diff --git a/.nojekyll b/.nojekyll index 701ac63..698f477 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -b8d9590b \ No newline at end of file +93deffdf \ No newline at end of file diff --git a/_tex/index.tex b/_tex/index.tex index 9f4f18c..b3bfc61 100644 --- a/_tex/index.tex +++ b/_tex/index.tex @@ -75,6 +75,39 @@ \makeatletter \def\fps@figure{htbp} \makeatother +% definitions for citeproc citations +\NewDocumentCommand\citeproctext{}{} +\NewDocumentCommand\citeproc{mm}{% + \begingroup\def\citeproctext{#2}\cite{#1}\endgroup} +\makeatletter + % allow citations to break across lines + \let\@cite@ofmt\@firstofone + % avoid brackets around text for \cite: + \def\@biblabel#1{} + \def\@cite#1#2{{#1\if@tempswa , #2\fi}} +\makeatother +\newlength{\cslhangindent} +\setlength{\cslhangindent}{1.5em} +\newlength{\csllabelwidth} +\setlength{\csllabelwidth}{3em} +\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing + {\begin{list}{}{% + \setlength{\itemindent}{0pt} + \setlength{\leftmargin}{0pt} + \setlength{\parsep}{0pt} + % turn on hanging indent if param 1 is 1 + \ifodd #1 + \setlength{\leftmargin}{\cslhangindent} + \setlength{\itemindent}{-1\cslhangindent} + \fi + % set entry spacing + \setlength{\itemsep}{#2\baselineskip}}} + {\end{list}} +\usepackage{calc} +\newcommand{\CSLBlock}[1]{\hfill\break\parbox[t]{\linewidth}{\strut\ignorespaces#1\strut}} +\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{\strut#1\strut}} +\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{\strut#1\strut}} +\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1} \usepackage{url} %this package should fix any errors with URLs in refs. \usepackage{lineno} @@ -173,9 +206,8 @@ \section{Data \& Methods}\label{sec-data-methods} \subsection{Metacommunity model}\label{metacommunity-model} -The metacommunity model developed by -(\textbf{thompsonDispersalGovernsReorganization2017a?}) is a good -starting point to use for this `case study' as it allows us some +The metacommunity model developed by Thompson \& Gonzalez (2017) is a +good starting point to use for this `case study' as it allows us some flexibility with how we want to parameterise the system. The model (Equation~\ref{eq-metacomm}) itself is based on a tritrophic community (`plants', `herbivores', and `carnivores') and is a collection of @@ -297,9 +329,9 @@ \subsection{Spatial wombling}\label{spatial-wombling} }\end{equation} The spatial wombling analyses were done using -\texttt{SpatialBoundaries.jl} -(\textbf{strydomSpatialBoundariesJlEdge2023?}). The docuemntation -provides a more detailed breakdown of the underlying methodology. +\texttt{SpatialBoundaries.jl} (Strydom \& Poisot, 2023). The +docuemntation provides a more detailed breakdown of the underlying +methodology. \section{Conclusion}\label{conclusion} @@ -312,6 +344,21 @@ \section*{References}\label{references} \href{https://PoisotLab.github.io/ms_womble_ya_net/index.qmd.html}{Article Notebook}} +\phantomsection\label{refs} +\begin{CSLReferences}{1}{0} +\bibitem[\citeproctext]{ref-Strydom2023Spatialboundariesa} +Strydom, T., \& Poisot, T. (2023). {SpatialBoundaries}.jl: Edge +detection using spatial wombling. \emph{Ecography}, \emph{2023}(5), +e06609. \url{https://doi.org/10.1111/ecog.06609} + +\bibitem[\citeproctext]{ref-Thompson2017Dispersala} +Thompson, P. L., \& Gonzalez, A. (2017). Dispersal governs the +reorganization of ecological networks under environmental change. +\emph{Nature Ecology \& Evolution}, \emph{1}(6). +\url{https://doi.org/10.1038/s41559-017-0162} + +\end{CSLReferences} + \end{document} diff --git a/index-meca.zip b/index-meca.zip index 8af81f9..b2e4256 100644 Binary files a/index-meca.zip and b/index-meca.zip differ diff --git a/index.docx b/index.docx index 22115f3..5a327c1 100644 Binary files a/index.docx and b/index.docx differ diff --git a/index.html b/index.html index 5312df9..3bcce94 100644 --- a/index.html +++ b/index.html @@ -28,6 +28,7 @@ div.csl-bib-body { } div.csl-entry { clear: both; + margin-bottom: 0em; } .hanging-indent div.csl-entry { margin-left:2em; @@ -216,7 +217,7 @@

