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 \IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
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 \hypersetup{
-  pdftitle={La Palma Earthquakes},
-  pdfauthor={Steve Purves; Rowan Cockett},
-  pdfkeywords={La Palma, Earthquakes},
+  pdftitle={T is for Topology},
+  pdfauthor={Tanya Strydom; Andrew P. Beckerman},
+  pdfkeywords={food web, network construction},
   colorlinks=true,
   linkcolor={blue},
   filecolor={Maroon},
@@ -178,143 +178,147 @@
 \draftfalse
 
 \begin{document}
-\title{La Palma Earthquakes}
+\title{T is for Topology}
 
-\authors{Steve Purves\affil{1}, Rowan Cockett\affil{1}}
-\affiliation{1}{Curvenote, }
-\correspondingauthor{Steve Purves}{steve@curvenote.com}
+\authors{Tanya Strydom\affil{1}, Andrew P. Beckerman\affil{1}}
+\affiliation{1}{University of Sheffield, }
+\correspondingauthor{Tanya Strydom}{t.strydom@sheffield.ac.uk}
 
 
 \begin{abstract}
-In September 2021, a significant jump in seismic activity on the island
-of La Palma (Canary Islands, Spain) signaled the start of a volcanic
-crisis that still continues at the time of writing. Earthquake data is
-continually collected and published by the Instituto Geográphico
-Nacional (IGN). \ldots{}
+Pending\ldots{}
 \end{abstract}
 
 \section*{Plain Language Summary}
-Earthquake data for the island of La Palma from the September 2021
-eruption is found \ldots{}
+We want to know a bit more about the different network topology
+generators (predict tools) and how they differ - \emph{i.e.,} their
+strengths and weaknesses
 
 
 
 \section{Introduction}\label{introduction}
 
-\textsubscript{Source:
-\href{https://BecksLab.github.io/ms_t_is_for_topology/index.qmd.html}{Article
-Notebook}}
-
-\textsubscript{Source:
-\href{https://BecksLab.github.io/ms_t_is_for_topology/index.qmd.html}{Article
-Notebook}}
-
-\begin{figure}[H]
-
-\centering{
-
-\includegraphics{index_files/figure-pdf/fig-timeline-output-1.pdf}
-
-}
-
-\caption{\label{fig-timeline}Timeline of recent earthquakes on La Palma}
-
-\end{figure}%
-
-\textsubscript{Source:
-\href{https://BecksLab.github.io/ms_t_is_for_topology/index.qmd.html}{Article
-Notebook}}
-
-\textsubscript{Source:
-\href{https://BecksLab.github.io/ms_t_is_for_topology/index.qmd.html}{Article
-Notebook}}
-
-Based on data up to and including 1971, eruptions on La Palma happen
-every 79.8 years on average.
-
-Studies of the magma systems feeding the volcano, such as Marrero et al.
-(2019), have proposed that there are two main magma reservoirs feeding
-the Cumbre Vieja volcano; one in the mantle (30-40km depth) which
-charges and in turn feeds a shallower crustal reservoir (10-20km depth).
-
-Eight eruptions have been recorded since the late 1400s
-(Figure~\ref{fig-timeline}).
+The standard run of the mill that we cannot always feasibly make network
+predictions because 1. hard, 2. time (prehistoric mostly), and 3.
+probably something else meaningful that's just slipping my mind at the
+moment.
+
+Maybe a brief history of the development of predictive tools? Sort of
+where the theory/body of work was based and how that has changed?
+
+Maybe start here already about discussing the core mechanistic
+differences that models will work at - some are really concerned (and
+thus constrained by) structure, others are more mechanistic in nature
+\emph{i.e.,} species \emph{a} had the capacity to eat species \emph{b},
+and then you get Rohr et al. (2010) and Strydom et al. (2022) that sit
+in the weird latent space\ldots{}
+
+At some point we are going to need to discuss the key difference and
+implication between a metaweb and a network realisation.
+
+\begin{quote}
+Do we need to delve into individual-based networks? (\emph{sensu} Tinker
+2012, Araújo 2008) I think its probably a step too far and one starts
+delving into apples and pears type of comparisons. Especially since
+these work off of already existing networks and its more about about
+`tweaking' those - so not so much \emph{de novo} predictions. Although
+this might be useful to keep in mind when it comes to re-wiring\ldots{}
+Also on that note do we opn the re-wiring door here in this ms or wait
+it out a bit.
+\end{quote}
 
