Added initial manuscript outline and README

README.md

+# Persefone paper
+
+This is the repository for preparing the initial Persefone.jl presentation paper.
+
+> Vedder, D., Matthies, M., Díaz Iturry, G., Pe'er, G. (*in prep*) Persefone.jl: Modelling Biodiversity in Dynamic Agricultural Landscapes
+
+To be submitted to [Environmental Modelling and Software](https://www.sciencedirect.com/journal/environmental-modelling-and-software/about/aims-and-scope)
+([guide for authors](https://www.sciencedirect.com/journal/environmental-modelling-and-software/publish/guide-for-authors)).
+
+## Repository structure
+
+- `paper.lyx` Main document file (download [LyX](https://www.lyx.org/) to edit)
+
+- `img` Figures and graphics for the main manuscript
+
+- `appendix` LaTeX files and images for the appendices

paper.lyx

+#LyX 2.4 created this file. For more info see https://www.lyx.org/
+\lyxformat 620
+\begin_document
+\begin_header
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+\pdf_title "Hybridisation may aid Evolutionary Rescue of an Endangered East African Passerine"
+\pdf_author "Vedder et al."
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+\index Index
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+\end_header
+
+\begin_body
+
+\begin_layout Title
+Persefone.jl:
+ Modelling Biodiversity in Dynamic Agricultural Landscapes
+\end_layout
+
+\begin_layout Author
+Daniel Vedder
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+1,2,3
+\end_layout
+
+\end_inset
+
+,
+ Marco Matthies
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+1,3
+\end_layout
+
+\end_inset
+
+,
+ Gabriel Díaz Iturry
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+1,3
+\end_layout
+
+\end_inset
+
+,
+ Guy Pe'er
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+1,3
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Abstract
+abstract here
+\begin_inset Newline newline
+\end_inset
+
+
+\series bold
+Keywords:
+ 
+\series default
+individual-based model,
+ agriculture,
+ biodiversity,
+ social-ecological system
+\end_layout
+
+\begin_layout Standard
+\begin_inset Note Note
+status open
+
+\begin_layout Plain Layout
+https://www.sciencedirect.com/journal/environmental-modelling-and-software/publish/guide-for-authors
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Standard
+
+\size footnotesize
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+
+\size footnotesize
+1 
+\end_layout
+
+\end_inset
+
+Department of Biodiversity and People,
+ Helmholtz Centre for Environmental Research - UFZ,
+ Permoserstraße 15,
+ 04318 Leipzig,
+ Germany
+\end_layout
+
+\begin_layout Standard
+
+\size footnotesize
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+
+\size footnotesize
+2 
+\end_layout
+
+\end_inset
+
+Institute of Biodiversity,
+ Friedrich Schiller University Jena,
+ Dornburger Straße 159,
+ 07743 Jena,
+ Germany
+\end_layout
+
+\begin_layout Standard
+
+\size footnotesize
+\begin_inset script superscript
+
+\begin_layout Plain Layout
+
+\size footnotesize
+3
+\end_layout
+
+\end_inset
+
+ German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig,
+ Puschstraße 4,
+ 04103 Leipzig,
+ Germany
+\end_layout
+
+\begin_layout Standard
+\begin_inset ERT
+status open
+
+\begin_layout Plain Layout
+
+
+\backslash
+linenumbers
+\end_layout
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Section
+Introduction
+\end_layout
+
+\begin_layout Itemize
+context
+\end_layout
+
+\begin_layout Itemize
+motivation
+\end_layout
+
+\begin_layout Section
+Methods
+\end_layout
+
+\begin_layout Subsection
+Model description
+\end_layout
+
+\begin_layout Itemize
+components:
+ farm,
+ crops,
+ species
+\end_layout
+
+\begin_layout Itemize
+input data,
+ parameters & variables,
+ sources
+\end_layout
+
+\begin_layout Itemize
+usage & availability
+\end_layout
+
+\begin_layout Subsection
+Model validation
+\end_layout
+
+\begin_layout Itemize
+AquaCrop:
+ yield & phenology
+\end_layout
+
+\begin_layout Itemize
+farm management cycle:
+ sowing,
+ mowing,
+ harvest
+\end_layout
+
+\begin_layout Itemize
+species:
+ habitat use,
+ territories,
+ life cycle
+\end_layout
+
+\begin_layout Subsection
+Model application
+\end_layout
+
+\begin_layout Itemize
+comparison of extensive & intensive management
+\end_layout
+
+\begin_layout Itemize
+ecological traps
+\end_layout
+
+\begin_layout Section
+Results
+\end_layout
+
+\begin_layout Subsection
+Model validation
+\end_layout
+
+\begin_layout Subsection
+Model application
+\end_layout
+
+\begin_layout Section
+Discussion
+\end_layout
+
+\begin_layout Itemize
+purpose,
+ possibilities,
+ strengths & weaknesses
+\end_layout
+
+\begin_layout Itemize
+comparison to ALMaSS and other models
+\end_layout
+
+\begin_layout Itemize
+future plans
+\end_layout
+
+\begin_layout Section
+Conclusion
+\end_layout
+
+\begin_layout Subsection*
+
+\size small
+Acknowledgments
+\end_layout
+
+\begin_layout Standard
+DV,
+ MM,
+ and GDI are funded through the project CAP4GI by the Federal Ministry of Education and Research (BMBF),
+ within the framework of the Strategy,
+ Research for Sustainability (FONA,
+ www.fona.de/en) as part of its Social-Ecological Research funding priority,
+ funding no.
+ 01UT2102A.
+ Responsibility for the content of this publication lies with the authors.
+ DV,
+ MM,
+ and GP gratefully acknowledge the support of iDiv,
+ funded by the German Research Foundation (DFG–FZT 118,
+ 202548816).
+\end_layout
+
+\begin_layout Subsection*
+
+\size small
+Data availability
+\end_layout
+
+\begin_layout Standard
+
+\size small
+The Persefone.jl source code and relevant input files are archived on Zenodo 
+\begin_inset Note Note
+status open
+
+\begin_layout Plain Layout
+todo
+\end_layout
+
+\end_inset
+
+.
+ The development version is available at 
+\begin_inset CommandInset href
+LatexCommand href
+target "https://git.idiv.de/persefone/persefone-model"
+literal "true"
+
+\end_inset
+
+.
+\end_layout
+
+\begin_layout Subsection*
+
+\size small
+Author contributions
+\end_layout
+
+\begin_layout Standard
+\begin_inset CommandInset bibtex
+LatexCommand bibtex
+btprint "btPrintCited"
+bibfiles "zosterops"
+options "apacitex"
+
+\end_inset
+
+
+\end_layout
+
+\end_body
+\end_document