2 Data & Methods

2.1 Metacommunity model

-

The metacommunity model developed by (thompsonDispersalGovernsReorganization2017a?) is a good starting point to use for this ‘case study’ as it allows us some flexibility with how we want to parameterise the system. The model (Equation 1) itself is based on a tritrophic community (‘plants’, ‘herbivores’, and ‘carnivores’) and is a collection of modified Lotka–Volterra equations and (broadly) models species abundance as a function of interaction strength, environmental effect, immigration, and emigration. The metacommunity consists of \(S\) species with \(M\) environmental patches and looks as follows:

+

The metacommunity model developed by Thompson and Gonzalez (2017) is a good starting point to use for this ‘case study’ as it allows us some flexibility with how we want to parameterise the system. The model (Equation 1) itself is based on a tritrophic community (‘plants’, ‘herbivores’, and ‘carnivores’) and is a collection of modified Lotka–Volterra equations and (broadly) models species abundance as a function of interaction strength, environmental effect, immigration, and emigration. The metacommunity consists of \(S\) species with \(M\) environmental patches and looks as follows:

\[ X_{ij}(t+1)=X_{ij}(t)exp\left[C_{i} + \sum_{k=1}^{S}B_{ik}X_{kj}(t)+A_{ij}(t)\right]+I_{ij}(t)-X_{ij}(t)a_{i} \tag{1}\]

@@ -332,7 +333,7 @@

\[ m = \sqrt{\frac{\partial f(x,y)}{\partial x}^2 + \frac{\partial f(x,y)}{\partial y}^2} \tag{4}\]

-

The spatial wombling analyses were done using SpatialBoundaries.jl (strydomSpatialBoundariesJlEdge2023?). The docuemntation provides a more detailed breakdown of the underlying methodology.

+

The spatial wombling analyses were done using SpatialBoundaries.jl (Strydom and Poisot 2023). The docuemntation provides a more detailed breakdown of the underlying methodology.

@@ -340,8 +341,13 @@

References

-
- +
+
+Strydom, Tanya, and Timothée Poisot. 2023. “SpatialBoundaries.jl: Edge Detection Using Spatial Wombling.” Ecography 2023 (5): e06609. https://doi.org/10.1111/ecog.06609. +
+
+Thompson, Patrick L., and Andrew Gonzalez. 2017. “Dispersal Governs the Reorganization of Ecological Networks Under Environmental Change.” Nature Ecology & Evolution 1 (6). https://doi.org/10.1038/s41559-017-0162. +

diff --git a/index.pdf b/index.pdf index 9c17822..ba9379f 100644 Binary files a/index.pdf and b/index.pdf differ diff --git a/index.xml b/index.xml index 3181e7d..8f752f5 100644 --- a/index.xml +++ b/index.xml @@ -140,8 +140,8 @@ Nacional (IGN). …

2 Data & Methods 2.1 Metacommunity model -

The metacommunity model developed by - (thompsonDispersalGovernsReorganization2017a?) +

The metacommunity model developed by Thompson and Gonzalez + (2017) is a good starting point to use for this ‘case study’ as it allows us some flexibility with how we want to parameterise the system. The model (Equation 1) @@ -432,20 +432,53 @@ Nacional (IGN). …

m=∂f(x,y)∂x2+∂f(x,y)∂y2(4)

The spatial wombling analyses were done using SpatialBoundaries.jl - (strydomSpatialBoundariesJlEdge2023?). - The docuemntation provides a more detailed breakdown of the - underlying methodology.

+ (Strydom + and Poisot 2023). The docuemntation provides a more detailed + breakdown of the underlying methodology.

 3 Conclusion - - References - + + References + + + + StrydomTanya + PoisotTimothée + + SpatialBoundaries.jl: Edge detection using spatial wombling + Ecography + 2023 + 2023 + 5 + 1600-0587 + 10.1111/ecog.06609 + e06609 + + + + + + + ThompsonPatrick L. + GonzalezAndrew + + Dispersal governs the reorganization of ecological networks under environmental change + Nature Ecology & Evolution + Nature Publishing Group + London, United States + 201706 + 1 + 6 + 10.1038/s41559-017-0162 + + + diff --git a/notebooks/data-screening-preview.html b/notebooks/data-screening-preview.html index ca1f1c9..6d61408 100644 --- a/notebooks/data-screening-preview.html +++ b/notebooks/data-screening-preview.html @@ -896,7 +896,7 @@

Timeline Plot

} } }); -