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Tag new Zenodo release + minor fixes for JOSS
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.zenodo.json

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"language": "eng",
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"license": "MIT",
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"upload_type": "software",
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"title": "AIBECS.jl: The ideal tool for exploring global marine biogeochemical cycles",
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"title": "AIBECS.jl: A tool for exploring global marine biogeochemical cycles",
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"creators": [
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{
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"orcid": "0000-0002-3838-5976",
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"affiliation": "previously UCI, now at USC",
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"affiliation": "Department of Earth Sciences, University of Southern California; (now at) School of Mathematics and Statistics, University of New South Wales, Sydney",
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"name": "Benoit Pasquier"
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},
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{
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"orcid": "0000-0001-7452-9415",
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"affiliation": "Department of Earth System Science, University of California, Irvine",
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"name": "François W. Primeau"
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},
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{
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"orcid": "0000-0002-8257-626X",
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"affiliation": "Department of Earth Sciences, University of Southern California",
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"name": "Seth G. John"
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}
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],
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"keywords": [

Project.toml

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name = "AIBECS"
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uuid = "ace601d6-714c-11e9-04e5-89b7fad23838"
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authors = ["Benoit Pasquier <[email protected]>"]
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version = "0.11.1"
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version = "0.11.2"
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[deps]
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Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"