-Data and methods are discussed in Section~\ref{sec-data-methods}.
-
-Let \(x\) denote the number of eruptions in a year. Then, \(x\) can be
-modeled by a Poisson distribution
+\section{Data \& Methods}\label{sec-data-methods}
 
-\begin{equation}\phantomsection\label{eq-poisson}{
-p(x) = \frac{e^{-\lambda} \lambda^{x}}{x !}
-}\end{equation}
+\subsection{Overview of topology
+generators}\label{overview-of-topology-generators}
 
-where \(\lambda\) is the rate of eruptions per year. Using
-Equation~\ref{eq-poisson}, the probability of an eruption in the next
-\(t\) years can be calculated.
+I know table are awful but in this case they may make more sense
 
-\begin{longtable}[]{@{}ll@{}}
-\caption{Recent historic eruptions on La
-Palma}\label{tbl-history}\tabularnewline
+\begin{longtable}[]{@{}
+  >{\raggedright\arraybackslash}p{(\columnwidth - 4\tabcolsep) * \real{0.2235}}
+  >{\raggedright\arraybackslash}p{(\columnwidth - 4\tabcolsep) * \real{0.5412}}
+  >{\raggedright\arraybackslash}p{(\columnwidth - 4\tabcolsep) * \real{0.2353}}@{}}
+\caption{Lets make a table that gives an overview of the different
+topology generators that we will look
+at}\label{tbl-history}\tabularnewline
 \toprule\noalign{}
-Name & Year \\
+\begin{minipage}[b]{\linewidth}\raggedright
+Model
+\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
+Reference
+\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
+Core Mechanism
+\end{minipage} \\
 \midrule\noalign{}
 \endfirsthead
 \toprule\noalign{}
-Name & Year \\
+\begin{minipage}[b]{\linewidth}\raggedright
+Model
+\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
+Reference
+\end{minipage} & \begin{minipage}[b]{\linewidth}\raggedright
+Core Mechanism
+\end{minipage} \\
 \midrule\noalign{}
 \endhead
 \bottomrule\noalign{}
 \endlastfoot
-Current & 2021 \\
-Teneguía & 1971 \\
-Nambroque & 1949 \\
-El Charco & 1712 \\
-Volcán San Antonio & 1677 \\
-Volcán San Martin & 1646 \\
-Tajuya near El Paso & 1585 \\
-Montaña Quemada & 1492 \\
+Niche model & Cohen et al. (1997) & structural \\
+Cascade model & Williams \& Martinez (2000) & structural \\
+PFIM & Shaw et al. (2024) & mechanistic \\
+Log-ratio & Rohr et al. (2010) & latent trait space \\
+Nested hierarchy & Cattin et al. (2004) & \\
+ADBM & Petchey et al. (2008) & mechanistic \\
+Stochastic & Rossberg et al. (2006) & \\
+Transfer learning & Strydom et al. (2022) & latent trait space \\
+Trait-based & Caron et al. (2022) & mechanistic \\
 \end{longtable}
 
