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<!DOCTYPE html>
<html >
<head>
<meta charset="UTF-8">
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<title>The Predictive Ecosystem Analyzer</title>
<meta name="description" content="The Predictive Ecosystem Analyzer">
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<meta property="og:title" content="The Predictive Ecosystem Analyzer" />
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<meta name="twitter:title" content="The Predictive Ecosystem Analyzer" />
<meta name="date" content="2018-09-21">
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<ul class="summary">
<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Welcome</a></li>
<li class="part"><span><b>I Introduction</b></span></li>
<li class="chapter" data-level="1" data-path="project-overview.html"><a href="project-overview.html"><i class="fa fa-check"></i><b>1</b> Project Overview</a></li>
<li class="chapter" data-level="2" data-path="contributor-covenant-code-of-conduct.html"><a href="contributor-covenant-code-of-conduct.html"><i class="fa fa-check"></i><b>2</b> Contributor Covenant Code of Conduct</a></li>
<li class="chapter" data-level="3" data-path="about-the-pecan-book.html"><a href="about-the-pecan-book.html"><i class="fa fa-check"></i><b>3</b> About the PEcAn Book</a><ul>
<li class="chapter" data-level="3.0.1" data-path="about-the-pecan-book.html"><a href="about-the-pecan-book.html#main-topics"><i class="fa fa-check"></i><b>3.0.1</b> Main Topics</a></li>
<li class="chapter" data-level="3.1" data-path="about-the-pecan-book.html"><a href="about-the-pecan-book.html#how-to-contribute"><i class="fa fa-check"></i><b>3.1</b> How to Contribute</a><ul>
<li class="chapter" data-level="3.1.1" data-path="about-the-pecan-book.html"><a href="about-the-pecan-book.html#editing-the-book-yourself"><i class="fa fa-check"></i><b>3.1.1</b> Editing the book yourself</a></li>
<li class="chapter" data-level="3.1.2" data-path="about-the-pecan-book.html"><a href="about-the-pecan-book.html#feedbackcommentssuggestions"><i class="fa fa-check"></i><b>3.1.2</b> Feedback/Comments/Suggestions</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>II Basic User Guide</b></span></li>
<li class="chapter" data-level="4" data-path="GettingStarted.html"><a href="GettingStarted.html"><i class="fa fa-check"></i><b>4</b> Getting Started</a><ul>
<li class="chapter" data-level="4.1" data-path="GettingStarted.html"><a href="GettingStarted.html#how-pecan-works-in-a-nutshell"><i class="fa fa-check"></i><b>4.1</b> How PEcAn Works in a nutshell</a></li>
<li class="chapter" data-level="4.2" data-path="GettingStarted.html"><a href="GettingStarted.html#download-the-pecan-vm"><i class="fa fa-check"></i><b>4.2</b> Download the PEcAn VM</a></li>
<li class="chapter" data-level="4.3" data-path="GettingStarted.html"><a href="GettingStarted.html#awsvm"><i class="fa fa-check"></i><b>4.3</b> Using AmazonWeb Services (AWS)</a></li>
<li class="chapter" data-level="4.4" data-path="GettingStarted.html"><a href="GettingStarted.html#dockervm"><i class="fa fa-check"></i><b>4.4</b> Working with the PEcAn Containers (Docker) [Experimental]</a></li>
<li class="chapter" data-level="4.5" data-path="GettingStarted.html"><a href="GettingStarted.html#pecan-demos"><i class="fa fa-check"></i><b>4.5</b> PEcAn Demos</a></li>
</ul></li>
<li class="chapter" data-level="5" data-path="web-workflow.html"><a href="web-workflow.html"><i class="fa fa-check"></i><b>5</b> Web workflow</a><ul>
<li class="chapter" data-level="5.1" data-path="web-workflow.html"><a href="web-workflow.html#site-and-model-selection"><i class="fa fa-check"></i><b>5.1</b> Site and model selection</a><ul>
<li class="chapter" data-level="5.1.1" data-path="web-workflow.html"><a href="web-workflow.html#selecting-a-model"><i class="fa fa-check"></i><b>5.1.1</b> Selecting a model</a></li>
<li class="chapter" data-level="5.1.2" data-path="web-workflow.html"><a href="web-workflow.html#selecting-a-site"><i class="fa fa-check"></i><b>5.1.2</b> Selecting a site</a></li>
</ul></li>
<li class="chapter" data-level="5.2" data-path="web-workflow.html"><a href="web-workflow.html#model-configuration"><i class="fa fa-check"></i><b>5.2</b> Model configuration</a><ul>
<li class="chapter" data-level="5.2.1" data-path="web-workflow.html"><a href="web-workflow.html#choosing-meteorology"><i class="fa fa-check"></i><b>5.2.1</b> Choosing meteorology</a></li>
<li class="chapter" data-level="5.2.2" data-path="web-workflow.html"><a href="web-workflow.html#selecting-plant-functional-types-pfts-and-other-parameter-groupings."><i class="fa fa-check"></i><b>5.2.2</b> Selecting Plant Functional Types (PFTs) and other parameter groupings.</a></li>
<li class="chapter" data-level="5.2.3" data-path="web-workflow.html"><a href="web-workflow.html#choosing-initial-vegetation"><i class="fa fa-check"></i><b>5.2.3</b> Choosing initial vegetation</a></li>
<li class="chapter" data-level="5.2.4" data-path="web-workflow.html"><a href="web-workflow.html#spin-up"><i class="fa fa-check"></i><b>5.2.4</b> Spin up</a></li>
<li class="chapter" data-level="5.2.5" data-path="web-workflow.html"><a href="web-workflow.html#selecting-a-soils-product"><i class="fa fa-check"></i><b>5.2.5</b> Selecting a soils product</a></li>
<li class="chapter" data-level="5.2.6" data-path="web-workflow.html"><a href="web-workflow.html#other-model-inputs"><i class="fa fa-check"></i><b>5.2.6</b> Other model inputs</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>III Intermediate user guide</b></span></li>
<li class="chapter" data-level="6" data-path="introduction.html"><a href="introduction.html"><i class="fa fa-check"></i><b>6</b> Introduction</a></li>
<li class="chapter" data-level="7" data-path="pecanXML.html"><a href="pecanXML.html"><i class="fa fa-check"></i><b>7</b> The PEcAn XML</a><ul>
<li class="chapter" data-level="7.1" data-path="pecanXML.html"><a href="pecanXML.html#pecan-folders"><i class="fa fa-check"></i><b>7.1</b> PEcAn folders</a></li>
<li class="chapter" data-level="7.2" data-path="pecanXML.html"><a href="pecanXML.html#database-access"><i class="fa fa-check"></i><b>7.2</b> Database Access</a></li>
<li class="chapter" data-level="7.3" data-path="pecanXML.html"><a href="pecanXML.html#bety-database-configuration"><i class="fa fa-check"></i><b>7.3</b> BETY Database Configuration</a></li>
<li class="chapter" data-level="7.4" data-path="pecanXML.html"><a href="pecanXML.html#brown-dog-configuration"><i class="fa fa-check"></i><b>7.4</b> Brown Dog Configuration</a></li>
<li class="chapter" data-level="7.5" data-path="pecanXML.html"><a href="pecanXML.html#pft-selection"><i class="fa fa-check"></i><b>7.5</b> PFT Selection</a></li>
<li class="chapter" data-level="7.6" data-path="pecanXML.html"><a href="pecanXML.html#meta-analysis"><i class="fa fa-check"></i><b>7.6</b> Meta Analysis</a></li>
<li class="chapter" data-level="7.7" data-path="pecanXML.html"><a href="pecanXML.html#ensemble-runs"><i class="fa fa-check"></i><b>7.7</b> Ensemble Runs</a></li>
<li class="chapter" data-level="7.8" data-path="pecanXML.html"><a href="pecanXML.html#sensitivity-runs"><i class="fa fa-check"></i><b>7.8</b> Sensitivity Runs</a></li>
<li class="chapter" data-level="7.9" data-path="pecanXML.html"><a href="pecanXML.html#model-setup"><i class="fa fa-check"></i><b>7.9</b> Model Setup</a></li>
<li class="chapter" data-level="7.10" data-path="pecanXML.html"><a href="pecanXML.html#run-setup"><i class="fa fa-check"></i><b>7.10</b> Run Setup</a></li>
<li class="chapter" data-level="7.11" data-path="pecanXML.html"><a href="pecanXML.html#state-data-assimilation-tags"><i class="fa fa-check"></i><b>7.11</b> State Data Assimilation Tags</a></li>
<li class="chapter" data-level="7.12" data-path="pecanXML.html"><a href="pecanXML.html#parameter-data-assimilation"><i class="fa fa-check"></i><b>7.12</b> Parameter Data Assimilation</a></li>
<li class="chapter" data-level="7.13" data-path="pecanXML.html"><a href="pecanXML.html#benchmarking"><i class="fa fa-check"></i><b>7.13</b> Benchmarking</a></li>
<li class="chapter" data-level="7.14" data-path="pecanXML.html"><a href="pecanXML.html#model-specific-configuration"><i class="fa fa-check"></i><b>7.14</b> Model-specific configuration</a></li>
</ul></li>
<li class="chapter" data-level="8" data-path="additional-web-configuration.html"><a href="additional-web-configuration.html"><i class="fa fa-check"></i><b>8</b> Additional web configuration</a><ul>
<li class="chapter" data-level="8.1" data-path="additional-web-configuration.html"><a href="additional-web-configuration.html#brown-dog"><i class="fa fa-check"></i><b>8.1</b> Brown Dog</a></li>
<li class="chapter" data-level="8.2" data-path="additional-web-configuration.html"><a href="additional-web-configuration.html#advanced-setup"><i class="fa fa-check"></i><b>8.2</b> Advanced Setup</a></li>
<li class="chapter" data-level="8.3" data-path="additional-web-configuration.html"><a href="additional-web-configuration.html#editing-model-configurations"><i class="fa fa-check"></i><b>8.3</b> Editing model configurations</a></li>
<li class="chapter" data-level="8.4" data-path="additional-web-configuration.html"><a href="additional-web-configuration.html#basic-setups"><i class="fa fa-check"></i><b>8.4</b> Basic Setups</a></li>
</ul></li>
<li class="chapter" data-level="9" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html"><i class="fa fa-check"></i><b>9</b> Settings-configured analyses</a><ul>
<li class="chapter" data-level="9.1" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#parameter-data-assimilation-pda"><i class="fa fa-check"></i><b>9.1</b> Parameter data assimilation (PDA)</a><ul>
