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The estimation of uncertainties in cosmological parameters is an important challenge in Large-Scale-Structure (LSS) analyses. For standard analyses such as Baryon Acoustic Oscillations (BAO) and Full Shape, two approaches are usually considered. First: analytical estimates of the covariance matrix use Gaussian approximations and (nonlinear) clustering measurements to estimate the matrix, which allows a relatively fast and computationally cheap way to generate matrices that adapt to an arbitrary clustering measurement. On the other hand, sample covariances are an empirical estimate of the matrix based on en ensemble of clustering measurements from fast and approximate simulations. While more computationally expensive due to the large amount of simulations and volume required, these allow us to take into account systematics that are impossible to model analytically. In this work we compare these two approaches in order to enable DESI's key analyses. We find that the configuration space analytical estimate performs satisfactorily in BAO analyses and its flexibility in terms of input clustering makes it the fiducial choice for DESI's 2024 BAO analysis. On the contrary, the analytical computation of the covariance matrix in Fourier space does not reproduce the expected measurements in terms of Full Shape analyses, which motivates the use of a corrected mock covariance for DESI's Full Shape analysis., Comment: 23 pages, 5 figures 7 tables, submitted to JCAP

We present three separate void catalogs created using a volume-limited sample of the DESI Year 1 Bright Galaxy Survey. We use the algorithms VoidFinder and V2 to construct void catalogs out to a redshift of z=0.24. We obtain 1,461 interior voids with VoidFinder, 420 with V2 using REVOLVER pruning, and 295 with V2 using VIDE pruning. Comparing our catalog with an overlapping SDSS void catalog, we find generally consistent void properties but significant differences in the void volume overlap, which we attribute to differences in the galaxy selection and survey masks. These catalogs are suitable for studying the variation in galaxy properties with cosmic environment and for cosmological studies., Comment: 17 pages, 6 figures

We measure the growth of cosmic density fluctuations on large scales and across the redshift range $0.3

The Large Magellanic Cloud (LMC) is a Milky Way (MW) satellite that is massive enough to gravitationally attract the MW disc and inner halo, causing significant motion of the inner MW with respect to the outer halo. In this work, we probe this interaction by constructing a sample of 9,866 blue horizontal branch (BHB) stars with radial velocities from the DESI spectroscopic survey out to 120 kpc from the Galactic centre. This is the largest spectroscopic set of BHB stars in the literature to date, and it contains four times more stars with Galactocentric distances beyond 50 kpc than previous BHB catalogues. Using the DESI BHB sample combined with SDSS BHBs, we measure the bulk radial velocity of stars in the outer halo and observe that the velocity in the Southern Galactic hemisphere is different by 3.7$\sigma$ from the North. Modelling the projected velocity field shows that its dipole component is directed at a point 22 degrees away from the LMC along its orbit, which we interpret as the travel direction of the inner MW. The velocity field includes a monopole term that is -24 km/s, which we refer to as compression velocity. This velocity is significantly larger than predicted by the current models of the MW and LMC interaction. This work uses DESI data from its first two years of observations, but we expect that with upcoming DESI data releases, the sample of BHB stars will increase and our ability to measure the MW-LMC interaction will improve significantly., Comment: 22 pages, 19 figures. Submitted to MNRAS

We explore correlations between the orientations of small galaxy groups, or "multiplets", and the large-scale gravitational tidal field. Using data from the Dark Energy Spectroscopic Instrument (DESI) Y1 survey, we detect the intrinsic alignment (IA) of multiplets to the galaxy-traced matter field out to separations of 100 Mpc/h. Unlike traditional IA measurements of individual galaxies, this estimator is not limited by imaging of galaxy shapes and allows for direct IA detection beyond redshift z = 1. Multiplet alignment is a form of higher-order clustering, for which the scale-dependence traces the underlying tidal field and amplitude is a result of small-scale (< 1 Mpc/h) dynamics. Within samples of bright galaxies (BGS), luminous red galaxies (LRG) and emission-line galaxies (ELG), we find similar scale-dependence regardless of intrinsic luminosity or colour. This is promising for measuring tidal alignment in galaxy samples that typically display no intrinsic alignment. DESI's LRG mock galaxy catalogues created from the AbacusSummit N-body simulations produce a similar alignment signal, though with a 33% lower amplitude at all scales. An analytic model using a non-linear power spectrum (NLA) only matches the signal down to 20 Mpc/h. Our detection demonstrates that galaxy clustering in the non-linear regime of structure formation preserves an interpretable memory of the large-scale tidal field. Multiplet alignment complements traditional two-point measurements by retaining directional information imprinted by tidal forces, and contains additional line-of-sight information compared to weak lensing. This is a more effective estimator than the alignment of individual galaxies in dense, blue, or faint galaxy samples., Comment: For an accessible summary of this paper, see https://cmlamman.github.io/doc/multipletIA_summary.pdf

