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 Submitting Workflow from Command Line
15 Workflow modules
- 15.1 Overview
- 15.2 Glossary
16 Adding to PEcAn
- 16.1 Case studies
- 16.2 Adding An Ecosystem Model
17 Formats records in BETY
18 Creating a new Format record in BETY
19 Reference Runs
20 Pecan Data Ingest via Web Interface
21 Working with the VM
- 21.1 Connecting to the VM via SSH
- 21.2 Connecting to bety on the VM via SSh
22 VM Desktop Conversion
- 22.0.1 Install RStudio Desktop
V Developer user guide
23 Introduction: Developer Guide
24 PEcAn Setup
25 Maintaining PEcAn
26 Git and GitHub Workflow
- 26.1 Using Git
- 26.2 GitHub use with PEcAn
27 Coding Practices
28 Directory structure
- 28.1 Overview of PEcAn repository as of PEcAn 1.5.3
- 28.2 Generic R package structure:
VI Reference Materials
29 PEcAn standard formats
- 29.1 Defining new input formats
  - 29.1.1 Input Standards
  - 29.1.2 Output Standards
30 PEcAn Models
31 Template MODEL page
32 Available Meteorological Drivers
33 Docker
34 SHINY
- 34.0.1 Debugging Shiny Apps
35 Debugging
36 RabbitMQ
37 Data assimilation with DART
VII Demos and Vignettes
38 PEcAn Hands-On Demo 01: Basic Run
39 Demo 02: Sensitivity and Uncertainty Analysis
- 39.1 Run Specification
- 39.2 Global Sensitivity: Shiny
40 PEcAn: Testing the Sensitivity Analysis Against Observations"
- 40.0.1 Author: “Ankur Desai”
- 40.1 Introduction
41 Simple Model-Data Comparisons
42 Parameter Data Assimilation
43 State-Variable Data Assimilation
44 Data Assimilation Concepts"
45 Introduction to the PEcAn R API
VIII Appendix
46 FAQ

The Predictive Ecosystem Analyzer

23 Introduction: Developer Guide

This section is for users who will be actively developing PEcAn.