<li class="chapter" data-level="9.1.1" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#pda.mcmc.r"><i class="fa fa-check"></i><b>9.1.1</b> <strong>pda.mcmc.R</strong></a></li>
<li class="chapter" data-level="9.1.2" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#pda.mcmc.bs.r"><i class="fa fa-check"></i><b>9.1.2</b> <strong>pda.mcmc.bs.R</strong></a></li>
<li class="chapter" data-level="9.1.3" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#pda.emulator"><i class="fa fa-check"></i><b>9.1.3</b> <strong>pda.emulator</strong></a></li>
<li class="chapter" data-level="9.1.4" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#pda.mcmc.recover.r"><i class="fa fa-check"></i><b>9.1.4</b> <strong>pda.mcmc.recover.R</strong></a></li>
<li class="chapter" data-level="9.1.5" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#pda.utils.r"><i class="fa fa-check"></i><b>9.1.5</b> <strong>pda.utils.R</strong></a></li>
<li class="chapter" data-level="9.1.6" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#get.da.data..r-plot.da.r"><i class="fa fa-check"></i><b>9.1.6</b> <strong>get.da.data.*.R, plot.da.R</strong></a></li>
</ul></li>
<li class="chapter" data-level="9.2" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#for-a-detailed-usage-of-the-module-please-see-the-vignette-under-modulesassim.batchvignettes"><i class="fa fa-check"></i><b>9.2</b> For a detailed usage of the module, please see the vignette under <strong>/modules/assim.batch/vignettes</strong></a></li>
<li class="chapter" data-level="9.3" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#state-data-assimilation-sda"><i class="fa fa-check"></i><b>9.3</b> State data assimilation (SDA)</a></li>
<li class="chapter" data-level="9.4" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#sda.enkf.r-is-housed-within-pecanmodulesassim.sequentialr"><i class="fa fa-check"></i><b>9.4</b> sda.enkf.R is housed within: <strong>/pecan/modules/assim.sequential/R</strong></a></li>
<li class="chapter" data-level="9.5" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#the-tree-ring-tutorial-is-housed-within-pecandocumentationtutorialsstateassimilation"><i class="fa fa-check"></i><b>9.5</b> The tree ring tutorial is housed within: <strong>/pecan/documentation/tutorials/StateAssimilation</strong></a></li>
<li class="chapter" data-level="9.6" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#more-descriptive-sda-methods-can-be-found-at-pecanbook_sourceadve_user_guide_websda_methods.rmd"><i class="fa fa-check"></i><b>9.6</b> More descriptive SDA methods can be found at: <strong>/pecan/book_source/adve_user_guide_web/SDA_Methods.Rmd</strong></a><ul>
<li class="chapter" data-level="9.6.1" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#sda.enkf.r-description"><i class="fa fa-check"></i><b>9.6.1</b> <strong>sda.enkf.R Description</strong></a></li>
<li class="chapter" data-level="9.6.2" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#sda.enkf.r-arguments"><i class="fa fa-check"></i><b>9.6.2</b> <strong>sda.enkf.R Arguments</strong></a></li>
<li class="chapter" data-level="9.6.3" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#state-data-assimilation-workflow"><i class="fa fa-check"></i><b>9.6.3</b> State Data Assimilation Workflow</a></li>
<li class="chapter" data-level="9.6.4" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#state-data-assimilation-tags-example"><i class="fa fa-check"></i><b>9.6.4</b> State Data Assimilation Tags Example</a></li>
<li class="chapter" data-level="9.6.5" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#state-data-assimilation-tags-descriptions"><i class="fa fa-check"></i><b>9.6.5</b> State Data Assimilation Tags Descriptions</a></li>
<li class="chapter" data-level="9.6.6" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#model-specific-functions-for-sda-workflow"><i class="fa fa-check"></i><b>9.6.6</b> Model Specific Functions for SDA Workflow</a></li>
<li class="chapter" data-level="9.6.7" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#analysis-options"><i class="fa fa-check"></i><b>9.6.7</b> Analysis Options</a></li>
<li class="chapter" data-level="9.6.8" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#the-generalized-ensemble-filter"><i class="fa fa-check"></i><b>9.6.8</b> The Generalized Ensemble Filter</a></li>
</ul></li>
<li class="chapter" data-level="9.7" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#sda_methods"><i class="fa fa-check"></i><b>9.7</b> SDA_Methods</a></li>
<li class="chapter" data-level="9.8" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#data-products"><i class="fa fa-check"></i><b>9.8</b> Data Products</a><ul>
<li class="chapter" data-level="9.8.1" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#tree-rings"><i class="fa fa-check"></i><b>9.8.1</b> Tree Rings</a></li>
<li class="chapter" data-level="9.8.2" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#pollen"><i class="fa fa-check"></i><b>9.8.2</b> Pollen</a></li>
</ul></li>
<li class="chapter" data-level="9.9" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#current-models"><i class="fa fa-check"></i><b>9.9</b> Current Models</a></li>
<li class="chapter" data-level="9.10" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#model-calibration"><i class="fa fa-check"></i><b>9.10</b> Model Calibration</a></li>
<li class="chapter" data-level="9.11" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#initial-conditions"><i class="fa fa-check"></i><b>9.11</b> Initial Conditions</a></li>
<li class="chapter" data-level="9.12" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#drivers"><i class="fa fa-check"></i><b>9.12</b> Drivers</a></li>
<li class="chapter" data-level="9.13" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#sequential-state-data-assimilation"><i class="fa fa-check"></i><b>9.13</b> Sequential State Data Assimilation</a><ul>
<li class="chapter" data-level="9.13.1" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#general-description"><i class="fa fa-check"></i><b>9.13.1</b> General Description</a></li>
<li class="chapter" data-level="9.13.2" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#enkf"><i class="fa fa-check"></i><b>9.13.2</b> EnKF</a></li>
<li class="chapter" data-level="9.13.3" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#generalized-ensemble-filter"><i class="fa fa-check"></i><b>9.13.3</b> Generalized Ensemble Filter</a></li>
<li class="chapter" data-level="9.13.4" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#ensemble-adjustment"><i class="fa fa-check"></i><b>9.13.4</b> Ensemble Adjustment</a></li>
<li class="chapter" data-level="9.13.5" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#diagnostics"><i class="fa fa-check"></i><b>9.13.5</b> Diagnostics</a></li>
</ul></li>
<li class="chapter" data-level="9.14" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#multisettings"><i class="fa fa-check"></i><b>9.14</b> MultiSettings</a></li>
<li class="chapter" data-level="9.15" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#Benchmarking"><i class="fa fa-check"></i><b>9.15</b> Benchmarking</a><ul>
<li class="chapter" data-level="9.15.1" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#data-preparation"><i class="fa fa-check"></i><b>9.15.1</b> Data Preparation</a></li>
<li class="chapter" data-level="9.15.2" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#model-runs"><i class="fa fa-check"></i><b>9.15.2</b> Model Runs</a></li>
<li class="chapter" data-level="9.15.3" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#the-benchmarking-shiny-app"><i class="fa fa-check"></i><b>9.15.3</b> The Benchmarking Shiny App</a></li>
<li class="chapter" data-level="9.15.4" data-path="settings-configured-analyses.html"><a href="settings-configured-analyses.html#benchmarking-in-pecan.xml"><i class="fa fa-check"></i><b>9.15.4</b> Benchmarking in pecan.xml</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="10" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html"><i class="fa fa-check"></i><b>10</b> Remote execution with PEcAn</a><ul>
<li class="chapter" data-level="10.1" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#basics-of-ssh"><i class="fa fa-check"></i><b>10.1</b> Basics of SSH</a></li>
<li class="chapter" data-level="10.2" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#ssh-authentication-password-vs.ssh-key"><i class="fa fa-check"></i><b>10.2</b> SSH authentication – password vs. SSH key</a><ul>
<li class="chapter" data-level="10.2.1" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#ssh-tunneling"><i class="fa fa-check"></i><b>10.2.1</b> SSH tunneling</a></li>
<li class="chapter" data-level="10.2.2" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#ssh-tunnels-and-pecan"><i class="fa fa-check"></i><b>10.2.2</b> SSH tunnels and PEcAn</a></li>
</ul></li>
<li class="chapter" data-level="10.3" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#basic-remote-execute-functions"><i class="fa fa-check"></i><b>10.3</b> Basic remote execute functions</a></li>
<li class="chapter" data-level="10.4" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#remote-model-execution-with-pecan"><i class="fa fa-check"></i><b>10.4</b> Remote model execution with PEcAn</a><ul>
<li class="chapter" data-level="10.4.1" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#xml-configuration"><i class="fa fa-check"></i><b>10.4.1</b> XML configuration</a></li>
<li class="chapter" data-level="10.4.2" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#configuration-for-pecan-web-interface"><i class="fa fa-check"></i><b>10.4.2</b> Configuration for PEcAn web interface</a></li>
</ul></li>