We study of the properties of a new class of circumgalactic medium absorbers identified in the Lyman-$\alpha$ forest: "Strong, Blended Lyman-$\alpha$" (or SBLA) absorption systems. We study SBLAs at $2.4 -2.40$ for $T=10^{3.5}$K and show gas clumping on $<210$ parsec scales. We fit multiphase models to this strong sub-population and find a low ionization phase with $n_H=1$cm$^{-3}$, $T=10^{3.5}$K and $[X/H]=0.8$, an intermediate ionization phase with $\log(n_H / $cm$^{-3}) = -3.05$, $T=10^{3.5}$K and $[X/H]=-0.8$, and a poorly constrained higher ionization phase. We find that the low ionization phase favours cold, dense super-solar metallicity gas with a clumping scale of just 0.009 parsecs., Comment: 28 pages, accepted for publication in MNRAS. Updated version of CLOUDY and UV background model. Many small changes to results with no impact on overall conclusions

We present a list of quasar candidates including photometric redshift estimates from the miniJPAS Data Release constructed using SQUEzE. This work is based on machine-learning classification of photometric data of quasar candidates using SQUEzE. It has the advantage that its classification procedure can be explained to some extent, making it less of a `black box' when compared with other classifiers. Another key advantage is that using user-defined metrics means the user has more control over the classification. While SQUEzE was designed for spectroscopic data, here we adapt it for multi-band photometric data, i.e. we treat multiple narrow-band filters as very low-resolution spectra. We train our models using specialized mocks from Queiroz et al. (2022). We estimate our redshift precision using the normalized median absolute deviation, $\sigma_{\rm NMAD}$ applied to our test sample. Our test sample returns an $f_1$ score (effectively the purity and completeness) of 0.49 for quasars down to magnitude $r=24.3$ with $z\geq2.1$ and 0.24 for quasars with $z<2.1$. For high-z quasars, this goes up to 0.9 for $r<21.0$. We present two catalogues of quasar candidates including redshift estimates: 301 from point-like sources and 1049 when also including extended sources. We discuss the impact of including extended sources in our predictions (they are not included in the mocks), as well as the impact of changing the noise model of the mocks. We also give an explanation of SQUEzE reasoning. Our estimates for the redshift precision using the test sample indicate a $\sigma_{NMAD}=0.92\%$ for the entire sample, reduced to 0.81\% for $r<22.5$ and 0.74\% for $r<21.3$. Spectroscopic follow-up of the candidates is required in order to confirm the validity of our findings., Comment: Accepted in A&A 24 pages, 24 figures, 7 tables

We present and validate the catalog of Lyman-$\alpha$ forest fluctuations for 3D analyses using the Early Data Release (EDR) from the Dark Energy Spectroscopic Instrument (DESI) survey. We used 88,511 quasars collected from DESI Survey Validation (SV) data and the first two months of the main survey (M2). We present several improvements to the method used to extract the Lyman-$\alpha$ absorption fluctuations performed in previous analyses from the Sloan Digital Sky Survey (SDSS). In particular, we modify the weighting scheme and show that it can improve the precision of the correlation function measurement by more than 20%. This catalog can be downloaded from https://data.desi.lbl.gov/public/edr/vac/edr/lya/fuji/v0.3 and it will be used in the near future for the first DESI measurements of the 3D correlations in the Lyman-$\alpha$ forest.

We present the one-dimensional Lyman-$\alpha$ forest power spectrum measurement using the first data provided by the Dark Energy Spectroscopic Instrument (DESI). The data sample comprises $26,330$ quasar spectra, at redshift $z > 2.1$, contained in the DESI Early Data Release and the first two months of the main survey. We employ a Fast Fourier Transform (FFT) estimator and compare the resulting power spectrum to an alternative likelihood-based method in a companion paper. We investigate methodological and instrumental contaminants associated to the new DESI instrument, applying techniques similar to previous Sloan Digital Sky Survey (SDSS) measurements. We use synthetic data based on log-normal approximation to validate and correct our measurement. We compare our resulting power spectrum with previous SDSS and high-resolution measurements. With relatively small number statistics, we successfully perform the FFT measurement, which is already competitive in terms of the scale range. At the end of the DESI survey, we expect a five times larger Lyman-$\alpha$ forest sample than SDSS, providing an unprecedented precise one-dimensional power spectrum measurement., Comment: 23 pages, 23 figures, Journal version

