Comparing Simulations and Observations of the Lyman-Alpha Forest I. Methodology

We describe techniques for comparing spectra extracted from cosmological simulations and observational data, using the same methodology to link Lyman-alpha properties derived from the simulations with properties derived from observational data. The eventual goal is to measure the coherence or clustering properties of Lyman-alpha absorbers using observations of quasar pairs and groups. We quantify the systematic underestimate in opacity that is inherent in the continuum fitting process of observed spectra over a range of resolution and signal-to-noise ratio. We present an automated process for detecting and selecting absorption features over the range of resolution and signal-to-noise of typical observational data on the Lyman-alpha "forest". Using these techniques, we detect coherence over transverse scales out to 500 h^{-1}_{50} kpc in spectra extracted from a cosmological simulation at z = 2