<li class="chapter" data-level="10.5" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#running-pecan-code-for-remotely"><i class="fa fa-check"></i><b>10.5</b> Running PEcAn code for remotely</a><ul>
<li class="chapter" data-level="10.5.1" data-path="remote-execution-with-pecan.html"><a href="remote-execution-with-pecan.html#geo.bu.edu"><i class="fa fa-check"></i><b>10.5.1</b> geo.bu.edu</a></li>
</ul></li>
</ul></li>
<li class="part"><span><b>IV Advanced user guide</b></span></li>
<li class="chapter" data-level="11" data-path="introduction-1.html"><a href="introduction-1.html"><i class="fa fa-check"></i><b>11</b> Introduction</a></li>
<li class="chapter" data-level="12" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html"><i class="fa fa-check"></i><b>12</b> PEcAn workflow (web/workflow.R)</a><ul>
<li class="chapter" data-level="12.1" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#read-settings"><i class="fa fa-check"></i><b>12.1</b> Read Settings</a></li>
<li class="chapter" data-level="12.2" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#input-conversions"><i class="fa fa-check"></i><b>12.2</b> Input Conversions</a><ul>
<li class="chapter" data-level="12.2.1" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#input-data"><i class="fa fa-check"></i><b>12.2.1</b> Input Data</a></li>
<li class="chapter" data-level="12.2.2" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#initial-conditions-1"><i class="fa fa-check"></i><b>12.2.2</b> Initial Conditions</a></li>
</ul></li>
<li class="chapter" data-level="12.3" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#meteorological-data"><i class="fa fa-check"></i><b>12.3</b> Meteorological Data</a><ul>
<li class="chapter" data-level="12.3.1" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#downloading-raw-data-description-of-process"><i class="fa fa-check"></i><b>12.3.1</b> Downloading Raw data (Description of Process)</a></li>
</ul></li>
<li class="chapter" data-level="12.4" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#traits"><i class="fa fa-check"></i><b>12.4</b> Traits</a></li>
<li class="chapter" data-level="12.5" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#meta-analysis-1"><i class="fa fa-check"></i><b>12.5</b> Meta Analysis</a></li>
<li class="chapter" data-level="12.6" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#model-configuration-1"><i class="fa fa-check"></i><b>12.6</b> Model Configuration</a></li>
<li class="chapter" data-level="12.7" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#run-execution"><i class="fa fa-check"></i><b>12.7</b> Run Execution</a></li>
<li class="chapter" data-level="12.8" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#post-run-analysis"><i class="fa fa-check"></i><b>12.8</b> Post Run Analysis</a></li>
<li class="chapter" data-level="12.9" data-path="pecan-workflow-webworkflow-r.html"><a href="pecan-workflow-webworkflow-r.html#advanced-analysis"><i class="fa fa-check"></i><b>12.9</b> Advanced Analysis</a></li>
</ul></li>
<li class="chapter" data-level="13" data-path="submitting-workflow-from-command-line.html"><a href="submitting-workflow-from-command-line.html"><i class="fa fa-check"></i><b>13</b> Submitting Workflow from Command Line</a></li>
<li class="chapter" data-level="14" data-path="workflow-modules.html"><a href="workflow-modules.html"><i class="fa fa-check"></i><b>14</b> Workflow modules</a><ul>
<li class="chapter" data-level="14.1" data-path="workflow-modules.html"><a href="workflow-modules.html#overview"><i class="fa fa-check"></i><b>14.1</b> Overview</a><ul>
<li class="chapter" data-level="14.1.1" data-path="workflow-modules.html"><a href="workflow-modules.html#load-settings"><i class="fa fa-check"></i><b>14.1.1</b> Load Settings:</a></li>
<li class="chapter" data-level="14.1.2" data-path="workflow-modules.html"><a href="workflow-modules.html#query-database"><i class="fa fa-check"></i><b>14.1.2</b> Query Database:</a></li>
<li class="chapter" data-level="14.1.3" data-path="workflow-modules.html"><a href="workflow-modules.html#meta-analysis-2"><i class="fa fa-check"></i><b>14.1.3</b> Meta Analysis:</a></li>
<li class="chapter" data-level="14.1.4" data-path="workflow-modules.html"><a href="workflow-modules.html#write-configuration-files"><i class="fa fa-check"></i><b>14.1.4</b> Write Configuration Files</a></li>
<li class="chapter" data-level="14.1.5" data-path="workflow-modules.html"><a href="workflow-modules.html#start-runs"><i class="fa fa-check"></i><b>14.1.5</b> Start Runs:</a></li>
<li class="chapter" data-level="14.1.6" data-path="workflow-modules.html"><a href="workflow-modules.html#get-model-output"><i class="fa fa-check"></i><b>14.1.6</b> Get Model Output</a></li>
<li class="chapter" data-level="14.1.7" data-path="workflow-modules.html"><a href="workflow-modules.html#ensemble-analysis"><i class="fa fa-check"></i><b>14.1.7</b> Ensemble Analysis</a></li>
<li class="chapter" data-level="14.1.8" data-path="workflow-modules.html"><a href="workflow-modules.html#sensitivity-analysis-variance-decomposition"><i class="fa fa-check"></i><b>14.1.8</b> Sensitivity Analysis, Variance Decomposition</a></li>
</ul></li>
<li class="chapter" data-level="14.2" data-path="workflow-modules.html"><a href="workflow-modules.html#glossary"><i class="fa fa-check"></i><b>14.2</b> Glossary</a></li>
</ul></li>
<li class="chapter" data-level="15" data-path="adding-to-pecan.html"><a href="adding-to-pecan.html"><i class="fa fa-check"></i><b>15</b> Adding to PEcAn</a><ul>
<li class="chapter" data-level="15.1" data-path="adding-to-pecan.html"><a href="adding-to-pecan.html#case-studies"><i class="fa fa-check"></i><b>15.1</b> Case studies</a></li>
<li class="chapter" data-level="15.2" data-path="adding-to-pecan.html"><a href="adding-to-pecan.html#adding-an-ecosystem-model"><i class="fa fa-check"></i><b>15.2</b> Adding An Ecosystem Model</a></li>
</ul></li>
<li class="chapter" data-level="16" data-path="NewFormat.html"><a href="NewFormat.html"><i class="fa fa-check"></i><b>16</b> Formats records in BETY</a></li>
<li class="chapter" data-level="17" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html"><i class="fa fa-check"></i><b>17</b> Creating a new Format record in BETY</a><ul>
<li class="chapter" data-level="17.1" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#formats---variables"><i class="fa fa-check"></i><b>17.1</b> Formats -> Variables</a><ul>
<li class="chapter" data-level="17.1.1" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#name-and-unit"><i class="fa fa-check"></i><b>17.1.1</b> Name and Unit</a></li>
<li class="chapter" data-level="17.1.2" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#storage-type"><i class="fa fa-check"></i><b>17.1.2</b> Storage Type</a></li>
<li class="chapter" data-level="17.1.3" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#column-number"><i class="fa fa-check"></i><b>17.1.3</b> Column Number</a></li>
</ul></li>
<li class="chapter" data-level="17.2" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#retrieving-format-information"><i class="fa fa-check"></i><b>17.2</b> Retrieving Format Information</a><ul>
<li class="chapter" data-level="17.2.1" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#inputs-1"><i class="fa fa-check"></i><b>17.2.1</b> Inputs</a></li>
<li class="chapter" data-level="17.2.2" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#output"><i class="fa fa-check"></i><b>17.2.2</b> Output</a></li>
</ul></li>
<li class="chapter" data-level="17.3" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#NewInput"><i class="fa fa-check"></i><b>17.3</b> Input records in BETY</a></li>
<li class="chapter" data-level="17.4" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#create-a-database-file-record-for-the-input-data"><i class="fa fa-check"></i><b>17.4</b> Create a database file record for the input data</a></li>
<li class="chapter" data-level="17.5" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#creating-a-new-input-record-in-bety"><i class="fa fa-check"></i><b>17.5</b> Creating a new Input record in BETY</a><ul>
<li class="chapter" data-level="17.5.1" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#InputConversions"><i class="fa fa-check"></i><b>17.5.1</b> Input Conversion</a></li>
<li class="chapter" data-level="17.5.2" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#vegetation-data"><i class="fa fa-check"></i><b>17.5.2</b> Vegetation Data</a></li>
<li class="chapter" data-level="17.5.3" data-path="creating-a-new-format-record-in-bety.html"><a href="creating-a-new-format-record-in-bety.html#soil-data"><i class="fa fa-check"></i><b>17.5.3</b> Soil Data</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="18" data-path="reference-runs.html"><a href="reference-runs.html"><i class="fa fa-check"></i><b>18</b> Reference Runs</a></li>
<li class="chapter" data-level="19" data-path="pecan-data-ingest-via-web-interface.html"><a href="pecan-data-ingest-via-web-interface.html"><i class="fa fa-check"></i><b>19</b> Pecan Data Ingest via Web Interface</a></li>
<li class="chapter" data-level="20" data-path="loading-data.html"><a href="loading-data.html"><i class="fa fa-check"></i><b>20</b> 1. Loading Data</a><ul>
<li class="chapter" data-level="20.1" data-path="loading-data.html"><a href="loading-data.html#selecting-ingest-method"><i class="fa fa-check"></i><b>20.1</b> Selecting Ingest Method</a><ul>
<li class="chapter" data-level="20.1.1" data-path="loading-data.html"><a href="loading-data.html#dataone-upload-example"><i class="fa fa-check"></i><b>20.1.1</b> DataONE Upload Example</a></li>
</ul></li>
<li class="chapter" data-level="20.2" data-path="loading-data.html"><a href="loading-data.html#local-upload-example"><i class="fa fa-check"></i><b>20.2</b> Local Upload Example</a></li>
