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<h2class="anchored" data-anchor-id="what-to-bring">What to bring</h2>
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<li>Laptop (highly, highly, <strong>highly</strong> recommend <code>macOS</code>) with internet connection. <strong>Please ensure you have administrator permissions</strong> - consult with your IT department on how to do this. Windows laptops are OK, but the instructors are all macOS natives - we will be using macOS during the workshop, and are unlikely to be able to fix any Windows-related software installation problems that are unfortunately common with some of the tools we’ll be using.</li>
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<li>Laptop (highly, highly, <strong>highly</strong> recommend <code>macOS</code>) with internet connection. <strong>Please ensure you have administrator permissions</strong> - consult with your IT department on how to do this.</li>
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<li>Install the necessary software, listed on the <code>Prerequisites</code> page.</li>
<p>Our course is not intended for absolute beginners in R. While participants don’t need to be highly proficient, a basic understanding of R and programming syntax is required. For example, participants should know how to create an R project and open a script, read in data using commands, make basic plots using <code>base</code> R, and write for loops. A basic understanding of the shell/command line is advantageous, but not required. Further, previous experience using the <code>terra</code> package and working with <code>netCDF</code> files is a plus, but again, not required.</p>
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<p>In addition to having R and RStudio already installed, you will need to install (i) <code>CDO</code>, (ii) <code>NCO</code>, (iii) <code>wget</code>, (iv) <code>Panoply</code> and (v) a suite of R packages.</p>
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<p>Our course is not intended for absolute beginners in <code>R</code>. While participants don’t need to be highly proficient, a basic understanding of <code>R</code> and programming syntax is required. For example, participants should know how to create an <code>R</code> project and open a script, read in data using commands, make basic plots using <code>base</code> R, and write for loops. A basic understanding of the shell/command line is advantageous, but not required. Further, previous experience using the <code>terra</code> package and working with <code>netCDF</code> files is a plus, but again, not required.</p>
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<p>In addition to having <code>R</code> and RStudio already installed, you will need to install (i) <code>CDO</code>, (ii) <code>NCO</code>, (iii) <code>wget</code>, (iv) <code>Panoply</code> and (v) a suite of R packages.</p>
<p>You will need <strong>CDO</strong> (Climate Data Operators) installed prior to the workshop. CDO comprises a suite of over 600 operators for standard (and speedy) processing of climate and forecast model outputs. More information on CDO found <ahref="https://code.mpimet.mpg.de/projects/cdo">here</a>.</p>
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<p>You will need <strong>CDO</strong> (Climate Data Operators) installed prior to the workshop. <code>CDO</code> comprises a suite of over 600 operators for standard (and speedy) processing of climate and forecast model outputs. More information on <code>CDO</code> found <ahref="https://code.mpimet.mpg.de/projects/cdo">here</a>.</p>
<p>The simplest way to install CDO is via Homebrew. If you haven’t already installed Homebrew, do so <ahref="https://brew.sh/">here</a>. Then, open terminal and run the following code:</p>
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<p>The simplest way to install <code>CDO</code> is via Homebrew. If you haven’t already installed Homebrew, do so <ahref="https://brew.sh/">here</a>. Then, open terminal and run the following code:</p>
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<divclass="cell">
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<divclass="sourceCode cell-code" id="cb1"><preclass="sourceCode r code-with-copy"><codeclass="sourceCode r"><spanid="cb1-1"><ahref="#cb1-1" aria-hidden="true" tabindex="-1"></a>brew install cdo</span></code><buttontitle="Copy to Clipboard" class="code-copy-button"><iclass="bi"></i></button></pre></div>
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<p>More information available on the <ahref="https://code.mpimet.mpg.de/projects/cdo/wiki/MacOS_Platform">CDO MacOS website</a>.</p>
<p>CDO is meant for use on POSIX-compatible operating systems (e.g., like Linux and MacOS), so downloading on Windows requires some extra steps.</p>
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<p><code>CDO</code> is meant for use on POSIX-compatible operating systems (e.g., like Linux and MacOS), so downloading on Windows requires some extra steps.</p>
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<p>Recent versions of Windows (>=10) includes an Ubuntu embedded Linux, offering the opportunity to install CDO via Ubuntu’s native package manager. First, install the Ubuntu app from the Microsoft Store application. Then open the Ubuntu terminal and type:</p>
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<divclass="cell">
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<divclass="sourceCode cell-code" id="cb2"><preclass="sourceCode r code-with-copy"><codeclass="sourceCode r"><spanid="cb2-1"><ahref="#cb2-1" aria-hidden="true" tabindex="-1"></a>sudo apt<spanclass="sc">-</span>get upgrade</span>
<p>Similar to CDO, we will install <ahref="https://nco.sourceforge.net/">NCO (netCDF operators)</a>, which are a suite of operators that take netCDF file formats and facilitate file manipulation.</p>
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<p>Similar to <code>CDO</code>, we will install <ahref="https://nco.sourceforge.net/">NCO (netCDF operators)</a>, which are a suite of operators that take netCDF file formats and facilitate file manipulation.</p>
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<h1class="unnumbered">Preface</h1><p><imgsrc="images/cmsi.png" title="R for marine ecologists: wrangling Earth System Model outputs" class="quarto-cover-image img-fluid"></p>
<strong>Instructors:</strong> Jessica Bolin, Mikaela Provost, Nerea Lezama-Ochoa and Mer Pozo Buil</p>