This paper is part of large effort within the J-PAS collaboration that aims to classify point-like sources in miniJPAS, which were observed in 60 optical bands over $\sim$ 1 deg$^2$ in the AEGIS field. We developed two algorithms based on artificial neural networks (ANN) to classify objects into four categories: stars, galaxies, quasars at low redshift ($z < 2.1)$, and quasars at high redshift ($z \geq 2.1$). As inputs, we used miniJPAS fluxes for one of the classifiers (ANN$_1$) and colours for the other (ANN$_2$). The ANNs were trained and tested using mock data in the first place. We studied the effect of augmenting the training set by creating hybrid objects, which combines fluxes from stars, galaxies, and quasars. Nevertheless, the augmentation processing did not improve the score of the ANN. We also evaluated the performance of the classifiers in a small subset of the SDSS DR12Q superset observed by miniJPAS. In the mock test set, the f1-score for quasars at high redshift with the ANN$_1$ (ANN$_2$) are $0.99$ ($0.99$), $0.93$ ($0.92$), and $0.63$ ($0.57$) for $17 < r \leq 20$, $20 < r \leq 22.5$, and $22.5 < r \leq 23.6$, respectively, where $r$ is the J-PAS rSDSS band. In the case of low-redshift quasars, galaxies, and stars, we reached $0.97$ ($0.97$), $0.82$ ($0.79$), and $0.61$ ($0.58$); $0.94$ ($0.94$), $0.90$ ($0.89$), and $0.81$ ($0.80$); and $1.0$ ($1.0$), $0.96$ ($0.94$), and $0.70$ ($0.52$) in the same r bins. In the SDSS DR12Q superset miniJPAS sample, the weighted f1-score reaches 0.87 (0.88) for objects that are mostly within $20 < r \leq 22.5$. Finally, we estimate the number of point-like sources that are quasars, galaxies, and stars in miniJPAS.

Astrophysical surveys rely heavily on the classification of sources as stars, galaxies or quasars from multi-band photometry. Surveys in narrow-band filters allow for greater discriminatory power, but the variety of different types and redshifts of the objects present a challenge to standard template-based methods. In this work, which is part of larger effort that aims at building a catalogue of quasars from the miniJPAS survey, we present a Machine Learning-based method that employs Convolutional Neural Networks (CNNs) to classify point-like sources including the information in the measurement errors. We validate our methods using data from the miniJPAS survey, a proof-of-concept project of the J-PAS collaboration covering $\sim$ 1 deg$^2$ of the northern sky using the 56 narrow-band filters of the J-PAS survey. Due to the scarcity of real data, we trained our algorithms using mocks that were purpose-built to reproduce the distributions of different types of objects that we expect to find in the miniJPAS survey, as well as the properties of the real observations in terms of signal and noise. We compare the performance of the CNNs with other well-established Machine Learning classification methods based on decision trees, finding that the CNNs improve the classification when the measurement errors are provided as inputs. The predicted distribution of objects in miniJPAS is consistent with the putative luminosity functions of stars, quasars and unresolved galaxies. Our results are a proof-of-concept for the idea that the J-PAS survey will be able to detect unprecedented numbers of quasars with high confidence., Comment: 16 pages, 15 figures, published by MNRAS

WEAVE, the new wide-field, massively multiplexed spectroscopic survey facility for the William Herschel Telescope, will see first light in late 2022. WEAVE comprises a new 2-degree field-of-view prime-focus corrector system, a nearly 1000-multiplex fibre positioner, 20 individually deployable 'mini' integral field units (IFUs), and a single large IFU. These fibre systems feed a dual-beam spectrograph covering the wavelength range 366$-$959\,nm at $R\sim5000$, or two shorter ranges at $R\sim20\,000$. After summarising the design and implementation of WEAVE and its data systems, we present the organisation, science drivers and design of a five- to seven-year programme of eight individual surveys to: (i) study our Galaxy's origins by completing Gaia's phase-space information, providing metallicities to its limiting magnitude for $\sim$3 million stars and detailed abundances for $\sim1.5$ million brighter field and open-cluster stars; (ii) survey $\sim0.4$ million Galactic-plane OBA stars, young stellar objects and nearby gas to understand the evolution of young stars and their environments; (iii) perform an extensive spectral survey of white dwarfs; (iv) survey $\sim400$ neutral-hydrogen-selected galaxies with the IFUs; (v) study properties and kinematics of stellar populations and ionised gas in $z<0.5$ cluster galaxies; (vi) survey stellar populations and kinematics in $\sim25\,000$ field galaxies at $0.3\lesssim z \lesssim 0.7$; (vii) study the cosmic evolution of accretion and star formation using $>1$ million spectra of LOFAR-selected radio sources; (viii) trace structures using intergalactic/circumgalactic gas at $z>2$. Finally, we describe the WEAVE Operational Rehearsals using the WEAVE Simulator., Comment: 41 pages, 27 figures, accepted for publication by MNRAS; updated version including information on individual grants in a revised Acknowledgements section, corrections to the affiliation list, and an updated references list

