paper: first section

.github/workflows/joss.yaml

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+on: 
+  push:
+    branches: [joss]
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v1
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          path: paper.md

joss_paper/paper.bib

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+@article{zhao2020GrasslandEcosystemServices,
+  title = {Grassland Ecosystem Services: A Systematic Review of Research Advances and Future Directions},
+  shorttitle = {Grassland Ecosystem Services},
+  author = {Zhao, Yuanyuan and Liu, Zhifeng and Wu, Jianguo},
+  year = {2020},
+  month = apr,
+  journal = {Landscape Ecology},
+  volume = {35},
+  number = {4},
+  pages = {793--814},
+  publisher = {{Springer Netherlands}},
+  issn = {1572-9761},
+  doi = {10.1007/s10980-020-00980-3},
+  urldate = {2023-04-06},
+  copyright = {2020 Springer Nature B.V.},
+  langid = {english},
+  keywords = {read}
+}
+
+@article{herrero2013BiomassUseProduction,
+  title = {Biomass Use, Production, Feed Efficiencies, and Greenhouse Gas Emissions from Global Livestock Systems},
+  author = {Herrero, Mario and Havl{\'i}k, Petr and Valin, Hugo and Notenbaert, An and Rufino, Mariana C. and Thornton, Philip K. and Bl{\"u}mmel, Michael and Weiss, Franz and Grace, Delia and Obersteiner, Michael},
+  year = {2013},
+  month = dec,
+  journal = {Proceedings of the National Academy of Sciences},
+  volume = {110},
+  number = {52},
+  pages = {20888--20893},
+  publisher = {{Proceedings of the National Academy of Sciences}},
+  doi = {10.1073/pnas.1308149110},
+  urldate = {2023-12-04}
+}
+
+@article{zhao2020GrasslandEcosystemServices,
+  title = {Grassland Ecosystem Services: A Systematic Review of Research Advances and Future Directions},
+  shorttitle = {Grassland Ecosystem Services},
+  author = {Zhao, Yuanyuan and Liu, Zhifeng and Wu, Jianguo},
+  year = {2020},
+  month = apr,
+  journal = {Landscape Ecology},
+  volume = {35},
+  number = {4},
+  pages = {793--814},
+  publisher = {{Springer Netherlands}},
+  issn = {1572-9761},
+  doi = {10.1007/s10980-020-00980-3},
+  urldate = {2023-04-06},
+  copyright = {2020 Springer Nature B.V.},
+  langid = {english}
+}
+
+@inbook{IPCC-2022-Chapter05,
+  author = {Bezner Kerr, R. and Hasegawa, T. and Lasco, R. and Bhatt, I. and Deryng, D. and Farrell, A. and Gurney-Smith, H. and Ju, H. and Lluch-Cota, S. and Meza, F. and Nelson, G. and Neufeldt, H. and Thornton, P.},
+  title = {Food, Fibre, and Other Ecosystem Products},
+  booktitle = {Climate Change 2022: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the Intergovernmental Panel on Climate Change},
+  editor = {Pörtner, H. O. and Roberts, D. C. and Tignor, M. and Poloczanska, E. S. and Mintenbeck, K. and Alegría, A. and Craig, M. and Langsdorf, S. and Löschke, S. and Möller, V. and Okem, A. and Rama, B.},
+  publisher = {Cambridge University Press},
+  address = {Cambridge, UK and New York, USA},
+  pages = {713-906},
+  ISBN = {9781009325844},
+  DOI = {10.1017/9781009325844.007.714},
+  year = {2022},
+  type = {Book Section}
+}
+
+@article{thornley1997TemperateGrasslandResponses,
+  title = {Temperate {{Grassland Responses}} to {{Climate Change}}: An {{Analysis}} Using the {{Hurley Pasture Model}}},
+  shorttitle = {Temperate {{Grassland Responses}} to {{Climate Change}}},
