inst/ms/som.md

In seananderson/metafolio: Metapopulation Simulations for Conserving Salmon Through Portfolio Optimization

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Appendices

Portfolio conservation of metapopulations under climate change

Sean C. Anderson, Jonathan W. Moore, Michelle M. McClure, Nicholas K. Dulvy, Andrew B. Cooper

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\textsc{Appendix A.} The metafolio \textsf{R} package.

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The metafolio \textsf{R} package contains the functions and code to carry out the analyses in our paper. metafolio. The package can be installed from CRAN with:

install.packages("metafolio")

Alternatively, you can view the code and install the package from http://github.com/seananderson/metafolio.

The included vignette describes the package and illustrates some example simulations. You can view the vignette with:

vignette("metafolio")

You can view the help for the package with:

?metafolio
help(package = "metafolio")

The figures from this paper can be re-created by downloading the code from GitHub and sourcing the file README.R in the inst/examples folder:

setwd("metafolio/inst/examples")
source("README.R")

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\textsc{Appendix B.} Simulation input parameters and default values.

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\textsc{Appendix C.} An example straying matrix.

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\begin{figure}[htbp] \centering \includegraphics[width=3.5in]{../examples/stray-matrix} \caption{An example straying matrix. The rows and columns represent different populations (indicated by population number). Dark blue indicates a high rate of straying and light blue indicates a low rate of straying.} \label{f:stray} \end{figure} \clearpage

\textsc{Appendix D.} Sensitivity illustration with alternative parameter values. \renewcommand{\thefigure}{D\arabic{figure}} \setcounter{figure}{0}

\begin{figure}[htbp] \centering \includegraphics[width=3.5in]{../examples/plot-various-options-ts-3pops} \caption{The impact of increasing or decreasing various parameter values on metapopulation return abundance. The different coloured lines represent three example salmon populations. The base case represents the base-case values for the short-term environmental fluctuation scenario.} \label{f:eg-sens} \end{figure} \clearpage

\textsc{Appendix E.} An illustration of the correlation between populations. \renewcommand{\thefigure}{E\arabic{figure}} \setcounter{figure}{0}

\begin{figure}[htbp] \centering \includegraphics[width=4.5in]{../examples/example-return-correlations} \caption{A comparison of the log(returns) between populations. The subpopulation IDs are coloured from warm tolerant (warm colours) to cool tolerant (cool colours). Note how populations 1 and 10 have asynchronous returns whereas populations with more similar thermal-tolerance curves (say populations 9 and 10) have more synchronous dynamics. Populations with thermal tolerance curves in the middle (e.g. population 6) are less correlated with other populations. Their population dynamics end up primarily driven by demographic stochasticity and less so by temperature-induced systematic changes in productivity.} \label{f:ret-corr} \end{figure} \clearpage

\textsc{Appendix F.} Example simulated time series from alternative conservation scenarios. \renewcommand{\thefigure}{F\arabic{figure}} \setcounter{figure}{0}

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/spatial-arma-sim-full-colour} \caption{Conserving a \textbf{full range} of response diversity (spatial conservation strategy) with \textbf{short-term} environmental fluctuations. This is the same as Fig.~3 but in colour.} \label{f:eg-sp-arma-full} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/spatial-arma-sim-onehalf} \caption{Conserving \textbf{one half} of response diversity (spatial conservation strategy) with \textbf{short-term} environmental fluctuations.} \label{f:eg-sp-arma-half} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/spatial-linear-sim-full} \caption{Conserving a \textbf{full range} of response diversity (spatial conservation strategy) with \textbf{long-term} environmental change.} \label{f:eg-sp-linear-full} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/spatial-linear-sim-onehalf} \caption{Conserving \textbf{one half} of response diversity (spatial conservation strategy) with \textbf{long-term} environmental change.} \label{f:eg-sp-linear-half} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/n-arma-sim-2} \caption{\textbf{Two populations} conserved with random response diversity and \textbf{short-term} environmental fluctuations.} \label{f:eg-n-arma-two} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/n-arma-sim-16} \caption{\textbf{Sixteen populations} conserved with random response diversity and \textbf{short-term} environmental fluctuations.} \label{f:eg-n-arma-sixteen} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/n-linear-sim-2} \caption{\textbf{Two populations} conserved with random response diversity and \textbf{long-term} environmental change.} \label{f:eg-n-linear-two} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/n-linear-sim-16} \caption{\textbf{Sixteen populations} conserved with random response diversity and \textbf{long-term} environmental change.} \label{f:eg-n-linear-sixteen} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/n-linear-arma-sim-2-squeeze} \caption{\textbf{Two populations} conserved with random response diversity and \textbf{long-term declining stream flow}.} \label{f:eg-n-squeeze-two} \end{figure} \clearpage

\begin{figure}[htbp] \centering \includegraphics[width=4.3in]{../examples/n-linear-arma-sim-16-squeeze} \caption{\textbf{Sixteen populations} conserved with random response diversity and \textbf{long-term declining stream flow}.} \label{f:eg-n-squeeze-twelve} \end{figure}

seananderson/metafolio documentation built on Feb. 13, 2024, 5:47 a.m.