We present the first clustering measurement of Strong Blended Lyman $\alpha$ (SBLA) absorption systems by measuring their cross-correlation with the Lyman $\alpha$ forest. SBLAs are a new population of absorbers detected within the Lyman $\alpha$ forest. We find a bias of $2.329\pm0.057$, consistent with that of Damped Lyman $\alpha$ absorbers (DLAs). For DLAs, we recover a bias of $2.331\pm0.057$ larger than previously reported (P\'erez-R\`afols et al. 2018b). We also find a redshift space distortion parameter $\beta=0.417\pm0.010$, also consistent with the recovered value for DLAs ($\beta=0.416\pm0.010$). This is consistent with SBLA and DLA systems tracing different portions of the circumgalactic medium of a broadly common population of galaxies. Given these common clustering properties, we combined them to perform a cross-correlation of galaxies in absorption with the Ly$\alpha$ forest. We find that the BAO scale uncertainty of this new measurement is $1.75\times$ that of Ly$\alpha$ auto-correlation and $1.6\times$ that of the quasar cross-correlation with the Ly$\alpha$ forest. We note that the current preferred metal contamination model for fitting the correlation functions with respect to the Ly$\alpha$ forest is not realistic enough for SBLA systems, likely due to their status as high redshift precision sites of high metal enrichment. Mock spectra including SBLA systems and their associated metal absorption are required to understand this sample fully. We conclude that SBLAs have the potential to complement the standard Ly$\alpha$ cosmological analyses in future surveys., Comment: accepted in MNRAS; 15 pages, 6 figures, 3 tables

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 quasar redshift have large uncertainties of a few hundred $\text{km s}^{-1}\,$ due to the broadness of the emission lines and the intrinsic shifts from other emission lines. We inject Gaussian random redshift errors into the mock quasar catalogues, and measure the auto-correlation and the Lyman-$\alpha$-quasar cross-correlation functions. We find a smearing of the BAO feature in the radial direction, but changes in the peak position are negligible. However, we see a significant unphysical correlation for small separations transverse to the line of sight which increases with the amplitude of the redshift errors. We interpret this contamination as a result of the broadening of emission lines in the measured mean continuum, caused by quasar redshift errors, combined with the unrealistically strong clustering of the simulated quasars on small scales., Comment: 13 pages, 8 figures, submitted to MNRAS

In this series of papers, we employ several machine learning (ML) methods to classify the point-like sources from the miniJPAS catalogue, and identify quasar candidates. Since no representative sample of spectroscopically confirmed sources exists at present to train these ML algorithms, we rely on mock catalogues. In this first paper we develop a pipeline to compute synthetic photometry of quasars, galaxies and stars using spectra of objects targeted as quasars in the Sloan Digital Sky Survey. To match the same depths and signal-to-noise ratio distributions in all bands expected for miniJPAS point sources in the range $17.5\leq r<24$, we augment our sample of available spectra by shifting the original $r$-band magnitude distributions towards the faint end, ensure that the relative incidence rates of the different objects are distributed according to their respective luminosity functions, and perform a thorough modeling of the noise distribution in each filter, by sampling the flux variance either from Gaussian realizations with given widths, or from combinations of Gaussian functions. Finally, we also add in the mocks the patterns of non-detections which are present in all real observations. Although the mock catalogues presented in this work are a first step towards simulated data sets that match the properties of the miniJPAS observations, these mocks can be adapted to serve the purposes of other photometric surveys., Comment: 20 pages, 18 figures, submitted to MNRAS