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<p><code>R</code> is undoubtedly the programming language of choice for many marine ecologists. However, navigating the complexities of downloading, processing and wrangling gridded oceanographic data within <code>R</code> can represent a steep learning curve. As climate-related projects continue to receive funding and the impacts of climate variability and change on our oceans become increasingly evident, <strong>the ability to efficiently interact with, and use, Earth System Model (ESM) outputs for our research is more critical than ever</strong>.</p>
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<p>The aim of our one-day <code>R</code> course is to train students, researchers and faculty in skills needed to be proficient in creating projections of physical variables from ESM outputs, with the goal of using them for ecological applications. <strong>Specifically, we’ll be creating projections of sea-surface temperature across two time periods out to 2100, across two climate scenarios, for the California Current region.</strong></p>
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<p>Our workshop is designed around Step 8 (pre-process the data) in the workflow of best practices for using ESMs for marine ecologists, as defined in Figure 1 within <spanclass="citation" data-cites="SCHOEMAN2023">(<ahref="_xxxxxx_references.html#ref-SCHOEMAN2023" role="doc-biblioref">Schoeman et al. 2023</a>)</span>.</p>
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<p>Our workshop is supported by CMSI, and is hosted by Bodega Marine Lab. We thank both organisations for their funding and support.</p>
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"title": "R for marine ecologists: wrangling Earth System Model outputs",
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"text": "Preface\nWorkshop date: 06/03/2025\nLocation: Lecture Hall, Bodega Marine Laboratory\nInstructors: Jessica Bolin, Mikaela Provost, Nerea Lezama-Ochoa and Mer Pozo Buil\nR is undoubtedly the programming language of choice for many marine ecologists. However, navigating the complexities of downloading, processing and wrangling gridded oceanographic data within R can represent a steep learning curve. As climate-related projects continue to receive funding and the impacts of climate variability and change on our oceans become increasingly evident, the ability to efficiently interact with, and use, Earth System Model (ESM) outputs for our research is more critical than ever.\nThe aim of our one-day R course is to train students, researchers and faculty in skills needed to be proficient in creating projections of physical variables from ESM outputs, with the goal of using them for ecological applications. Specifically, we’ll be creating projections of sea-surface temperature across two time periods out to 2100, across two climate scenarios, for the California Current region.\nOur workshop is designed around Step 8 (pre-process the data) in the workflow of best practices for using ESMs for marine ecologists, as defined in Figure 1 within (Schoeman et al. 2023).\nOur workshop is supported by CMSI, and is hosted by Bodega Marine Lab. We thank both organisations for their funding and support.\n\n\n\n\nSchoeman, David S., Alex Sen Gupta, Cheryl S. Harrison, Jason D. Everett, Isaac Brito-Morales, Lee Hannah, Laurent Bopp, Patrick R. Roehrdanz, and Anthony J. Richardson. 2023. “Demystifying Global Climate Models for Use in the Life Sciences.” Trends in Ecology & Evolution 38 (9): 843–58. https://doi.org/https://doi.org/10.1016/j.tree.2023.04.005.",
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"text": "Preface\nPilot workshop date: 06/03/2025\nLocation: Lecture Hall, Bodega Marine Laboratory\nInstructors: Jessica Bolin, Mikaela Provost, Nerea Lezama-Ochoa and Mer Pozo Buil\nR is undoubtedly the programming language of choice for many marine ecologists. However, navigating the complexities of downloading, processing and wrangling gridded oceanographic data within R can represent a steep learning curve. As climate-related projects continue to receive funding and the impacts of climate variability and change on our oceans become increasingly evident, the ability to efficiently interact with, and use, Earth System Model (ESM) outputs for our research is more critical than ever.\nThe aim of our one-day R course is to train students, researchers and faculty in skills needed to be proficient in creating projections of physical variables from ESM outputs, with the goal of using them for ecological applications. Specifically, we’ll be creating projections of sea-surface temperature across two time periods out to 2100, across two climate scenarios, for the California Current region.\nOur workshop is designed around Step 8 (pre-process the data) in the workflow of best practices for using ESMs for marine ecologists, as defined in Figure 1 within (Schoeman et al. 2023).\nOur workshop is supported by CMSI, and is hosted by Bodega Marine Lab. We thank both organisations for their funding and support.\n\n\n\n\n\n\n\n\n\nSchoeman, David S., Alex Sen Gupta, Cheryl S. Harrison, Jason D. Everett, Isaac Brito-Morales, Lee Hannah, Laurent Bopp, Patrick R. Roehrdanz, and Anthony J. Richardson. 2023. “Demystifying Global Climate Models for Use in the Life Sciences.” Trends in Ecology & Evolution 38 (9): 843–58. https://doi.org/https://doi.org/10.1016/j.tree.2023.04.005.",
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"href": "_xx_about.html#what-to-bring",
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"title": "About",
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"section": "What to bring",
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"text": "What to bring\n\nLaptop (highly, highly, highly recommend macOS) with internet connection. Please ensure you have administrator permissions - consult with your IT department on how to do this. Windows laptops are OK, but the instructors are all macOS natives - we will be using macOS during the workshop, and are unlikely to be able to fix any Windows-related software installation problems that are unfortunately common with some of the tools we’ll be using.\nInstall the necessary software, listed on the Prerequisites page.",
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"text": "What to bring\n\nLaptop (highly, highly, highly recommend macOS) with internet connection. Please ensure you have administrator permissions - consult with your IT department on how to do this.\nInstall the necessary software, listed on the Prerequisites page.",
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