We review the study of inhomogeneous perturbations about a homogeneous and
isotropic background cosmology. We adopt a coordinate based approach, but give
geometrical interpretations of metric perturbations in terms of the expansion,
shear and curvature of constant-time hypersurfaces and the orthogonal timelike
vector field. We give the gauge transformation rules for metric and matter
variables at first and second order. We show how gauge invariant variables are
constructed by identifying geometric or matter variables in physically-defined
coordinate systems, and give the relations between many commonly used
gauge-invariant variables. In particular we show how the Einstein equations or
energy-momentum conservation can be used to obtain simple evolution equations
at linear order, and discuss extensions to non-linear order. We present
evolution equations for systems with multiple interacting fluids and scalar
fields, identifying adiabatic and entropy perturbations. As an application we
consider the origin of primordial curvature and isocurvature perturbations from
field perturbations during inflation in the very early universe.Comment: 96 pages, submitted to Phys. Rep; v2: minor changes, typos corrected,
references added, 1 figure added, corresponds to published versio