docs/paper.bib

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@article{Amante_Eakins_2009,
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@dataset{Amante_Eakins_2009,
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title = {{ETOPO1} 1 arc-minute global relief model: procedures, data sources and analysis},
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author = {Amante, Christopher and Eakins, Barry W},
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year = {2009},
@@ -141,9 +141,9 @@ @article{Chien_etal_2016
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year = {2016}
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}
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@misc{Dai_2017,
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@dataset{Dai_2017,
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author = {Aiguo {Dai}},
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title = {Dai and Trenberth Global River Flow and Continental Discharge Dataset},
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title = {Global River Flow and Continental Discharge Dataset},
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publisher = {Research Data Archive at the National Center for Atmospheric Research, Computational and Information Systems Laboratory},
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address = {Boulder CO},
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year = {2017},
@@ -290,7 +290,7 @@ @article{DeVries_GBC_2014
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year = {2014}
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}
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@misc{Distributions.jl-2019,
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@software{Distributions.jl-2019,
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author = {Dahua Lin and
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John Myles White and
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Simon Byrne and
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@inbook{Kelley_2003_1,
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author = {Kelley, C. T.},
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chapter = {1. Introduction},
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title = {Solving Nonlinear Equations with Newton's Method},
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title = {Solving Nonlinear Equations with {Newton}'s Method},
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pages = {1-25},
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doi = {10.1137/1.9780898718898.ch1},
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year = {2003},
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author = {Xingwen Li and François Primeau}
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}
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@misc{Luijendijk_etal_2019,
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@dataset{Luijendijk_etal_2019,
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author = {Elco {Luijendijk} and Tom {Gleeson} and Nils {Moosdorf}},
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title = {{Geospatial data and model results for a global model study of coastal groundwater discharge}},
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year = {2019},
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doi = {10.1594/PANGAEA.907641},
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note = {Supplement to: Luijendijk, E et al. (2019): The Flow of Fresh Groundwater and Solutes to the World's Oceans and Coastal Ecosystems. EarthArXiv Preprints, https://doi.org/10.31223/osf.io/sw8r4},
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type = {data set},
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publisher = {PANGAEA}
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}
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}
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@article{Rackauckas_Nie_JORS_2017,
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title = {Differentialequations.jl--a performant and feature-rich ecosystem for solving differential equations in julia},
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title = {{DifferentialEquations.jl --- A performant and feature-rich ecosystem for solving differential equations in Julia}},
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author = {Rackauckas, Christopher and Nie, Qing},
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journal = {Journal of Open Research Software},
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volume = {5},
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number = {1},
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year = {2017},
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publisher = {Ubiquity Press}
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pages = {15},
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publisher = {Ubiquity Press},
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doi = {http://doi.org/10.5334/jors.151}
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}
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@article{RevelsLubinPapamarkou2016,
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}
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@article{Schlitzer_etal_ChemGeo_2018,
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@dataset{Schlitzer_etal_ChemGeo_2018,
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author = {Schlitzer, Reiner and Anderson, Robert F. and Dodas, Elena Masferrer and Lohan, Maeve and Geibert, Walter and Tagliabue, Alessandro and Bowie, Andrew and Jeandel, Catherine and Maldonado, Maria T and Landing, William M and Cockwell, Donna and Abadie, Cyril and Abouchami, Wafa and Achterberg, Eric P and Agather, Alison and Aguliar-Islas, Ana and van Aken, Hendrik M and Andersen, Morten and Archer, Corey and Auro, Maureen and de Baar, Hein J and Baars, Oliver and Baker, Alex R and Bakker, Karel and Basak, Chandranath and Baskaran, Mark and Bates, Nicholas R and Bauch, Dorothea and van Beek, Pieter and Behrens, Melanie K and Black, Erin and Bluhm, Katrin and Bopp, Laurent and Bouman, Heather and Bowman, Katlin and Bown, Johann and Boyd, Philip and Boye, Marie and Boyle, Edward A. and Branellec, Pierre and Bridgestock, Luke and Brissebrat, Guillaume and Browning, Thomas and Bruland, Kenneth W and Brumsack, Hans-J{\"u}rgen and Brzezinski, Mark and Buck, Clifton S and Buck, Kristen N and Buesseler, Ken and Bull, Abby and Butler, Edward and Cai, Pinghe and Mor, Patricia C{\'a}mara and Cardinal, Damien and Carlson, Craig and Carrasco, Gonzalo and Casacuberta, N{\'u}ria and Casciotti, Karen L and Castrillejo, Maxi and Chamizo, Elena and Chance, Rosie and Charette, Matthew A and Chaves, Joaquin E and Cheng, Hai and Chever, Fanny and Christl, Marcus and Church, Thomas M and Closset, Ivia and Colman, Albert and Conway, Tim M and Cossa, Daniel and Croot, Peter and Cullen, Jay T and Cutter, Gregory A and Daniels, Chris and Dehairs, Frank and Deng, Feifei and Dieu, Huong Thi and Duggan, Brian and Dulaquais, Gabriel and Dumousseaud, Cynthia and Echegoyen-Sanz, Yolanda and Edwards, R Lawrence and Ellwood, Michael and Fahrbach, Eberhard and Fitzsimmons, Jessica N and Flegal, A Russell and Fleisher, Martin Q and van de Flierdt, Tina and Frank, Martin and Friedrich, Jana and Fripiat, François and Fr{\"o}llje, Henning and Galer, Stephen J G and Gamo, Toshitaka and Ganeshram, Raja S and Garcia-Orellana, Jordi and Garcia-Solsona, Ester and Gault-Ringold, Melanie and George, Ejin and Gerringa, Loes J A and Gilbert, Melissa and Godoy, Jose M and Goldstein, Steven L. and Gonzalez, Santiago R and Grissom, Karen and Hammerschmidt, Chad and Hartman, Alison and Hassler, Christel S and Hathorne, Ed C and Hatta, Mariko and Hawco, Nicholas and Hayes, Christopher T and Heimb{\"u}rger, Lars-Eric and Helgoe, Josh and Heller, Maija and Henderson, Gideon M and