<li class="chapter" data-level="20.3" data-path="loading-data.html"><a href="loading-data.html#creating-an-input-record"><i class="fa fa-check"></i><b>20.3</b> 2. Creating an Input Record</a></li>
<li class="chapter" data-level="20.4" data-path="loading-data.html"><a href="loading-data.html#creating-a-format-record"><i class="fa fa-check"></i><b>20.4</b> 3. Creating a format record</a></li>
<li class="chapter" data-level="20.5" data-path="loading-data.html"><a href="loading-data.html#formats_variables-record"><i class="fa fa-check"></i><b>20.5</b> 4. Formats_Variables Record</a></li>
<li class="chapter" data-level="20.6" data-path="loading-data.html"><a href="loading-data.html#editing-records"><i class="fa fa-check"></i><b>20.6</b> Editing records</a></li>
<li class="chapter" data-level="20.7" data-path="loading-data.html"><a href="loading-data.html#standalone-tools-modules"><i class="fa fa-check"></i><b>20.7</b> Standalone tools (modules)</a></li>
<li class="chapter" data-level="20.8" data-path="loading-data.html"><a href="loading-data.html#LoadData"><i class="fa fa-check"></i><b>20.8</b> Loading Data in PEcAn</a><ul>
<li class="chapter" data-level="20.8.1" data-path="loading-data.html"><a href="loading-data.html#function-load_data"><i class="fa fa-check"></i><b>20.8.1</b> Function <code>load_data</code></a></li>
<li class="chapter" data-level="20.8.2" data-path="loading-data.html"><a href="loading-data.html#example"><i class="fa fa-check"></i><b>20.8.2</b> Example</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="21" data-path="working-with-the-vm.html"><a href="working-with-the-vm.html"><i class="fa fa-check"></i><b>21</b> Working with the VM</a><ul>
<li class="chapter" data-level="21.1" data-path="working-with-the-vm.html"><a href="working-with-the-vm.html#connecting-to-the-vm-via-ssh"><i class="fa fa-check"></i><b>21.1</b> Connecting to the VM via SSH</a></li>
<li class="chapter" data-level="21.2" data-path="working-with-the-vm.html"><a href="working-with-the-vm.html#connecting-to-bety-on-the-vm-via-ssh"><i class="fa fa-check"></i><b>21.2</b> Connecting to bety on the VM via SSh</a></li>
</ul></li>
<li class="chapter" data-level="22" data-path="vm-desktop-conversion.html"><a href="vm-desktop-conversion.html"><i class="fa fa-check"></i><b>22</b> VM Desktop Conversion</a><ul>
<li class="chapter" data-level="22.0.1" data-path="vm-desktop-conversion.html"><a href="vm-desktop-conversion.html#install-rstudio-desktop"><i class="fa fa-check"></i><b>22.0.1</b> Install RStudio Desktop</a></li>
</ul></li>
<li class="part"><span><b>V Developer user guide</b></span></li>
<li class="chapter" data-level="23" data-path="introduction-developer-guide.html"><a href="introduction-developer-guide.html"><i class="fa fa-check"></i><b>23</b> Introduction: Developer Guide</a></li>
<li class="chapter" data-level="24" data-path="pecan-setup.html"><a href="pecan-setup.html"><i class="fa fa-check"></i><b>24</b> PEcAn Setup</a><ul>
<li class="chapter" data-level="24.1" data-path="pecan-setup.html"><a href="pecan-setup.html#installing-the-pecan-vm"><i class="fa fa-check"></i><b>24.1</b> Installing the PEcAn VM</a></li>
<li class="chapter" data-level="24.2" data-path="pecan-setup.html"><a href="pecan-setup.html#install-pecan-by-hand"><i class="fa fa-check"></i><b>24.2</b> Install PEcAn by hand</a><ul>
<li class="chapter" data-level="24.2.1" data-path="pecan-setup.html"><a href="pecan-setup.html#installation-prerequisites"><i class="fa fa-check"></i><b>24.2.1</b> Installation Prerequisites</a></li>
<li class="chapter" data-level="24.2.2" data-path="pecan-setup.html"><a href="pecan-setup.html#os-specific-installations"><i class="fa fa-check"></i><b>24.2.2</b> OS Specific Installations</a></li>
<li class="chapter" data-level="24.2.3" data-path="pecan-setup.html"><a href="pecan-setup.html#installing-bety"><i class="fa fa-check"></i><b>24.2.3</b> Installing BETY</a></li>
<li class="chapter" data-level="24.2.4" data-path="pecan-setup.html"><a href="pecan-setup.html#install-models"><i class="fa fa-check"></i><b>24.2.4</b> Install Models</a></li>
<li class="chapter" data-level="24.2.5" data-path="pecan-setup.html"><a href="pecan-setup.html#download-and-compile-pecan"><i class="fa fa-check"></i><b>24.2.5</b> Download and Compile PEcAn</a></li>
<li class="chapter" data-level="24.2.6" data-path="pecan-setup.html"><a href="pecan-setup.html#pecan-testrun"><i class="fa fa-check"></i><b>24.2.6</b> PEcAn Testrun</a></li>
<li class="chapter" data-level="24.2.7" data-path="pecan-setup.html"><a href="pecan-setup.html#pecan-customizations"><i class="fa fa-check"></i><b>24.2.7</b> PEcAn Customizations</a></li>
</ul></li>
<li class="chapter" data-level="24.3" data-path="pecan-setup.html"><a href="pecan-setup.html#aws-setup"><i class="fa fa-check"></i><b>24.3</b> AWS Setup</a><ul>
<li class="chapter" data-level="24.3.1" data-path="pecan-setup.html"><a href="pecan-setup.html#porting-vm-to-aws"><i class="fa fa-check"></i><b>24.3.1</b> Porting VM to AWS</a></li>
<li class="chapter" data-level="24.3.2" data-path="pecan-setup.html"><a href="pecan-setup.html#set-up-multiple-instances-optional"><i class="fa fa-check"></i><b>24.3.2</b> Set up multiple instances (optional)</a></li>
</ul></li>
<li class="chapter" data-level="24.4" data-path="pecan-setup.html"><a href="pecan-setup.html#shiny-setup"><i class="fa fa-check"></i><b>24.4</b> Shiny Setup</a><ul>
<li class="chapter" data-level="24.4.1" data-path="pecan-setup.html"><a href="pecan-setup.html#install-the-shiny-r-package-and-shiny-server"><i class="fa fa-check"></i><b>24.4.1</b> Install the Shiny R package and Shiny server</a></li>
<li class="chapter" data-level="24.4.2" data-path="pecan-setup.html"><a href="pecan-setup.html#modify-the-shiny-configuration-file"><i class="fa fa-check"></i><b>24.4.2</b> Modify the shiny configuration file</a></li>
<li class="chapter" data-level="24.4.3" data-path="pecan-setup.html"><a href="pecan-setup.html#set-the-apache-proxy"><i class="fa fa-check"></i><b>24.4.3</b> Set the Apache proxy</a></li>
<li class="chapter" data-level="24.4.4" data-path="pecan-setup.html"><a href="pecan-setup.html#enable-and-start-the-shiny-server-and-restart-apache"><i class="fa fa-check"></i><b>24.4.4</b> Enable and start the shiny server, and restart apache</a></li>
<li class="chapter" data-level="24.4.5" data-path="pecan-setup.html"><a href="pecan-setup.html#troubleshooting-1"><i class="fa fa-check"></i><b>24.4.5</b> Troubleshooting</a></li>
<li class="chapter" data-level="24.4.6" data-path="pecan-setup.html"><a href="pecan-setup.html#further-reading"><i class="fa fa-check"></i><b>24.4.6</b> Further reading</a></li>
</ul></li>
<li class="chapter" data-level="24.5" data-path="pecan-setup.html"><a href="pecan-setup.html#thredds-setup"><i class="fa fa-check"></i><b>24.5</b> Thredds Setup</a><ul>
<li class="chapter" data-level="24.5.1" data-path="pecan-setup.html"><a href="pecan-setup.html#install-the-tomcat-8-and-thredds-webapp"><i class="fa fa-check"></i><b>24.5.1</b> Install the Tomcat 8 and Thredds webapp</a></li>
<li class="chapter" data-level="24.5.2" data-path="pecan-setup.html"><a href="pecan-setup.html#ubuntu-1"><i class="fa fa-check"></i><b>24.5.2</b> Ubuntu</a></li>
<li class="chapter" data-level="24.5.3" data-path="pecan-setup.html"><a href="pecan-setup.html#customize-the-thredds-server"><i class="fa fa-check"></i><b>24.5.3</b> Customize the Thredds server</a></li>
<li class="chapter" data-level="24.5.4" data-path="pecan-setup.html"><a href="pecan-setup.html#update-the-catalog"><i class="fa fa-check"></i><b>24.5.4</b> Update the catalog</a></li>
<li class="chapter" data-level="24.5.5" data-path="pecan-setup.html"><a href="pecan-setup.html#troubleshooting-2"><i class="fa fa-check"></i><b>24.5.5</b> Troubleshooting</a></li>
<li class="chapter" data-level="24.5.6" data-path="pecan-setup.html"><a href="pecan-setup.html#further-reading-1"><i class="fa fa-check"></i><b>24.5.6</b> Further reading</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="25" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html"><i class="fa fa-check"></i><b>25</b> Maintaining PEcAn</a><ul>
<li class="chapter" data-level="25.1" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#updating-pecan-code-and-bety-database"><i class="fa fa-check"></i><b>25.1</b> Updating PEcAn Code and Bety Database</a><ul>
<li class="chapter" data-level="25.1.1" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#updating-pecan"><i class="fa fa-check"></i><b>25.1.1</b> Updating PEcAn</a></li>
</ul></li>
<li class="chapter" data-level="25.2" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#updating-bety"><i class="fa fa-check"></i><b>25.2</b> Updating BETY</a></li>
<li class="chapter" data-level="25.3" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#database-synchronization"><i class="fa fa-check"></i><b>25.3</b> Database synchronization</a><ul>
<li class="chapter" data-level="25.3.1" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#how-does-it-work"><i class="fa fa-check"></i><b>25.3.1</b> How does it work?</a></li>
<li class="chapter" data-level="25.3.2" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#set-up"><i class="fa fa-check"></i><b>25.3.2</b> Set up</a></li>
<li class="chapter" data-level="25.3.3" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#fetch-latest-data"><i class="fa fa-check"></i><b>25.3.3</b> Fetch latest data</a></li>
<li class="chapter" data-level="25.3.4" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#sharing-data"><i class="fa fa-check"></i><b>25.3.4</b> Sharing data</a></li>