-Table~\ref{tbl-history} summarises the eruptions recorded since the
-colonization of the islands by Europeans in the late 1400s.
-
-\begin{figure}
-
-\centering{
-
-\includegraphics{images/la-palma-map.png}
-
-}
-
-\caption{\label{fig-map}Map of La Palma}
-
-\end{figure}%
-
-La Palma is one of the west most islands in the Volcanic Archipelago of
-the Canary Islands (Figure~\ref{fig-map}).
-
-\begin{figure}[H]
-
-\centering{
-
-\includegraphics{index_files/figure-latex/notebooks-data-screening-fig-spatial-plot-output-1.png}
-
-}
-
-\caption{\label{fig-spatial-plot}Locations of earthquakes on La Palma
-since 2017.}
-
-\end{figure}%
-
-\textsubscript{Source:
-\href{https://BecksLab.github.io/ms_t_is_for_topology/index.qmd.html}{Article
-Notebook}}
-
-Figure~\ref{fig-spatial-plot} shows the location of recent Earthquakes
-on La Palma.
-
-\section{Data \& Methods}\label{sec-data-methods}
+\subsection{Datasets used}\label{datasets-used}
+
+Here I think we need to span a variety of domains, at minimum aquatic
+and terrestrial but maybe there should be a `scale' element as well
+\emph{i.e.,} a regional and local network. I think there is going to be
+a `turning point' where structural will take over from mechanistic in
+terms of performance. More specifically at local scales bioenergetic
+constraints (and co-occurrence) may play a bigger role in structuring a
+network whereas at the metaweb level then mechanistic may make more
+(since by default its about who can potentially interact and obviously
+not constrained by real-world scenarios) \emph{sensu} Caron et al.
+(2023)
+
+\section{Results}\label{results}
+
+How we want to compare and contrast. I think there won't be a `winner'
+and thus we need to think of `tests' that are going to measure
+performance in different situations/settings. With that in mind I think
+some valuable points to consider would be:
+
+\begin{itemize}
+\tightlist
+\item
+  Structural vs pairwise link predictions (graph vs node level)
+
+  \begin{itemize}
+  \tightlist
+  \item
+    \% of links correctly retrieved
+  \item
+    connectence
+  \item
+    trophic level
+  \item
+    generalism vs specialism
+  \item
+    something related to false positives/negatives
+  \end{itemize}
+\item
+  Data `cost' (some methods might need a lot lot of supporting data vs
+  something very light weight)
+\item
+  I think it would be remiss to also take into consideration
+  computational cost
+\end{itemize}
 
 \section{Conclusion}\label{conclusion}
 
@@ -329,12 +333,65 @@ \section*{References}\label{references}
 
 \phantomsection\label{refs}
 \begin{CSLReferences}{1}{0}
-\bibitem[\citeproctext]{ref-marrero2019}
-Marrero, J., García, A., Berrocoso, M., Llinares, Á., Rodríguez-Losada,
-A., \& Ortiz, R. (2019). Strategies for the development of volcanic
-hazard maps in monogenetic volcanic fields: The example of {La} {Palma}
-({Canary} {Islands}). \emph{Journal of Applied Volcanology}, \emph{8}.
-\url{https://doi.org/10.1186/s13617-019-0085-5}
+\bibitem[\citeproctext]{ref-caronAddressingEltonianShortfall2022}
+Caron, D., Maiorano, L., Thuiller, W., \& Pollock, L. J. (2022).
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+
+\bibitem[\citeproctext]{ref-caronTrophicInteractionModels2023}
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+
+\bibitem[\citeproctext]{ref-cattinPhylogeneticConstraintsAdaptation2004}
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+
+\bibitem[\citeproctext]{ref-cohenStochasticTheoryCommunity1997}
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+
+\bibitem[\citeproctext]{ref-petcheySizeForagingFood2008}
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+National Academy of Sciences}, \emph{105}(11), 4191--4196.
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+
+\bibitem[\citeproctext]{ref-rohrModelingFoodWebs2010}
+Rohr, R. P., Scherer, H., Kehrli, P., Mazza, C., \& Bersier, L.-F.
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+
+\bibitem[\citeproctext]{ref-rossbergFoodWebsExperts2006}
+Rossberg, A. G., Matsuda, H., Amemiya, T., \& Itoh, K. (2006). Food
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+
+\bibitem[\citeproctext]{ref-shawFrameworkReconstructingAncient2024}
+Shaw, J. O., Dunhill, A. M., Beckerman, A. P., Dunne, J. A., \& Hull, P.
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+
+\bibitem[\citeproctext]{ref-strydomFoodWebReconstruction2022}
+Strydom, T., Bouskila, S., Banville, F., Barros, C., Caron, D., Farrell,
+M. J., et al. (2022). Food web reconstruction through phylogenetic
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+\url{https://doi.org/10.1111/2041-210X.13835}
+
+\bibitem[\citeproctext]{ref-williamsSimpleRulesYield2000}
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 \end{CSLReferences}