This handbook is organized into five chapters that provide an overview of the theoretical underpinnings and history of systems research, give concrete examples of existing systems research projects, and offer detailed practical guidance on how to organize and execute a collaborative systems project. Each chapter includes a case study that highlights key facets of a systems research approach. An extensive list of recommended resources for each chapter can be found at the back of the book on p. 87–91.

Chapter 1, Introduction to Agricultural Systems and Agricultural Systems Research: A Paradigm Change, defines agricultural systems for the purpose of systems research, compares systems research with reductionist research methods, briefly describes the background and theory of agroecological and agricultural systems research, and provides concrete examples for shifting to a systems research paradigm.

Chapter 2, Collaboration, Decision Making and Organizational Structure for Agricultural Systems Research, provides guidance on how to develop leadership, teamwork and collaboration, build an interdisciplinary research team, instill a culture of collaboration, engage farmers and other nonacademic stakeholders in the research process, be an effective facilitator, conduct productive meetings, and manage inevitable tensions and disagreements.

Chapter 3, Planning Interdisciplinary Agricultural Systems Research, focuses on the process of planning a systems research project, including goal setting, hypothesis development, experimental design, site selection, statistical method considerations, and financial planning.

Chapter 4, Analyzing the Performance and Sustainability of Agricultural Systems, considers methods for managing complex data sets generated by systems projects, including statistical and mathematical tools (univariate and multivariate analyses and mathematical modeling), natural resource accounting methods (life cycle assessments, ecological footprints and carbon footprints), and sustainability indicators.

Chapter 5, Implementing a Systems Research Project: Troubleshooting and Putting It All Together, assembles the remaining pieces, with an emphasis on moving a project from startup to final publication, and provides a roadmap for developing and confirming plans, dealing with budget and accountability issues, and building flexible, resilient organizational structures.