test citation

paper.bib

@@ -1,59 +1,45 @@
-@article{Pearson:2017,
-  	url = {http://adsabs.harvard.edu/abs/2017arXiv170304627P},
-  	Archiveprefix = {arXiv},
-  	Author = {{Pearson}, S. and {Price-Whelan}, A.~M. and {Johnston}, K.~V.},
-  	Eprint = {1703.04627},
-  	Journal = {ArXiv e-prints},
-  	Keywords = {Astrophysics - Astrophysics of Galaxies},
-  	Month = mar,
-  	Title = {{Gaps in Globular Cluster Streams: Pal 5 and the Galactic Bar}},
-  	Year = 2017
+@article{scheffer2009early,
+  title={Early-warning signals for critical transitions},
+  author={Scheffer, Marten and Bascompte, Jordi and Brock, William A and Brovkin, Victor and Carpenter, Stephen R and Dakos, Vasilis and Held, Hermann and Van Nes, Egbert H and Rietkerk, Max and Sugihara, George},
+  journal={Nature},
+  volume={461},
+  number={7260},
+  pages={53--59},
+  year={2009},
+  publisher={Nature Publishing Group}
 }
 
-@book{Binney:2008,
-  	url = {http://adsabs.harvard.edu/abs/2008gady.book.....B},
-  	Author = {{Binney}, J. and {Tremaine}, S.},
-  	Booktitle = {Galactic Dynamics: Second Edition, by James Binney and Scott Tremaine.~ISBN 978-0-691-13026-2 (HB).~Published by Princeton University Press, Princeton, NJ USA, 2008.},
-  	Publisher = {Princeton University Press},
-  	Title = {{Galactic Dynamics: Second Edition}},
-  	Year = 2008
+@article{clements2018indicators,
+  title={Indicators of transitions in biological systems},
+  author={Clements, Christopher F and Ozgul, Arpat},
+  journal={Ecology letters},
+  volume={21},
+  number={6},
+  pages={905--919},
+  year={2018},
+  publisher={Wiley Online Library}
 }
 
-@article{gaia,
-    author = {{Gaia Collaboration}},
-    title = "{The Gaia mission}",
-    journal = {Astronomy and Astrophysics},
-    archivePrefix = "arXiv",
-    eprint = {1609.04153},
-    primaryClass = "astro-ph.IM",
-    keywords = {space vehicles: instruments, Galaxy: structure, astrometry, parallaxes, proper motions, telescopes},
-    year = 2016,
-    month = nov,
-    volume = 595,
-    doi = {10.1051/0004-6361/201629272},
-    url = {http://adsabs.harvard.edu/abs/2016A%26A...595A...1G},
+@article{bury2020detecting,
+  title={Detecting and distinguishing tipping points using spectral early warning signals},
+  author={Bury, Thomas M and Bauch, Chris T and Anand, Madhur},
+  journal={Journal of the Royal Society Interface},
+  volume={17},
+  number={170},
+  pages={20200482},
+  year={2020},
+  publisher={The Royal Society}
 }
 
-@article{astropy,
-    author = {{Astropy Collaboration}},
-    title = "{Astropy: A community Python package for astronomy}",
-    journal = {Astronomy and Astrophysics},
-    archivePrefix = "arXiv",
-    eprint = {1307.6212},
-    primaryClass = "astro-ph.IM",
-    keywords = {methods: data analysis, methods: miscellaneous, virtual observatory tools},
-    year = 2013,
-    month = oct,
-    volume = 558,
-    doi = {10.1051/0004-6361/201322068},
-    url = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A}
+@article{bury2021deep,
+  title={Deep learning for early warning signals of tipping points},
+  author={Bury, Thomas M and Sujith, RI and Pavithran, Induja and Scheffer, Marten and Lenton, Timothy M and Anand, Madhur and Bauch, Chris T},
+  journal={Proceedings of the National Academy of Sciences},
+  volume={118},
+  number={39},
+  pages={e2106140118},
+  year={2021},
+  publisher={National Acad Sciences}
 }
 
-@misc{fidgit,
-  author = {A. M. Smith and K. Thaney and M. Hahnel},
-  title = {Fidgit: An ungodly union of GitHub and Figshare},
-  year = {2020},
-  publisher = {GitHub},
-  journal = {GitHub repository},
-  url = {https://github.com/arfon/fidgit}
-}
+

paper.md

@@ -1,115 +1,55 @@
 ---
-title: 'Gala: A Python package for galactic dynamics'
+title: 'ewstools: A Python package for early warning signals of bifurcations in time series data.'
 tags:
   - Python
-  - astronomy
-  - dynamics
-  - galactic dynamics
-  - milky way
+  - time series
+  - early warning signal
+  - tipping point
+  - dynamical system
+  - bifurcation
+
 authors:
-  - name: Adrian M. Price-Whelan
-    orcid: 0000-0000-0000-0000
-    equal-contrib: true
+  - name: Thomas M. Bury
+    orcid: 0000-0003-1595-9444
     affiliation: "1, 2" # (Multiple affiliations must be quoted)
-  - name: Author Without ORCID
-    equal-contrib: true # (This is how you can denote equal contributions between multiple authors)
-    affiliation: 2
-  - name: Author with no affiliation
-    corresponding: true # (This is how to denote the corresponding author)
-    affiliation: 3
 affiliations:
- - name: Lyman Spitzer, Jr. Fellow, Princeton University, USA
+ - name: Department of Physiology, McGill University, Montréal, Canada
    index: 1
- - name: Institution Name, Country
+ - name: Department of Applied Mathematics, University of Waterloo, Waterloo, Canada
    index: 2
- - name: Independent Researcher, Country
-   index: 3
-date: 13 August 2017
+date: 17 August 2022
 bibliography: paper.bib
 