<li class="chapter" data-level="25.3.5" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#automation"><i class="fa fa-check"></i><b>25.3.5</b> Automation</a></li>
<li class="chapter" data-level="25.3.6" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#network-status-map"><i class="fa fa-check"></i><b>25.3.6</b> Network Status Map</a></li>
<li class="chapter" data-level="25.3.7" data-path="maintaining-pecan.html"><a href="maintaining-pecan.html#tasks"><i class="fa fa-check"></i><b>25.3.7</b> Tasks</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="26" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html"><i class="fa fa-check"></i><b>26</b> Git and GitHub Workflow</a><ul>
<li class="chapter" data-level="26.1" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#using-git"><i class="fa fa-check"></i><b>26.1</b> Using Git</a><ul>
<li class="chapter" data-level="26.1.1" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#git"><i class="fa fa-check"></i><b>26.1.1</b> Git</a></li>
<li class="chapter" data-level="26.1.2" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#pecan-project-and-github"><i class="fa fa-check"></i><b>26.1.2</b> PEcAn Project and Github</a></li>
<li class="chapter" data-level="26.1.3" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#pecan-project-branches"><i class="fa fa-check"></i><b>26.1.3</b> PEcAn Project Branches</a></li>
<li class="chapter" data-level="26.1.4" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#git-rstudio"><i class="fa fa-check"></i><b>26.1.4</b> Git + Rstudio</a></li>
<li class="chapter" data-level="26.1.5" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#for-development"><i class="fa fa-check"></i><b>26.1.5</b> For development:</a></li>
<li class="chapter" data-level="26.1.6" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#references"><i class="fa fa-check"></i><b>26.1.6</b> References</a></li>
</ul></li>
<li class="chapter" data-level="26.2" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#github-use-with-pecan"><i class="fa fa-check"></i><b>26.2</b> GitHub use with PEcAn</a><ul>
<li class="chapter" data-level="26.2.1" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#bugs-issues-features-etc."><i class="fa fa-check"></i><b>26.2.1</b> Bugs, Issues, Features, etc.</a></li>
<li class="chapter" data-level="26.2.2" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#requesting-a-feature"><i class="fa fa-check"></i><b>26.2.2</b> Requesting a feature</a></li>
<li class="chapter" data-level="26.2.3" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#closing-an-issue"><i class="fa fa-check"></i><b>26.2.3</b> Closing an issue</a></li>
<li class="chapter" data-level="26.2.4" data-path="git-and-github-workflow.html"><a href="git-and-github-workflow.html#when-to-submit-an-issue"><i class="fa fa-check"></i><b>26.2.4</b> When to submit an issue?</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="27" data-path="coding-practices.html"><a href="coding-practices.html"><i class="fa fa-check"></i><b>27</b> Coding Practices</a><ul>
<li class="chapter" data-level="27.1" data-path="coding-practices.html"><a href="coding-practices.html#coding-style"><i class="fa fa-check"></i><b>27.1</b> Coding Style</a><ul>
<li class="chapter" data-level="27.1.1" data-path="coding-practices.html"><a href="coding-practices.html#use-roxygen2-documentation"><i class="fa fa-check"></i><b>27.1.1</b> Use Roxygen2 documentation</a></li>
<li class="chapter" data-level="27.1.2" data-path="coding-practices.html"><a href="coding-practices.html#write-your-name-at-the-top"><i class="fa fa-check"></i><b>27.1.2</b> Write your name at the top</a></li>
<li class="chapter" data-level="27.1.3" data-path="coding-practices.html"><a href="coding-practices.html#use-testthat-testing-package"><i class="fa fa-check"></i><b>27.1.3</b> Use testthat testing package</a></li>
<li class="chapter" data-level="27.1.4" data-path="coding-practices.html"><a href="coding-practices.html#dont-use-shortcuts"><i class="fa fa-check"></i><b>27.1.4</b> Don’t use shortcuts</a></li>
<li class="chapter" data-level="27.1.5" data-path="coding-practices.html"><a href="coding-practices.html#package-dependencies"><i class="fa fa-check"></i><b>27.1.5</b> Package Dependencies:</a></li>
</ul></li>
<li class="chapter" data-level="27.2" data-path="coding-practices.html"><a href="coding-practices.html#logging"><i class="fa fa-check"></i><b>27.2</b> Logging</a><ul>
<li class="chapter" data-level="27.2.1" data-path="coding-practices.html"><a href="coding-practices.html#pecan-logging-functions"><i class="fa fa-check"></i><b>27.2.1</b> PEcAn logging functions</a></li>
<li class="chapter" data-level="27.2.2" data-path="coding-practices.html"><a href="coding-practices.html#other-r-logging-packages"><i class="fa fa-check"></i><b>27.2.2</b> Other R logging packages</a></li>
<li class="chapter" data-level="27.2.3" data-path="coding-practices.html"><a href="coding-practices.html#example-usage"><i class="fa fa-check"></i><b>27.2.3</b> Example Usage</a></li>
</ul></li>
<li class="chapter" data-level="27.3" data-path="coding-practices.html"><a href="coding-practices.html#package-data"><i class="fa fa-check"></i><b>27.3</b> Package Data</a><ul>
<li class="chapter" data-level="27.3.1" data-path="coding-practices.html"><a href="coding-practices.html#summary"><i class="fa fa-check"></i><b>27.3.1</b> Summary:</a></li>
<li class="chapter" data-level="27.3.2" data-path="coding-practices.html"><a href="coding-practices.html#accessing-data"><i class="fa fa-check"></i><b>27.3.2</b> Accessing data</a></li>
</ul></li>
<li class="chapter" data-level="27.4" data-path="coding-practices.html"><a href="coding-practices.html#packages-used-in-development"><i class="fa fa-check"></i><b>27.4</b> Packages used in development</a></li>
<li class="chapter" data-level="27.5" data-path="coding-practices.html"><a href="coding-practices.html#roxygen2-1"><i class="fa fa-check"></i><b>27.5</b> Roxygen2</a><ul>
<li class="chapter" data-level="27.5.1" data-path="coding-practices.html"><a href="coding-practices.html#canonical-references"><i class="fa fa-check"></i><b>27.5.1</b> Canonical references:</a></li>
<li class="chapter" data-level="27.5.2" data-path="coding-practices.html"><a href="coding-practices.html#basic-roxygen2-instructions"><i class="fa fa-check"></i><b>27.5.2</b> Basic Roxygen2 instructions:</a></li>
<li class="chapter" data-level="27.5.3" data-path="coding-practices.html"><a href="coding-practices.html#example-1"><i class="fa fa-check"></i><b>27.5.3</b> Example</a></li>
<li class="chapter" data-level="27.5.4" data-path="coding-practices.html"><a href="coding-practices.html#updating-documentation"><i class="fa fa-check"></i><b>27.5.4</b> Updating documentation</a></li>
</ul></li>
<li class="chapter" data-level="27.6" data-path="coding-practices.html"><a href="coding-practices.html#testing"><i class="fa fa-check"></i><b>27.6</b> Testing</a><ul>
<li class="chapter" data-level="27.6.1" data-path="coding-practices.html"><a href="coding-practices.html#rationale"><i class="fa fa-check"></i><b>27.6.1</b> Rationale</a></li>
<li class="chapter" data-level="27.6.2" data-path="coding-practices.html"><a href="coding-practices.html#tests-makes-development-easier-and-less-error-prone"><i class="fa fa-check"></i><b>27.6.2</b> Tests makes development easier and less error prone</a></li>
<li class="chapter" data-level="27.6.3" data-path="coding-practices.html"><a href="coding-practices.html#quick-start"><i class="fa fa-check"></i><b>27.6.3</b> Quick Start:</a></li>
<li class="chapter" data-level="27.6.4" data-path="coding-practices.html"><a href="coding-practices.html#test-files"><i class="fa fa-check"></i><b>27.6.4</b> Test files</a></li>
<li class="chapter" data-level="27.6.5" data-path="coding-practices.html"><a href="coding-practices.html#testing-the-shiny-server"><i class="fa fa-check"></i><b>27.6.5</b> Testing the Shiny Server</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="28" data-path="directory-structure.html"><a href="directory-structure.html"><i class="fa fa-check"></i><b>28</b> Directory structure</a><ul>
<li class="chapter" data-level="28.1" data-path="directory-structure.html"><a href="directory-structure.html#overview-of-pecan-repository-as-of-pecan-1.5.3"><i class="fa fa-check"></i><b>28.1</b> Overview of PEcAn repository as of PEcAn 1.5.3</a></li>
<li class="chapter" data-level="28.2" data-path="directory-structure.html"><a href="directory-structure.html#generic-r-package-structure"><i class="fa fa-check"></i><b>28.2</b> Generic R package structure:</a></li>
</ul></li>
<li class="part"><span><b>VI Reference Materials</b></span></li>
<li class="chapter" data-level="29" data-path="pecan-standard-formats.html"><a href="pecan-standard-formats.html"><i class="fa fa-check"></i><b>29</b> PEcAn standard formats</a><ul>
<li class="chapter" data-level="29.1" data-path="pecan-standard-formats.html"><a href="pecan-standard-formats.html#defining-new-input-formats"><i class="fa fa-check"></i><b>29.1</b> Defining new input formats</a><ul>
<li class="chapter" data-level="29.1.1" data-path="pecan-standard-formats.html"><a href="pecan-standard-formats.html#input-standards"><i class="fa fa-check"></i><b>29.1.1</b> Input Standards</a></li>
<li class="chapter" data-level="29.1.2" data-path="pecan-standard-formats.html"><a href="pecan-standard-formats.html#output-standards"><i class="fa fa-check"></i><b>29.1.2</b> Output Standards</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="30" data-path="models-in-pecan.html"><a href="models-in-pecan.html"><i class="fa fa-check"></i><b>30</b> Models in PEcAn</a></li>