+  author = {Thornley, J. H. M. and Cannell, M. G. R.},
+  year = {1997},
+  month = aug,
+  journal = {Annals of Botany},
+  volume = {80},
+  number = {2},
+  pages = {205--221},
+  issn = {0305-7364},
+  doi = {10.1006/anbo.1997.0430},
+  urldate = {2023-10-26},
+  keywords = {hurley pasture model,read,source of references}
+}
+
+@article{jenkinson1994TrendsHerbageYields,
+  title = {Trends in Herbage Yields over the Last Century on the {{Rothamsted Long-term Continuous Hay Experiment}}},
+  author = {Jenkinson, D. S. and Potts, J. M. and Perry, J. N. and Barnett, V. and Coleman, K. and Johnston, A. E.},
+  year = {1994},
+  month = jun,
+  journal = {The Journal of Agricultural Science},
+  volume = {122},
+  number = {3},
+  pages = {365--374},
+  publisher = {{Cambridge University Press}},
+  issn = {1469-5146, 0021-8596},
+  doi = {10.1017/S0021859600067290},
+  urldate = {2023-12-04},
+  langid = {english},
+  keywords = {RothC}
+}
+
+@article{jouven2006ModelPredictingDynamics,
+  title = {Model Predicting Dynamics of Biomass, Structure and Digestibility of Herbage in Managed Permanent Pastures. 1. {{Model}} Description},
+  author = {Jouven, M. and Carr{\`e}re, P. and Baumont, R.},
+  year = {2006},
+  journal = {Grass and Forage Science},
+  volume = {61},
+  number = {2},
+  pages = {112--124},
+  issn = {1365-2494},
+  doi = {10.1111/j.1365-2494.2006.00515.x},
+  urldate = {2023-01-04},
+  langid = {english},
+  keywords = {functional traits,mechanistic dynamic model,permanent grassland}
+}
+
+@article{ruelle2018DevelopmentMooreparkSt,
+  title = {Development of the {{Moorepark St Gilles}} Grass Growth Model ({{MoSt GG}} Model): {{A}} Predictive Model for Grass Growth for Pasture Based Systems},
+  shorttitle = {Development of the {{Moorepark St Gilles}} Grass Growth Model ({{MoSt GG}} Model)},
+  author = {Ruelle, E. and Hennessy, D. and Delaby, L.},
+  year = {2018},
+  month = sep,
+  journal = {European Journal of Agronomy},
+  volume = {99},
+  pages = {80--91},
+  issn = {1161-0301},
+  doi = {10.1016/j.eja.2018.06.010},
+  urldate = {2023-11-03},
+  keywords = {Grass growth model,Grazing,Nitrogen fluxes,readlist,Soil model}
+}
+
+@article{kokah2023ModelingDailyDynamics,
+  title = {Modeling the Daily Dynamics of Grass Growth of Several Species According to Their Functional Type, Based on Soil Water and Nitrogen Dynamics: {{Gras-sim}} Model Definition, Parametrization and Evaluation},
+  shorttitle = {Modeling the Daily Dynamics of Grass Growth of Several Species According to Their Functional Type, Based on Soil Water and Nitrogen Dynamics},
+  author = {Kokah, Essomandan Urbain and Knoden, David and Lambert, Richard and Himdi, Hamza and Dumont, Benjamin and Bindelle, J{\'e}r{\^o}me},
+  year = {2023},
+  month = nov,
+  journal = {Journal of Agriculture and Food Research},
+  pages = {100875},
+  issn = {2666-1543},
+  doi = {10.1016/j.jafr.2023.100875},
+  urldate = {2023-11-20},
+  keywords = {Biomass,Functional group,Grassland,Model,modvege,Nitrogen,readlist,Water}
+}
+
+@book{rcoreteam2021LanguageEnvironmentStatistical,
+  title = {R: {{A Language Environment}} for {{Statistical Computing}}},
+  author = {{R Core Team}},
+  year = {2021},
+  publisher = {{R Foundation for Statistical Computing}},
+  address = {{Vienna, Austria}},
+  url = {https://www.R-project.org/}
+}
+