The upcoming WEAVE-QSO survey will target a high density of quasars over a large area, enabling the reconstruction of the 3D density field through Lyman-$\alpha$ tomography over unprecedented volumes smoothed on intermediate scales ($\approx$ 16 Mpc/$h$). We produce mocks of the Lyman-$\alpha$ forest using LyMAS, and reconstruct the 3D density field between sightlines through Wiener filtering in a configuration compatible with the future WEAVE-QSO observations. The fidelity of the reconstruction is assessed by measuring one- and two-point statistics from the distribution of critical points in the cosmic web. In addition, initial Lagrangian statistics are predicted from first principles, and measurements of the connectivity of the cosmic web are performed. The reconstruction captures well the expected features in the auto- and cross-correlations of the critical points. This remains true after a realistic noise is added to the synthetic spectra, even though sparsity of sightlines introduces systematics, especially in the cross-correlations of points with mixed signature. Specifically, for walls and filaments, the most striking clustering features could be measured with up to 4 sigma of significance with a WEAVE-QSO-like survey. Moreover, the connectivity of each peak identified in the reconstructed field is globally consistent with its counterpart in the original field, indicating that the reconstruction preserves the geometry of the density field not only statistically, but also locally. Hence the critical points relative positions within the tomographic reconstruction could be used as standard rulers for dark energy by WEAVE-QSO and similar surveys., Comment: 26 pages, 22 figures, submitted to MNRAS

Correlations in and with the flux transmission of the Lyman$-\alpha$ (Ly$\alpha$) forest in the spectra of high-redshift quasars are powerful cosmological tools, yet these measurements can be compromised if the intrinsic quasar continuum is significantly uncertain. One particularly problematic case is broad absorption line (BAL) quasars, which exhibit blueshifted absorption associated with many spectral features that are consistent with outflows of up to $\sim0.1c$. As these absorption features can both fall in the forest region and be difficult to distinguish from Ly$\alpha$ absorption, cosmological analyses eliminate the 12 - 16% of quasars that exhibit BALs. In this paper we explore an alternate approach that includes BALs in the Ly$\alpha$ auto correlation function, with the exception of the expected locations of the BAL absorption troughs. This procedure returns over 95% of the pathlength that is lost by the exclusion of BALs, as well as increases the density of sightlines. We show that including BAL quasars reduces the fractional uncertainty in the covariance matrix and correlation function and does not significantly change the shape of the correlation function relative to analyses that exclude BAL quasars. We also evaluate different definitions of BALs, masking strategies, and potential differences in the quasar continuum in the forest region for BALs with different amounts of absorption., Comment: 10 pages, 10 figures

We present the characteristics of the Damped Lyman-$\alpha$ (DLA) systems found in the data release DR16 of the extended Baryon Oscillation Spectroscopic Survey (eBOSS) of the Sloan Digital Sky Survey (SDSS). DLAs were identified using the convolutional neural network (CNN) of~\cite{Parks2018}. A total of 117,458 absorber candidates were found with $2 \leq \zdla \leq 5.5$ and $19.7 \leq \lognhi \leq 22$, including 57,136 DLA candidates with $\lognhi \geq 20.3$. Mock quasar spectra were used to estimate DLA detection efficiency and the purity of the resulting catalog. Restricting the quasar sample to bright forests, i.e. those with mean forest fluxes $\meanflux>2\times\fluxunit$, the completeness and purity are greater than 90\% for DLAs with column densities in the range $20.1\leq \lognhi \leq 22$., Comment: Submitted to ApJS

We study large-scale UV background inhomogeneity in three-dimensions associated with the observed quasar populations at high redshift. We do this by measuring metal absorption through quasar absorption spectrum stacking as a function distance to closest quasar in SDSS-IV/eBOSS on 10s of comoving megaparsec scales. We study both intergalactic medium absorbers and mixed circumgalactic medium absorbers and probe absorption in O VI, C IV, and Si IV, and Si III. Overall stronger high ionization species absorption is seen closer to quasars at $2.4