<li class="chapter" data-level="31" data-path="template-model-page.html"><a href="template-model-page.html"><i class="fa fa-check"></i><b>31</b> Template MODEL page</a><ul>
<li class="chapter" data-level="31.1" data-path="template-model-page.html"><a href="template-model-page.html#biocro-configuration"><i class="fa fa-check"></i><b>31.1</b> BioCro Configuration</a></li>
<li class="chapter" data-level="31.2" data-path="template-model-page.html"><a href="template-model-page.html#biocro-1"><i class="fa fa-check"></i><b>31.2</b> BioCro</a></li>
<li class="chapter" data-level="31.3" data-path="template-model-page.html"><a href="template-model-page.html#clm"><i class="fa fa-check"></i><b>31.3</b> CLM</a></li>
<li class="chapter" data-level="31.4" data-path="template-model-page.html"><a href="template-model-page.html#dalec-1"><i class="fa fa-check"></i><b>31.4</b> DALEC</a></li>
<li class="chapter" data-level="31.5" data-path="template-model-page.html"><a href="template-model-page.html#ed"><i class="fa fa-check"></i><b>31.5</b> ED</a><ul>
<li class="chapter" data-level="31.5.1" data-path="template-model-page.html"><a href="template-model-page.html#introduction-2"><i class="fa fa-check"></i><b>31.5.1</b> Introduction</a></li>
<li class="chapter" data-level="31.5.2" data-path="template-model-page.html"><a href="template-model-page.html#pecan-configuration-file-additions"><i class="fa fa-check"></i><b>31.5.2</b> PEcAn configuration file additions</a></li>
<li class="chapter" data-level="31.5.3" data-path="template-model-page.html"><a href="template-model-page.html#model-specific-input-files"><i class="fa fa-check"></i><b>31.5.3</b> Model specific input files</a></li>
<li class="chapter" data-level="31.5.4" data-path="template-model-page.html"><a href="template-model-page.html#model-configuration-files"><i class="fa fa-check"></i><b>31.5.4</b> Model configuration files</a></li>
<li class="chapter" data-level="31.5.5" data-path="template-model-page.html"><a href="template-model-page.html#installation-notes"><i class="fa fa-check"></i><b>31.5.5</b> Installation notes</a></li>
</ul></li>
<li class="chapter" data-level="31.6" data-path="template-model-page.html"><a href="template-model-page.html#gday-1"><i class="fa fa-check"></i><b>31.6</b> GDAY</a></li>
<li class="chapter" data-level="31.7" data-path="template-model-page.html"><a href="template-model-page.html#linkages-1"><i class="fa fa-check"></i><b>31.7</b> LINKAGES</a></li>
<li class="chapter" data-level="31.8" data-path="template-model-page.html"><a href="template-model-page.html#lpj-guess-1"><i class="fa fa-check"></i><b>31.8</b> LPJ-GUESS</a></li>
<li class="chapter" data-level="31.9" data-path="template-model-page.html"><a href="template-model-page.html#maespa-1"><i class="fa fa-check"></i><b>31.9</b> MAESPA</a></li>
</ul></li>
<li class="chapter" data-level="32" data-path="pecan-models.html"><a href="pecan-models.html"><i class="fa fa-check"></i><b>32</b> PEcAn Models</a><ul>
<li class="chapter" data-level="32.1" data-path="pecan-models.html"><a href="pecan-models.html#preles"><i class="fa fa-check"></i><b>32.1</b> PRELES</a></li>
<li class="chapter" data-level="32.2" data-path="pecan-models.html"><a href="pecan-models.html#sipnet-configuration"><i class="fa fa-check"></i><b>32.2</b> SIPNET configuration</a></li>
<li class="chapter" data-level="32.3" data-path="pecan-models.html"><a href="pecan-models.html#sipnet-1"><i class="fa fa-check"></i><b>32.3</b> Sipnet</a><ul>
<li class="chapter" data-level="32.3.1" data-path="pecan-models.html"><a href="pecan-models.html#download-gfdl"><i class="fa fa-check"></i><b>32.3.1</b> Download GFDL</a></li>
<li class="chapter" data-level="32.3.2" data-path="pecan-models.html"><a href="pecan-models.html#cm3"><i class="fa fa-check"></i><b>32.3.2</b> CM3</a></li>
<li class="chapter" data-level="32.3.3" data-path="pecan-models.html"><a href="pecan-models.html#esm2m-esm2g"><i class="fa fa-check"></i><b>32.3.3</b> ESM2M & ESM2G</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="33" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html"><i class="fa fa-check"></i><b>33</b> Available Meteorological Drivers</a><ul>
<li class="chapter" data-level="33.1" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#ameriflux"><i class="fa fa-check"></i><b>33.1</b> Ameriflux</a></li>
<li class="chapter" data-level="33.2" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#amerifluxlbl"><i class="fa fa-check"></i><b>33.2</b> AmerifluxLBL</a></li>
<li class="chapter" data-level="33.3" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#fluxnet2015"><i class="fa fa-check"></i><b>33.3</b> Fluxnet2015</a></li>
<li class="chapter" data-level="33.4" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#narr"><i class="fa fa-check"></i><b>33.4</b> NARR</a></li>
<li class="chapter" data-level="33.5" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#cruncep"><i class="fa fa-check"></i><b>33.5</b> CRUNCEP</a></li>
<li class="chapter" data-level="33.6" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#cmip5"><i class="fa fa-check"></i><b>33.6</b> CMIP5</a></li>
<li class="chapter" data-level="33.7" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#nldas"><i class="fa fa-check"></i><b>33.7</b> NLDAS</a></li>
<li class="chapter" data-level="33.8" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#gldas"><i class="fa fa-check"></i><b>33.8</b> GLDAS</a></li>
<li class="chapter" data-level="33.9" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#paleon"><i class="fa fa-check"></i><b>33.9</b> PalEON</a></li>
<li class="chapter" data-level="33.10" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#fluxnetlathuile"><i class="fa fa-check"></i><b>33.10</b> FluxnetLaThuile</a></li>
<li class="chapter" data-level="33.11" data-path="available-meteorological-drivers.html"><a href="available-meteorological-drivers.html#geostreams"><i class="fa fa-check"></i><b>33.11</b> Geostreams</a></li>
</ul></li>
<li class="chapter" data-level="34" data-path="what-is-docker.html"><a href="what-is-docker.html"><i class="fa fa-check"></i><b>34</b> What is Docker?</a><ul>
<li class="chapter" data-level="34.1" data-path="what-is-docker.html"><a href="what-is-docker.html#working-with-docker"><i class="fa fa-check"></i><b>34.1</b> Working with Docker</a></li>
<li class="chapter" data-level="34.2" data-path="what-is-docker.html"><a href="what-is-docker.html#working-with-docker-compose"><i class="fa fa-check"></i><b>34.2</b> Working with docker-compose</a></li>
</ul></li>
<li class="chapter" data-level="35" data-path="pecan-docker-architecture.html"><a href="pecan-docker-architecture.html"><i class="fa fa-check"></i><b>35</b> PEcAn Docker Architecture</a></li>
<li class="chapter" data-level="36" data-path="quickstart-for-docker-and-pecan-.html"><a href="quickstart-for-docker-and-pecan-.html"><i class="fa fa-check"></i><b>36</b> Quickstart for Docker and PEcAn.</a><ul>
<li class="chapter" data-level="36.1" data-path="quickstart-for-docker-and-pecan-.html"><a href="quickstart-for-docker-and-pecan-.html#install-docker"><i class="fa fa-check"></i><b>36.1</b> Install Docker</a></li>
<li class="chapter" data-level="36.2" data-path="quickstart-for-docker-and-pecan-.html"><a href="quickstart-for-docker-and-pecan-.html#running-pecan"><i class="fa fa-check"></i><b>36.2</b> Running PEcAn</a></li>
<li class="chapter" data-level="36.3" data-path="quickstart-for-docker-and-pecan-.html"><a href="quickstart-for-docker-and-pecan-.html#testing-pecan"><i class="fa fa-check"></i><b>36.3</b> Testing PEcAn</a></li>
</ul></li>
<li class="chapter" data-level="37" data-path="dockerfiles-for-models.html"><a href="dockerfiles-for-models.html"><i class="fa fa-check"></i><b>37</b> Dockerfiles for Models</a><ul>
<li class="chapter" data-level="37.1" data-path="dockerfiles-for-models.html"><a href="dockerfiles-for-models.html#common-problems"><i class="fa fa-check"></i><b>37.1</b> Common problems</a><ul>
<li class="chapter" data-level="37.1.1" data-path="dockerfiles-for-models.html"><a href="dockerfiles-for-models.html#debugging-missing-libraries"><i class="fa fa-check"></i><b>37.1.1</b> Debugging missing libraries</a></li>
<li class="chapter" data-level="37.1.2" data-path="dockerfiles-for-models.html"><a href="dockerfiles-for-models.html#using-the-pecan-download.file-function"><i class="fa fa-check"></i><b>37.1.2</b> Using the PEcAn download.file() function</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="38" data-path="debugging.html"><a href="debugging.html"><i class="fa fa-check"></i><b>38</b> Debugging</a><ul>
<li class="chapter" data-level="38.0.1" data-path="debugging.html"><a href="debugging.html#using-testsworkflow.r"><i class="fa fa-check"></i><b>38.0.1</b> Using <code>tests/workflow.R</code></a></li>
<li class="chapter" data-level="38.0.2" data-path="debugging.html"><a href="debugging.html#useful-scripts"><i class="fa fa-check"></i><b>38.0.2</b> Useful scripts</a></li>
<li class="chapter" data-level="38.0.3" data-path="debugging.html"><a href="debugging.html#debugging-shiny-apps"><i class="fa fa-check"></i><b>38.0.3</b> Debugging Shiny Apps</a></li>
<li class="chapter" data-level="38.1" data-path="debugging.html"><a href="debugging.html#troubleshooting-pecan"><i class="fa fa-check"></i><b>38.1</b> Troubleshooting PEcAn</a><ul>
<li class="chapter" data-level="38.1.1" data-path="debugging.html"><a href="debugging.html#cookies-and-pecan-web-pages"><i class="fa fa-check"></i><b>38.1.1</b> Cookies and pecan web pages</a></li>
<li class="chapter" data-level="38.1.2" data-path="debugging.html"><a href="debugging.html#warning-mkdir-function.mkdir-no-such-file-or-directory"><i class="fa fa-check"></i><b>38.1.2</b> <code>Warning: mkdir() [function.mkdir]: No such file or directory</code></a></li>