-# Optional fields if submitting to a AAS journal too, see this blog post:
-# https://blog.joss.theoj.org/2018/12/a-new-collaboration-with-aas-publishing
-aas-doi: 10.3847/xxxxx <- update this with the DOI from AAS once you know it.
-aas-journal: Astrophysical Journal <- The name of the AAS journal.
----
 
 # Summary
 
-The forces on stars, galaxies, and dark matter under external gravitational
-fields lead to the dynamical evolution of structures in the universe. The orbits
-of these bodies are therefore key to understanding the formation, history, and
-future state of galaxies. The field of "galactic dynamics," which aims to model
-the gravitating components of galaxies to study their structure and evolution,
-is now well-established, commonly taught, and frequently used in astronomy.
-Aside from toy problems and demonstrations, the majority of problems require
-efficient numerical tools, many of which require the same base code (e.g., for
-performing numerical orbit integration).
-
-# Statement of need
-
-`Gala` is an Astropy-affiliated Python package for galactic dynamics. Python
-enables wrapping low-level languages (e.g., C) for speed without losing
-flexibility or ease-of-use in the user-interface. The API for `Gala` was
-designed to provide a class-based and user-friendly interface to fast (C or
-Cython-optimized) implementations of common operations such as gravitational
-potential and force evaluation, orbit integration, dynamical transformations,
-and chaos indicators for nonlinear dynamics. `Gala` also relies heavily on and
-interfaces well with the implementations of physical units and astronomical
-coordinate systems in the `Astropy` package [@astropy] (`astropy.units` and
-`astropy.coordinates`).
-
-`Gala` was designed to be used by both astronomical researchers and by
-students in courses on gravitational dynamics or astronomy. It has already been
-used in a number of scientific publications [@Pearson:2017] and has also been
-used in graduate courses on Galactic dynamics to, e.g., provide interactive
-visualizations of textbook material [@Binney:2008]. The combination of speed,
-design, and support for Astropy functionality in `Gala` will enable exciting
-scientific explorations of forthcoming data releases from the *Gaia* mission
-[@gaia] by students and experts alike.
-
-# Mathematics
-
-Single dollars ($) are required for inline mathematics e.g. $f(x) = e^{\pi/x}$
+Many systems across nature and society have the capacity to undergo an abrupt and 
+profound change in their dynamics. From a dynamical systemes perspective, these events 
+are often associated with the crossing of a bifurcation. Early warning signals (EWS) 
+for bifurcations are therefore in high demand. Two commonly used EWS for bifurcations 
+are variance and lag-1 autocorrelation, that are expected to increase prior to many 
+bifurcations due to critical slowing down [@scheffer2009early]. There now exist a 
+wealth of other EWS based on changes in time series dynamics that are expected to occur 
+prior to bifurcations [@clements2018indicators]. More recently, deep learning 
+classifiers have been trained and applied to detect bifurcations, with promising 
+results [@bury2021deep]
 
-Double dollars make self-standing equations:
 
-$$\Theta(x) = \left\{\begin{array}{l}
-0\textrm{ if } x < 0\cr
-1\textrm{ else}
-\end{array}\right.$$
 
-You can also use plain \LaTeX for equations
-\begin{equation}\label{eq:fourier}
-\hat f(\omega) = \int_{-\infty}^{\infty} f(x) e^{i\omega x} dx
-\end{equation}
-and refer to \autoref{eq:fourier} from text.
-
-# Citations
-
-Citations to entries in paper.bib should be in
-[rMarkdown](http://rmarkdown.rstudio.com/authoring_bibliographies_and_citations.html)
-format.
-
-If you want to cite a software repository URL (e.g. something on GitHub without a preferred
-citation) then you can do it with the example BibTeX entry below for @fidgit.
-
-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)"
+# Statement of need
 
-# Figures
+`ewstools` is a Python package for computing, analysing, and visualising
+early warning signals in time series data.
 
-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
 
-We acknowledge contributions from Brigitta Sipocz, Syrtis Major, and Semyeong
-Oh, and support from Kathryn Johnston during the genesis of this project.
+TB acknowledge contributions from Chris Bauch on code for training deep learning 
+classifiers. This project is currently supported by the
+Fonds de recherche du Québec (FRQ), 
+and has received funding in the past from the
+Natural Sciences and Engineering Research Council of Canada (NSERC).
+
 
 # References