joss_paper/paper.md

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+---
+title: 'growR: R Implementation of the Vegetation Model ModVege'
+tags:
+  - R
+  - agronomy
+  - grasslands
+  - agroecology
+  - modelling
+authors:
+  - name: Kevin P. Kramer
+    orcid: 0000-0001-5523-6924
+    equal-contrib: true
+    affiliation: 1
+    corresponding: true # (This is how to denote the corresponding author)
+  - name: Pierluigi Calanca
+    equal-contrib: true
+    affiliation: 1
+affiliations:
+ - name: Agroscope, Federal Department of Economic Affairs, Education and Research, Switzerland
+   index: 1
+date: 13 December 2023
+bibliography: paper.bib
+
+---
+
+# Summary and Statement of Need
+
+Grasslands constitute one of Earth's most widespread terrestrial ecosystems 
+[@zhao2020GrasslandEcosystemServices] and managed grasslands are a core 
+element in global agriculture, providing roughly half the feed inputs for 
+global livestock systems [@herrero2013BiomassUseProduction].
+Beside their importance for global food production, they provide a catalogue 
+of other ecosystem services, such as water flow and erosion regulation, 
+pollination service, carbon sequestration and climate regulation 
+[@zhao2020GrasslandEcosystemServices].
+The latter two examples have radically grown in urgency in light of 
+anthropogenic climate change [@IPCC-2002-Chapter05].
+
+There is thus ample motivation to study the properties and dynamics of 
+grasslands.
+Experimental approaches, while of fundamental importance, suffer from high 
+costs in time resources required, as a study site typically has to be maintained 
+over several year in order to make a scientific observation.
+For this reason, the method of investigating grassland dynamics by means of 
+mathematical models and simulationist approaches has found widespread 
+application, with dozens of models being formulated, employed and further 
+developed.
+Each of these models has been developed with different applications in mind 
+and thus comes with its own focal points and a set of advantages and 
+disadvantages.
+To give just a few examples:
+
+- [The Hurley Pasture Model](@thornley1997TemperateGrasslandResponses) is a 
+  rather complete and detailed mechanistic model for managed pastures.
+- [RothC](https://www.rothamsted.ac.uk/rothamsted-carbon-model-rothc) was 
+  developed for the long-term 
+  [Rothamsted Parkgrass Experiment](@jenkinson1994TrendsHerbageYields) and 
+  thus uses comparatively long time scales with a focus on the carbon balance.
+- [ModVege](@jouven2006ModelPredictingDynamics) is another mechanistic model 
+  that is designed to capture the dominant processes with a minimum of 
+  required input parameters.
+- [The Moorepark St Gilles](@ruelle2018DevelopmentMooreparkSt) and 
+  [Gras-sim](@kokah2023ModelingDailyDynamics) models both extend 
+  [ModVege](@jouven2006ModelPredictingDynamics) by adding more processes and 
+  therefore complexity.
+
+The different existing grassland models vary in their formulation, but also 
+in the way they are implemented.
+With this large variability in models, model implementations and 
+implementation versions, transparency and becomes critical for the 
+reproduction of scientific results.
+
+This paper describes the software package `growR`.
+`growR` is an implementation of the vegetation model 
+[ModVege](@jouven2006ModelPredictingDynamics) in the `R` language 
+[@rcoreteam2021LanguageEnvironmentStatistical].
+It is packaged and distributed via the 
+[comprehensive R archive network (CRAN)](https://cran.r-project.org/) with 
+the [source code freely and openly 
+available](https://github.com/kuadrat/growr) and thus presents a contribution 
+to the above formulated need for reproducible practices in ecosystems modelling.
+
+
+# Citations
+
+Citations to entries in paper.bib should be in
+[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
+format.
+
+For a quick reference, the following citation commands can be used:
+- `@author:2001`  ->  "Author et al. (2001)"
+- `[@author:2001]` -> "(Author et al., 2001)"
+- `[@author1:2001; @author2:2001]` -> "(Author1 et al., 2001; Author2 et al., 2002)"
+
+# Figures
+
+Figures can be included like this:
+![Caption for example figure.\label{fig:example}](figure.png)
+and referenced from text using \autoref{fig:example}.
+
+Figure sizes can be customized by adding an optional second parameter:
+![Caption for example figure.](figure.png){ width=20% }
+
+# Acknowledgements
+
+
+# References
+