<li class="chapter" data-level="38.1.3" data-path="debugging.html"><a href="debugging.html#after-creating-a-new-pft-the-tag-for-pft-not-passed-to-config.xml-in-ed"><i class="fa fa-check"></i><b>38.1.3</b> After creating a new PFT the <num> tag for PFT not passed to config.xml in ED</a></li>
</ul></li>
<li class="chapter" data-level="38.2" data-path="debugging.html"><a href="debugging.html#pecan-project-use-to-teach-ecological-model-data-synthesis"><i class="fa fa-check"></i><b>38.2</b> PEcAn Project use to teach Ecological model-data synthesis</a><ul>
<li class="chapter" data-level="38.2.1" data-path="debugging.html"><a href="debugging.html#university-classes"><i class="fa fa-check"></i><b>38.2.1</b> University classes</a></li>
<li class="chapter" data-level="38.2.2" data-path="debugging.html"><a href="debugging.html#summer-courses-workshops"><i class="fa fa-check"></i><b>38.2.2</b> Summer Courses / Workshops</a></li>
<li class="chapter" data-level="38.2.3" data-path="debugging.html"><a href="debugging.html#selected-publications"><i class="fa fa-check"></i><b>38.2.3</b> Selected Publications</a></li>
</ul></li>
<li class="chapter" data-level="38.3" data-path="debugging.html"><a href="debugging.html#data-assimilation-with-dart"><i class="fa fa-check"></i><b>38.3</b> Data assimilation with DART</a></li>
</ul></li>
<li class="part"><span><b>VII Demos and Vignettes</b></span></li>
<li class="chapter" data-level="39" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html"><i class="fa fa-check"></i><b>39</b> PEcAn Hands-On Demo 01: Basic Run</a><ul>
<li class="chapter" data-level="39.1" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#objective"><i class="fa fa-check"></i><b>39.1</b> Objective</a><ul>
<li class="chapter" data-level="39.1.1" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#pecan-url"><i class="fa fa-check"></i><b>39.1.1</b> PEcAn URL</a></li>
</ul></li>
<li class="chapter" data-level="39.2" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#basic-run"><i class="fa fa-check"></i><b>39.2</b> Basic Run</a><ul>
<li class="chapter" data-level="39.2.1" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#start-pecan"><i class="fa fa-check"></i><b>39.2.1</b> Start PEcAn:</a></li>
<li class="chapter" data-level="39.2.2" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#site-selection"><i class="fa fa-check"></i><b>39.2.2</b> Site Selection</a></li>
<li class="chapter" data-level="39.2.3" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#host"><i class="fa fa-check"></i><b>39.2.3</b> Host</a></li>
<li class="chapter" data-level="39.2.4" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#mode"><i class="fa fa-check"></i><b>39.2.4</b> Mode</a></li>
<li class="chapter" data-level="39.2.5" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#site-group"><i class="fa fa-check"></i><b>39.2.5</b> Site Group</a></li>
<li class="chapter" data-level="39.2.6" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#conversion"><i class="fa fa-check"></i><b>39.2.6</b> Conversion:</a></li>
<li class="chapter" data-level="39.2.7" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#site"><i class="fa fa-check"></i><b>39.2.7</b> Site:</a></li>
<li class="chapter" data-level="39.2.8" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#model-run-workflow"><i class="fa fa-check"></i><b>39.2.8</b> Model Run Workflow</a></li>
</ul></li>
<li class="chapter" data-level="39.3" data-path="pecan-hands-on-demo-01-basic-run.html"><a href="pecan-hands-on-demo-01-basic-run.html#next-steps"><i class="fa fa-check"></i><b>39.3</b> Next steps</a></li>
</ul></li>
<li class="chapter" data-level="40" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html"><i class="fa fa-check"></i><b>40</b> Demo 02: Sensitivity and Uncertainty Analysis</a><ul>
<li class="chapter" data-level="40.1" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#run-specification-1"><i class="fa fa-check"></i><b>40.1</b> Run Specification</a><ul>
<li class="chapter" data-level="40.1.1" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#additional-outputs"><i class="fa fa-check"></i><b>40.1.1</b> Additional Outputs:</a></li>
<li class="chapter" data-level="40.1.2" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#run-id"><i class="fa fa-check"></i><b>40.1.2</b> 1. Run ID:</a></li>
<li class="chapter" data-level="40.1.3" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#inputs-3"><i class="fa fa-check"></i><b>40.1.3</b> 2. Inputs:</a></li>
<li class="chapter" data-level="40.1.4" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#outputs"><i class="fa fa-check"></i><b>40.1.4</b> 3. Outputs:</a></li>
<li class="chapter" data-level="40.1.5" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#pfts"><i class="fa fa-check"></i><b>40.1.5</b> 4. PFTs:</a></li>
<li class="chapter" data-level="40.1.6" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#pecan-files"><i class="fa fa-check"></i><b>40.1.6</b> PEcAn Files:</a></li>
</ul></li>
<li class="chapter" data-level="40.2" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#global-sensitivity-shiny"><i class="fa fa-check"></i><b>40.2</b> Global Sensitivity: Shiny</a><ul>
<li class="chapter" data-level="40.2.1" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#next-steps-1"><i class="fa fa-check"></i><b>40.2.1</b> Next Steps</a></li>
<li class="chapter" data-level="40.2.2" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#assimilation-by-hand"><i class="fa fa-check"></i><b>40.2.2</b> Assimilation ‘by hand’</a></li>
<li class="chapter" data-level="40.2.3" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#mcmc-concepts"><i class="fa fa-check"></i><b>40.2.3</b> MCMC Concepts</a></li>
<li class="chapter" data-level="40.2.4" data-path="demo-02-sensitivity-and-uncertainty-analysis.html"><a href="demo-02-sensitivity-and-uncertainty-analysis.html#more-info-about-tools-analyses-and-specific-tasks"><i class="fa fa-check"></i><b>40.2.4</b> More info about tools, analyses, and specific tasks…</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="41" data-path="pecan-testing-the-sensitivity-analysis-against-observations.html"><a href="pecan-testing-the-sensitivity-analysis-against-observations.html"><i class="fa fa-check"></i><b>41</b> PEcAn: Testing the Sensitivity Analysis Against Observations"</a><ul>
<li class="chapter" data-level="41.0.1" data-path="pecan-testing-the-sensitivity-analysis-against-observations.html"><a href="pecan-testing-the-sensitivity-analysis-against-observations.html#author-ankur-desai"><i class="fa fa-check"></i><b>41.0.1</b> Author: “Ankur Desai”</a></li>
<li class="chapter" data-level="41.1" data-path="pecan-testing-the-sensitivity-analysis-against-observations.html"><a href="pecan-testing-the-sensitivity-analysis-against-observations.html#introduction-3"><i class="fa fa-check"></i><b>41.1</b> Introduction</a></li>
</ul></li>
<li class="chapter" data-level="42" data-path="simple-model-data-comparisons.html"><a href="simple-model-data-comparisons.html"><i class="fa fa-check"></i><b>42</b> Simple Model-Data Comparisons</a><ul>
<li class="chapter" data-level="42.0.1" data-path="simple-model-data-comparisons.html"><a href="simple-model-data-comparisons.html#author-istem-fer-tess-mccabe"><i class="fa fa-check"></i><b>42.0.1</b> Author: Istem Fer, Tess McCabe</a></li>
<li class="chapter" data-level="42.1" data-path="simple-model-data-comparisons.html"><a href="simple-model-data-comparisons.html#starting-rstudio-server"><i class="fa fa-check"></i><b>42.1</b> Starting RStudio Server</a></li>
<li class="chapter" data-level="42.2" data-path="simple-model-data-comparisons.html"><a href="simple-model-data-comparisons.html#read-in-settings-from-an-xml-file"><i class="fa fa-check"></i><b>42.2</b> Read in settings From an XML file</a></li>
<li class="chapter" data-level="42.3" data-path="simple-model-data-comparisons.html"><a href="simple-model-data-comparisons.html#read-in-model-output-from-specific-variables"><i class="fa fa-check"></i><b>42.3</b> Read in model output from specific variables</a></li>
<li class="chapter" data-level="42.4" data-path="simple-model-data-comparisons.html"><a href="simple-model-data-comparisons.html#compare-model-to-flux-observations"><i class="fa fa-check"></i><b>42.4</b> Compare model to flux observations</a></li>
</ul></li>
<li class="chapter" data-level="43" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html"><i class="fa fa-check"></i><b>43</b> Parameter Data Assimilation</a><ul>
<li class="chapter" data-level="43.1" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#objectives"><i class="fa fa-check"></i><b>43.1</b> Objectives</a></li>
<li class="chapter" data-level="43.2" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#larger-context"><i class="fa fa-check"></i><b>43.2</b> Larger Context</a></li>
<li class="chapter" data-level="43.3" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#connect-to-rstudio"><i class="fa fa-check"></i><b>43.3</b> Connect to Rstudio</a></li>
<li class="chapter" data-level="43.4" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#defining-variables"><i class="fa fa-check"></i><b>43.4</b> Defining variables</a></li>
<li class="chapter" data-level="43.5" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#initial-ensemble-analysis"><i class="fa fa-check"></i><b>43.5</b> Initial Ensemble Analysis</a><ul>
<li class="chapter" data-level="43.5.1" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#questions"><i class="fa fa-check"></i><b>43.5.1</b> Questions:</a></li>
</ul></li>