Henderson, Paul B and van Heuven, Steven and Ho, Peng and Horner, Tristan J and Hsieh, Yu-Te and Huang, Kuo-Fang and Humphreys, Matthew P and Isshiki, Kenji and Jacquot, Jeremy E and Janssen, David J and Jenkins, William J and John, Seth and Jones, Elizabeth M and Jones, Janice L and Kadko, David C and Kayser, Rick and Kenna, Timothy C and Khondoker, Roulin and Kim, Taejin and Kipp, Lauren and Klar, Jessica K and Klunder, Maarten and Kretschmer, Sven and Kumamoto, Yuichiro and Laan, Patrick and Labatut, Marie and Lacan, François and Lam, Phoebe J and Lambelet, Myriam and Lamborg, Carl H and Le Moigne, Fr{\'e}d{\'e}ric A C and Le Roy, Emilie and Lechtenfeld, Oliver J and Lee, Jong-Mi and Lherminier, Pascale and Little, Susan and L{\'o}pez-Lora, Mercedes and Lu, Yanbin and Masque, Pere and Mawji, Edward and Mcclain, Charles R and Measures, Christopher and Mehic, Sanjin and Barraqueta, Jan-Lukas Menzel and van der Merwe, Pier and Middag, Rob and Mieruch, Sebastian and Milne, Angela and Minami, Tomoharu and Moffett, James W and Moncoiffe, Gwenaelle and Moore, Willard S and Morris, Paul J and Morton, Peter L and Nakaguchi, Yuzuru and Nakayama, Noriko and Niedermiller, John and Nishioka, Jun and Nishiuchi, Akira and Noble, Abigail and Obata, Hajime and Ober, Sven and Ohnemus, Daniel C and van Ooijen, Jan and O'Sullivan, Jeanette and Owens, Stephanie and Pahnke, Katharina and Paul, Maxence and Pavia, Frank and Pena, Leopoldo D and Peters, Brian and Planchon, Frederic and Planquette, Helene and Pradoux, Catherine and Puigcorb{\'e}, Viena and Quay, Paul and Queroue, Fabien and Radic, Amandine and Rauschenberg, S and Rehk{\"a}mper, Mark and Rember, Robert and Remenyi, Tomas and Resing, Joseph A and Rickli, Joerg and Rigaud, Sylvain and Rijkenberg, Micha J A and Rintoul, Stephen and Robinson, Laura F. and Roca-Mart{\'\i}, Montserrat and Rodellas, Valenti and Roeske, Tobias and Rolison, John M and Rosenberg, Mark and Roshan, Saeed and van der Loeff, Michiel M Rutgers and Ryabenko, Evgenia and Saito, Mak A and Salt, Lesley A and Sanial, Virginie and Sarthou, Geraldine and Schallenberg, Christina and Schauer, Ursula and Scher, Howie and Schlosser, Christian and Schnetger, Bernhard and Scott, Peter and Sedwick, Peter N and Semiletov, Igor and Shelley, Rachel...},
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title = {{The GEOTRACES Intermediate Data Product 2017}},
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journal = {Chemical Geology},
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@article{Schlitzer_JPO_1993,
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author = {Reiner Schlitzer},
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title = {Determining the Mean, Large-Scale Circulation of the Atlantic with the Adjoint Method},
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title = {Determining the Mean, Large-Scale Circulation of the {Atlantic} with the Adjoint Method},
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journal = {Journal of Physical Oceanography},
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year = {1993},
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publisher = {American Meteorological Society},
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@article{Schlitzer_GeoMonoAGU_2000,
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title = {Applying the adjoint method for biogeochemical modeling: export of particulate organic matter in the world ocean},
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author = {Schlitzer, Reiner},
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journal = {GEOPHYSICAL MONOGRAPH-AMERICAN GEOPHYSICAL UNION},
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journal = {Geophysical Monograph-American Geophysical Union},
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volume = {114},
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pages = {107--124},
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year = {2000},
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publisher = {AGU AMERICAN GEOPHYSICAL UNION}
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publisher = {AGU}
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}
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@article{Thacker_JGRO_1989,
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author = {Thacker, William Carlisle},
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title = {The role of the Hessian matrix in fitting models to measurements},
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title = {The role of the {H}essian matrix in fitting models to measurements},
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journal = {Journal of Geophysical Research: Oceans},
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volume = {94},
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number = {C5},
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@article{WOA_2018_nut,
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author = {H. E. Garcia and K. Weathers and C. R. Paver and I. Smolyar and T. P. Boyer and R. A. Locarnini and M. M. Zweng and A. V. Mishonov and O. K. Baranova and D. Seidov and J. R. Reagan},
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title = {{World Ocean Atlas 2018}},
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volume = {{Volume 4}: Dissolved Inorganic Nutrients (phosphate, nitrate and nitrate+nitrite, silicate)},
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title = {{World Ocean Atlas 2018: Dissolved Inorganic Nutrients (phosphate, nitrate and nitrate+nitrite, silicate)}},
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volume = {4},
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year = {2018},
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publisher = {NOAA National Centers for Environmental Information},
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note = {A. Mishonov Technical Ed.}
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}
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@misc{WorldOceanAtlasTools.jl-2019,
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@software{WorldOceanAtlasTools.jl-2019,
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author = {Benoît Pasquier},
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title = {WorldOceanAtlasTools.jl: Download and process World Ocean Data in Julia},
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month = may,

docs/paper.md

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the Ocean Circulation Inverse Model (OCIM) v0.1 [@Primeau_etal_JGRO_2013],
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v1.0 [@DeVries_Primeau_JPO_2011; @DeVries_GBC_2014],
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and v2.0 [@DeVries_Holzer_JGRO_2019],
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and the MITgcm-built Ocean Comprehensible Atlas (OCCA) ocean-state estimate model [@Forget:2010], of which the downloads are handled by the [DataDeps.jl](https://github.com/oxinabox/DataDeps.jl) package [@DataDeps:2018; @White_etal:2019].
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and the MITgcm-built Ocean Comprehensible Atlas (OCCA) ocean-state estimate model [@Forget:2010], of which the downloads are handled by the [DataDeps.jl](https://github.com/oxinabox/DataDeps.jl) package [@White_etal:2019].
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AIBECS.jl also offers classic two-box and three-box models [@Sarmiento_Gruber:2006; @Archer_etal_GBC_2000].
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The [OceanGrids.jl](https://github.com/briochemc/OceanGrids.jl) package, on which AIBECS depends, provides the underlying grid configuration types as well as regridding and interpolating routines.
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Swapping the underlying circulation model and grid requires a single-line-of-code change, facilitating intercomparison projects.

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