Welcome
I Introduction
1 Project Overview
2 Contributor Covenant Code of Conduct
3 About the PEcAn Book
- 3.0.1 Main Topics
- 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
8 Additional web configuration
9 Settings-configured analyses
10 Remote execution with PEcAn
IV Advanced user guide
11 Introduction
12 PEcAn workflow (web/workflow.R)
13 Submitting Workflow from Command Line
14 Workflow modules
- 14.1 Overview
- 14.2 Glossary
15 Adding to PEcAn
- 15.1 Case studies
- 15.2 Adding An Ecosystem Model
16 Formats records in BETY
17 Creating a new Format record in BETY
18 Reference Runs
19 Working with the VM
- 19.1 Connecting to the VM via SSH
- 19.2 Connecting to bety on the VM via SSh
20 VM Desktop Conversion
- 20.0.1 Install RStudio Desktop
V Developer user guide
21 Introduction: Developer Guide
22 PEcAn Setup
23 Maintaining PEcAn
24 Git and GitHub Workflow
25 Coding Practices
26 Directory structure
- 26.1 Overview of PEcAn repository as of PEcAn 1.5.3
- 26.2 Generic R package structure:
VI Reference Materials
27 PEcAn standard formats
- 27.1 Defining new input formats
  - 27.1.1 Outputs
28 Models in PEcAn
29 PEcAn Models
30 Template MODEL page
- 30.1 Model Variables
31 Available Meteorological Drivers
32 PEcAn Docker Architecture
33 What is Docker?
34 Dockerfiles for Models
- 34.1 SIPNET
  - 34.1.1 Using the PEcAn download.file() function
35 Debugging
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"
39 Simple Model-Data Comparisons
40 Parameter Data Assimilation
41 State-Variable Data Assimilation
42 Data Assimilation Concepts"
VIII Appendix
43 FAQ

The Predictive Ecosystem Analyzer

21 Introduction: Developer Guide

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