<li class="chapter" data-level="43.6" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#choosing-parameters"><i class="fa fa-check"></i><b>43.6</b> Choosing Parameters</a><ul>
<li class="chapter" data-level="43.6.1" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#questions-1"><i class="fa fa-check"></i><b>43.6.1</b> Questions:</a></li>
</ul></li>
<li class="chapter" data-level="43.7" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#editing-pecan-settings"><i class="fa fa-check"></i><b>43.7</b> Editing PEcAn settings</a></li>
<li class="chapter" data-level="43.8" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#investigating-pecan-function-pda.emulator-optional"><i class="fa fa-check"></i><b>43.8</b> Investigating PEcAn function pda.emulator (optional)</a></li>
<li class="chapter" data-level="43.9" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#running-a-demo-pda"><i class="fa fa-check"></i><b>43.9</b> Running a demo PDA</a></li>
<li class="chapter" data-level="43.10" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#outputs-from-pecans-parameter-data-assimilation"><i class="fa fa-check"></i><b>43.10</b> Outputs from PEcAn’s Parameter Data Assimilation</a><ul>
<li class="chapter" data-level="43.10.1" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#questions-2"><i class="fa fa-check"></i><b>43.10.1</b> Questions:</a></li>
</ul></li>
<li class="chapter" data-level="43.11" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#post-pda-analyses"><i class="fa fa-check"></i><b>43.11</b> Post-PDA analyses</a><ul>
<li class="chapter" data-level="43.11.1" data-path="parameter-data-assimilation-1.html"><a href="parameter-data-assimilation-1.html#questions-3"><i class="fa fa-check"></i><b>43.11.1</b> Questions:</a></li>
</ul></li>
</ul></li>
<li class="chapter" data-level="44" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html"><i class="fa fa-check"></i><b>44</b> State-Variable Data Assimilation</a><ul>
<li class="chapter" data-level="44.1" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#objectives-1"><i class="fa fa-check"></i><b>44.1</b> Objectives:</a></li>
<li class="chapter" data-level="44.2" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#overview-1"><i class="fa fa-check"></i><b>44.2</b> Overview:</a><ul>
<li class="chapter" data-level="44.2.1" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#initial-run"><i class="fa fa-check"></i><b>44.2.1</b> Initial Run</a></li>
<li class="chapter" data-level="44.2.2" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#settings-1"><i class="fa fa-check"></i><b>44.2.2</b> Settings:</a></li>
<li class="chapter" data-level="44.2.3" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#loading-data-1"><i class="fa fa-check"></i><b>44.2.3</b> Loading data</a></li>
<li class="chapter" data-level="44.2.4" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#estimating-tree-level-data-uncertainties"><i class="fa fa-check"></i><b>44.2.4</b> Estimating tree-level data uncertainties</a></li>
</ul></li>
<li class="chapter" data-level="44.3" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#allometric-equations"><i class="fa fa-check"></i><b>44.3</b> Allometric equations</a></li>
<li class="chapter" data-level="44.4" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#estimate-stand-level-npp"><i class="fa fa-check"></i><b>44.4</b> Estimate stand-level NPP</a></li>
<li class="chapter" data-level="44.5" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#build-initial-conditions"><i class="fa fa-check"></i><b>44.5</b> Build Initial Conditions</a></li>
<li class="chapter" data-level="44.6" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#load-priors"><i class="fa fa-check"></i><b>44.6</b> Load Priors</a></li>
<li class="chapter" data-level="44.7" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#ensemble-kalman-filter"><i class="fa fa-check"></i><b>44.7</b> Ensemble Kalman Filter</a></li>
<li class="chapter" data-level="44.8" data-path="state-variable-data-assimilation.html"><a href="state-variable-data-assimilation.html#finishing-up"><i class="fa fa-check"></i><b>44.8</b> Finishing up</a></li>
</ul></li>
<li class="chapter" data-level="45" data-path="data-assimilation-concepts.html"><a href="data-assimilation-concepts.html"><i class="fa fa-check"></i><b>45</b> Data Assimilation Concepts"</a><ul>
<li class="chapter" data-level="45.1" data-path="data-assimilation-concepts.html"><a href="data-assimilation-concepts.html#fitting-the-model"><i class="fa fa-check"></i><b>45.1</b> Fitting the model</a></li>
<li class="chapter" data-level="45.2" data-path="data-assimilation-concepts.html"><a href="data-assimilation-concepts.html#whats-going-on"><i class="fa fa-check"></i><b>45.2</b> What’s going on</a></li>
<li class="chapter" data-level="45.3" data-path="data-assimilation-concepts.html"><a href="data-assimilation-concepts.html#evaluating-the-model-output"><i class="fa fa-check"></i><b>45.3</b> Evaluating the model output</a></li>
<li class="chapter" data-level="45.4" data-path="data-assimilation-concepts.html"><a href="data-assimilation-concepts.html#additional-information"><i class="fa fa-check"></i><b>45.4</b> Additional information</a></li>
<li class="chapter" data-level="45.5" data-path="data-assimilation-concepts.html"><a href="data-assimilation-concepts.html#citations"><i class="fa fa-check"></i><b>45.5</b> Citations</a></li>
</ul></li>
<li class="part"><span><b>VIII Appendix</b></span></li>
<li class="chapter" data-level="46" data-path="faq.html"><a href="faq.html"><i class="fa fa-check"></i><b>46</b> FAQ</a></li>
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<div id="available-meteorological-drivers" class="section level1">
<h1><span class="header-section-number">33</span> Available Meteorological Drivers</h1>
<div id="ameriflux" class="section level2">
<h2><span class="header-section-number">33.1</span> Ameriflux</h2>
<p>Scale: site</p>
<p>Resolution: 30 or 60 min</p>
<p>Availability: varies by site <a href="http:\/\/ameriflux.lbl.gov\/data\/data-availability\/" class="uri">http:\/\/ameriflux.lbl.gov\/data\/data-availability\/</a></p>
<p>Notes: Old ORNL server, use is deprecated</p>
</div>
<div id="amerifluxlbl" class="section level2">
<h2><span class="header-section-number">33.2</span> AmerifluxLBL</h2>
<p>Scale: site</p>
<p>Resolution: 30 or 60 min</p>
<p>Availability: varies by site <a href="http:\/\/ameriflux.lbl.gov\/data\/data-availability\/" class="uri">http:\/\/ameriflux.lbl.gov\/data\/data-availability\/</a></p>
<p>Notes: new Lawrence Berkeley Lab server</p>
</div>
<div id="fluxnet2015" class="section level2">
<h2><span class="header-section-number">33.3</span> Fluxnet2015</h2>
<p>Scale: site</p>
<p>Resolution: 30 or 60 min</p>
<p>Availability: varies by site <a href="http://fluxnet.fluxdata.org/sites/site-list-and-pages/">http://fluxnet.fluxdata.org/sites/site-list-and-pages</a></p>
<p>Notes: Fluxnet 2015 synthesis product. Does not cover all FLUXNET sites</p>
</div>
<div id="narr" class="section level2">
<h2><span class="header-section-number">33.4</span> NARR</h2>
<p>Scale: North America</p>
<p>Resolution: 3 hr, approx. 32km <span class="math inline">\(Lambert conical projection\)</span></p>
<p>Availability: 1979-present</p>
</div>
<div id="cruncep" class="section level2">
<h2><span class="header-section-number">33.5</span> CRUNCEP</h2>
<p>Scale: global</p>
<p>Resolution: 6hr, 0.5 degree</p>
<p>Availability: 1901-2010</p>
</div>
<div id="cmip5" class="section level2">
<h2><span class="header-section-number">33.6</span> CMIP5</h2>
<p>Scale: varies by model</p>
<p>Resolution: 3 hr</p>
<p>Availability: 2006-2100</p>
<p>Currently only GFDL available. Different scenerios and ensemble members can be set via Advanced Edit.</p>
</div>
<div id="nldas" class="section level2">
<h2><span class="header-section-number">33.7</span> NLDAS</h2>
<p>Scale: Lower 48 + buffer,</p>
<p>Resolution: 1 hour, .125 degree</p>
<p>Availability: 1980-present</p>
</div>
<div id="gldas" class="section level2">
<h2><span class="header-section-number">33.8</span> GLDAS</h2>
<p>Scale: Global</p>
<p>Resolution: 3hr, 1 degree</p>
<p>Availability: 1948-2010</p>
</div>
<div id="paleon" class="section level2">
<h2><span class="header-section-number">33.9</span> PalEON</h2>
<p>Scale: -100 to -60 W Lon, 35 to 50 N Latitude <span class="math inline">\(US northern hardwoods + buffer\)</span></p>
<p>Resolution: 6hr, 0.5 degree</p>
<p>Availability: 850-2010</p>
</div>
<div id="fluxnetlathuile" class="section level2">
<h2><span class="header-section-number">33.10</span> FluxnetLaThuile</h2>
<p>Scale: site</p>
<p>Resolution: 30 or 60 min</p>
<p>Availability: varies by site <a href="http:\/\/www.fluxdata.org\/DataInfo\/Dataset%20Doc%20Lib\/SynthDataSummary.aspx">http:\/\/www.fluxdata.org\/DataInfo\/Dataset%20Doc%20Lib\/SynthDataSummary.aspx</a></p>
<p>Notes: 2007 synthesis. Fluxnet2015 supercedes this for sites that have been updated</p>
</div>
<div id="geostreams" class="section level2">
<h2><span class="header-section-number">33.11</span> Geostreams</h2>
<p>Scale: site</p>
<p>Resolution: varies</p>
<p>Availability: varies by site</p>
<p>Notes: This is a protocol, not a single archive. The PEcAn functions currently default to querying [<a href="https://terraref.ncsa.illinois.edu/clowder/api/geostreams" class="uri">https://terraref.ncsa.illinois.edu/clowder/api/geostreams</a>], which requires login and contains data from only two sites (Urbana IL and Maricopa AZ). However the interface can be used with any server that supports the <a href="https://opensource.ncsa.illinois.edu/confluence/display/CATS/Geostreams+API">Geostreams API</a>.</p>
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