
\chapter{Installation, configuration, basic usage}\label{ch:0}

\chapter{Climate dynamics \& experimental design}\label{ch:climate-dynamics}

\chapter{Ocean circulation}\label{ch:ocean-circulation}

\chapter{Climates of Past Worlds}\label{ch:past-worlds}

\chapter{Alternative Worlds}\label{ch:alternative-worlds}

\chapter{Fossil fuel CO$_{2}$ and ‘ocean acidification’}\label{ch:fossil-fuel-co2}

\chapter{Ocean biogeochemical cycles}\label{ch:ocean=biogeochem}

\chapter{Marine ecosystems and dynamics}\label{ch:marine-ecosystems}

\chapter{The land surface}\label{ch:land-surface}

\chapter{Atmospheric dynamics}\label{ch:atmospheric-dynamics}

\chapter{Geological carbon processes}\label{ch:geological-carbon}

\chapter{Proxies and Reconstructing the Past}\label{ch:proxies}

\chapter{Synthesis: Earth system dynamics}\label{ch:earth-system-dynamics}

\chapter{muffin model output}\label{ch:model-output}

\chapter{Introduction to model results analysis}\label{ch:results-analysis}

\chapter{muffinplot}\label{ch:muffinplot}

\chapter{muffindata}\label{ch:muffindata}

\chapter{muffingen}\label{ch:muffingen}

\chapter{FAQ}\label{ch:faq}
\label{faq:installation}

\chapter{HOW-TO (technical)}\label{ch:how-to-technical}

\chapter{HOW-TO (experiment)}\label{ch:how-to-experiment}
\label{howto:weatheringfeedback1}
\label{howto:weatheringfeedback2}
\label{howto:OMEN-SED}

\chapter{Model Code}\label{ch:model-code}

\chapter{Examples}\label{ch:examples}

\chapter{Appendix I -- Tables}\label{ch:appendix-i}
