Welcome
I Introduction
1 Project Overview
2 Contributor Covenant Code of Conduct
3 About the PEcAn Book
- 3.1 How to Contribute
  - 3.1.1 Editing the book yourself
  - 3.1.2 Feedback/Comments/Suggestions
II Basic User Guide
4 Getting Started
5 Web workflow
- 5.1 Site and model selection
  - 5.1.1 Selecting a model
  - 5.1.2 Selecting a site
- 5.2 Model configuration
III Intermediate user guide
6 Introduction
7 The PEcAn XML
- 7.1 Core configuration
- 7.2 Advanced features
8 Additional web configuration
9 Settings-configured analyses
10 Remote execution with PEcAn
11 The PEcAn Docker API
- 11.1 Installation
- 11.2 Creating and submitting a workflow
IV Advanced user guide
12 Introduction
13 PEcAn workflow (web/workflow.R)
14 Adding to PEcAn
15 Standalone tools (modules)
- 15.1 Loading Data in PEcAn
  - 15.1.1 Function load_data
  - 15.1.2 Example
16 Working with the VM
- 16.1 Connecting to the VM via SSH
- 16.2 Connecting to bety on the VM via SSh
17 Workflow modules
- 17.1 Overview
- 17.2 Glossary
18 Submitting Workflow from Command Line
19 VM Desktop Conversion
- 19.0.1 Install RStudio Desktop
V Developer user guide
20 Introduction: Developer Guide
21 PEcAn Setup
22 Maintaining PEcAn
23 Git and GitHub Workflow
- 23.1 Using Git
- 23.2 GitHub use with PEcAn
24 Coding Practices
25 Directory structure
- 25.1 Overview of PEcAn repository as of PEcAn 1.5.3
- 25.2 Generic R package structure:
VI Reference Materials
26 PEcAn standard formats
- 26.1 Defining new input formats
  - 26.1.1 Input Standards
  - 26.1.2 Output Standards
27 PEcAn Models
28 Template MODEL page
29 Available Meteorological Drivers
30 Docker
31 SHINY
- 31.0.1 Debugging Shiny Apps
32 Debugging
33 RabbitMQ
34 Editing this book
35 Data assimilation with DART
VII Demos and Vignettes
36 PEcAn Hands-On Demo 01: Basic Run
37 Demo 02: Sensitivity and Uncertainty Analysis
- 37.1 Run Specification
- 37.2 Global Sensitivity: Shiny
38 PEcAn: Testing the Sensitivity Analysis Against Observations"
- 38.0.1 Author: “Ankur Desai”
- 38.1 Introduction
39 Simple Model-Data Comparisons
40 Parameter Data Assimilation
41 State-Variable Data Assimilation
42 Data Assimilation Concepts"
43 Introduction to the PEcAn R API
VIII Appendix
44 FAQ

The Predictive Ecosystem Analyzer

44 FAQ