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We explore several physical effects on the power spectrum of the Lyman-alpha forest transmitted flux. The effects we investigate here are usually not part of hydrodynamic simulations and so need to be estimated separately. The most…
The analysis of the Lyman-alpha forest of absorption lines in quasar spectra has emerged as a potentially powerful technique to constrain the linear matter power spectrum. In most previous work, the amplitude of the ionizing background was…
Trend filtering---first introduced into the astronomical literature in Paper I of this series---is a state-of-the-art statistical tool for denoising one-dimensional signals that possess varying degrees of smoothness. In this work, we…
Lyman-alpha forest data probing the post-reionization Universe shows surprisingly large opacity fluctuations over rather large ($\ge$50 comoving Mpc/h) spatial scales. We model these fluctuations using a hybrid approach utilizing the large…
We have developed two independent methods to measure the one-dimensional power spectrum of the transmitted flux in the Lyman-$\alpha$ forest. The first method is based on a Fourier transform, and the second on a maximum likelihood…
We present the measurement of Baryon Acoustic Oscillations (BAO) from the Lyman-$\alpha$ (Ly$\alpha$) forest of high-redshift quasars with the first-year dataset of the Dark Energy Spectroscopic Instrument (DESI). Our analysis uses over…
We investigate the properties of the Lyman alpha forest as predicted by numerical simulations for a range of currently viable cosmological models. This is done in order to understand the dependencies of the forest on cosmological…
On large scales, the Lyman-$\alpha$ forest provides insights into the expansion history of the Universe, while on small scales, it imposes strict constraints on the growth history, the nature of dark matter, and the sum of neutrino masses.…
We derive and numerically implement an algorithm for estimating the 3D power spectrum of the Lyman-$\alpha$ (Ly-$\alpha$) forest flux fluctuations. The algorithm exploits the unique geometry of Ly-$\alpha$ forest data to efficiently measure…
We study and compare fitting methods for the Lyman-$\alpha$ (Ly$\alpha$) forest 3D correlation function. We use the nested sampler PolyChord and the community code picca to perform a Bayesian analysis which we compare with previous…
Using a sample of approximately 14,000 z>2.1 quasars observed in the first year of the Baryon Oscillation Spectroscopic Survey (BOSS), we measure the three-dimensional correlation function of absorption in the Lyman-alpha forest. The…
Using synthetic Lyman-$\alpha$ forests from the Dark Energy Spectroscopic Instrument (DESI) survey, we present a study of the impact of errors in the estimation of quasar redshift on the Lyman-$\alpha$ correlation functions. Estimates of…
We measure the power spectrum, P_F(k,z), of the transmitted flux in the Ly-alpha forest using 3035 high redshift quasar spectra from the Sloan Digital Sky Survey. This sample is almost two orders of magnitude larger than any previously…
The flux/transmission power spectrum has become a popular statistical tool in studies of the high redshift ($z > 2$) Lyman-alpha forest. At low redshifts, where the forest has thinned out into a series of well-isolated absorption lines, the…
We present the Baryon Acoustic Oscillation (BAO) measurements with the Lyman-alpha (LyA) forest from the second data release (DR2) of the Dark Energy Spectroscopic Instrument (DESI) survey. Our BAO measurements include both the…
A shift of the baryon acoustic oscillation (BAO) scale to smaller values than predicted by linear theory was observed in simulations. In this paper, we try to provide an intuitive physical understanding of why this shift occurs, explaining…
We discuss the determination of the linear power spectrum of dark matter fluctuations from measurements of the transmitted flux Ly-alpha Forest power spectrum. We show that at most scales probed by current measurements, the flux power…
[abridged] We describe LyMAS (Ly-alpha Mass Association Scheme), a method of predicting clustering statistics in the Ly-alpha forest on large scales from moderate resolution simulations of the dark matter distribution, with calibration from…
Fluctuations in Lyman-$\alpha$ (Ly$\alpha$) forest transmission towards high-$z$ quasars are partially sourced from spatial fluctuations in the ultraviolet background (UVB), the level of which are set by the mean free path of ionizing…
Random forests are a statistical learning technique that use bootstrap aggregation to average high-variance and low-bias trees. Improvements to random forests, such as applying Lasso regression to the tree predictions, have been proposed in…