garcia2015evaluating
 }
 
 @article{almonacid2016evaluation,
-  title={Evaluation of annual mean shoreline position deduced from Landsat imagery as a mid-term coastal evolution indicator},
+  title={Evaluation of annual mean shoreline position deduced from {Landsat} imagery as a mid-term coastal evolution indicator},
   author={Almonacid-Caballer, J. and Sanchez-Garcia, E. and Pardo-Pascual, J. E. and Balaguer-Beser, A. A. and Palomar-Vazquez, J.},
   journal={Marine Geology},
   volume={372},
@@ -353,4 +336,4 @@ @article{almonacid2016evaluation
   publisher={Elsevier},
   doi={10.1016/j.margeo.2015.12.015},
   url={https://doi.org/10.1016/j.margeo.2015.12.015}
-}
+}
diff --git a/paper/paper.md b/paper/paper.md
@@ -43,7 +43,7 @@ bibliography: paper.bib
 
 So-called `instantaneous' SDS workflows, where shorelines are extracted from each individual satellite image rather than temporal composites [@pardopascual20121; @bishop2021mapping], follow a basic recipe, namely 1) waterline estimation, where the 2D (x,y) location of the land-sea interface is determined, and 2) water-level correction, where the waterline location is mapped onto a shore-perpendicular transect, converted to a linear distance along that transect, then corrected for water level, and referenced to a particular elevation contour on the beach [@vos2019coastsat]. The resulting measurement is called a 'shoreline' and it is the location that the waterline intersects a particular elevation datum. Water level corrections typically only account for tide [@vos2019coastsat] but recently SDS workflows have incorporated both wave setup and runup correction, which are a function of the instantaneous wave field at the time of image acquisition [@konstantinou2023satellite; @vitousek2023future; @vitousek2023model; @castelle2021satellite].
 
-`CoastSeg` has three broad aims. The first aim is to be an toolkit consisting functions that operate the core SDS workflow functionalities. This includes file input/output, image downloading, geospatial conversion, tidal model API handling, mapping 2D shorelines to 1D transect-based measurements, and numerous other functions common to a basic SDS workflow, regardless of a particular waterline estimation methodology. This waterline detection algorithm will be crucial to the success of any SDS workflow because it is the step that identifies the the boundary between sea and land which serves as the basis for shoreline mapping. The idea behind the design of `CoastSeg` is that users could extend or customize functionality using scripts and notebooks.
+`CoastSeg` has three broad aims. The first aim is to be a toolkit consisting functions that operate the core SDS workflow functionalities. This includes file input/output, image downloading, geospatial conversion, tidal model API handling, mapping 2D shorelines to 1D transect-based measurements, and numerous other functions common to a basic SDS workflow, regardless of a particular waterline estimation methodology. This waterline detection algorithm will be crucial to the success of any SDS workflow because it identifies the boundary between sea and land, which serves as the basis for shoreline mapping. The idea behind the design of `CoastSeg` is that users could extend or customize functionality using scripts and notebooks.
 
 The second aim of `CoastSeg` is therefore to provide fully functioning SDS implementations in an accessible browser notebook format. Our principal objective to date has been to re-implement and improve upon a popular existing toolbox, `CoastSat` [@vos2019coastsat], allowing the user to carry out the well-established `CoastSat` SDS workflow with a well-supported literature [@castelle2021satellite; @castelle2022primary; @vos2023pacific; @vos2023benchmarking; @warrick2023large; @konstantinou2023satellite; @vitousek2023model; @mclean202350; @vandenhove2024secular], but in a more accessible and convenient way within the `CoastSeg` platform. In order to achieve this, we developed `CoastSat-package` [@voscoastsat], a Python package that is installed into the `CoastSeg` `conda` environment. `CoastSat-package` contains re-implemented versions of the original `CoastSat` codes, addresses the lack of pip or conda installability of `CoastSat`, and isolates the CoastSeg-specific enhancements from the original `CoastSat` code. These improvements include additional image download filtering, such as by cloud coverage in the scene, additional parameters to control shoreline extraction, and more accessible output formats, all while retaining the foundational elements of the original `CoastSat` code. The `CoastSeg` re-implementation of the `CoastSat` workflow is end-to-end within a single notebook. That notebook allows the user to, among other tasks: a) define a Region of Interest (ROI) on a webmap and upload geospatial vector format files; b) define, download and post-process satellite imagery; c) identify waterlines in that imagery using the `CoastSat` method [@vos2019coastsat]; d) correct those waterlines to elevation-based shorelines using tidal elevation-datum corrections provided through interaction with the pyTMD [@tyler_sutterley_2024] API; and e) save output files in a variety of modern geospatial and other formats for subsequent analysis. Additionally, CoastSeg's toolkit-based design enables it to run as non-interactive scripts, catering to larger scale shoreline analysis projects.This flexibility ensures that CoastSeg can accommodate a wide range of research needs, from detailed, interactive exploration to extensive, automated analyses.