We present a measurement of baryonic acoustic oscillations (BAO) from Lyman-$\alpha$ (Ly$\alpha$) absorption and quasars at an effective redshift $z=2.33$ using the complete extended Baryonic Oscillation Spectroscopic Survey (eBOSS). The sixteenth and final eBOSS data release (SDSS DR16) contains all data from eBOSS and its predecessor, the Baryonic Oscillation Spectroscopic Survey (BOSS), providing $210,005$ quasars with $z_{q}>2.10$ that are used to measure Ly$\alpha$ absorption. We measure the BAO scale both in the auto-correlation of Ly$\alpha$ absorption and in its cross correlation with $341,468$ quasars with redshift $z_{q}>1.77$. Apart from the statistical gain from new quasars and deeper observations, the main improvements over previous work come from more accurate modeling of physical and instrumental correlations and the use of new sets of mock data. Combining the BAO measurement from the auto- and cross-correlation yields the constraints of the two ratios $D_{H}(z=2.33)/r_{d} = 8.99 \pm 0.19$ and $D_{M}(z=2.33)/r_{d} = 37.5 \pm 1.1$, where the error bars are statistical. These results are within $1.5\sigma$ of the prediction of the flat-$\Lambda$CDM cosmology of Planck~(2016). The analysis code, \texttt{picca}, the catalog of the flux-transmission field measurements, and the $\Delta \chi^{2}$ surfaces are publicly available., Comment: 37 pages, 23 figures, Matches the published version by ApJ

We present the cosmological implications from final measurements of clustering using galaxies, quasars, and Ly$\alpha$ forests from the completed Sloan Digital Sky Survey (SDSS) lineage of experiments in large-scale structure. These experiments, composed of data from SDSS, SDSS-II, BOSS, and eBOSS, offer independent measurements of baryon acoustic oscillation (BAO) measurements of angular-diameter distances and Hubble distances relative to the sound horizon, $r_d$, from eight different samples and six measurements of the growth rate parameter, $f\sigma_8$, from redshift-space distortions (RSD). This composite sample is the most constraining of its kind and allows us to perform a comprehensive assessment of the cosmological model after two decades of dedicated spectroscopic observation. We show that the BAO data alone are able to rule out dark-energy-free models at more than eight standard deviations in an extension to the flat, $\Lambda$CDM model that allows for curvature. When combined with Planck Cosmic Microwave Background (CMB) measurements of temperature and polarization the BAO data provide nearly an order of magnitude improvement on curvature constraints. The RSD measurements indicate a growth rate that is consistent with predictions from Planck primary data and with General Relativity. When combining the results of SDSS BAO and RSD with external data, all multiple-parameter extensions remain consistent with a $\Lambda$CDM model. Regardless of cosmological model, the precision on $\Omega_\Lambda$, $H_0$, and $\sigma_8$, remains at roughly 1\%, showing changes of less than 0.6\% in the central values between models. The inverse distance ladder measurement under a o$w_0w_a$CDM yields $H_0= 68.20 \pm 0.81 \, \rm km\, s^{-1} Mpc^{-1}$, remaining in tension with several direct determination methods. (abridged), Comment: A summary of all SDSS BAO and RSD measurements with accompanying legacy figures can be found here: https://www.sdss.org/science/final-bao-and-rsd-measurements/ . The full cosmological interpretation of these measurements can be found here: https://www.sdss.org/science/cosmology-results-from-eboss/

This paper documents the sixteenth data release (DR16) from the Sloan Digital Sky Surveys; the fourth and penultimate from the fourth phase (SDSS-IV). This is the first release of data from the southern hemisphere survey of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2); new data from APOGEE-2 North are also included. DR16 is also notable as the final data release for the main cosmological program of the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), and all raw and reduced spectra from that project are released here. DR16 also includes all the data from the Time Domain Spectroscopic Survey (TDSS) and new data from the SPectroscopic IDentification of ERosita Survey (SPIDERS) programs, both of which were co-observed on eBOSS plates. DR16 has no new data from the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey (or the MaNGA Stellar Library "MaStar"). We also preview future SDSS-V operations (due to start in 2020), and summarize plans for the final SDSS-IV data release (DR17)., Comment: DR16 release: Monday Dec 9th 2019. This is the alphabetical order SDSS-IV collaboration data release paper. 25 pages, 6 figures, accepted by ApJS on 11th May 2020. Minor changes clarify or improve text and figures relative to v1

The statistical power of Lyman-${\alpha}$ forest Baryon Acoustic Oscillation (BAO) measurements is set to increase significantly in the coming years as new instruments such as the Dark Energy Spectroscopic Instrument deliver progressively more constraining data. Generating mock datasets for such measurements will be important for validating analysis pipelines and evaluating the effects of systematics. With such studies in mind, we present LyaCoLoRe: a package for producing synthetic Lyman-${\alpha}$ forest survey datasets for BAO analyses. LyaCoLoRe transforms initial Gaussian random field skewers into skewers of transmitted flux fraction via a number of fast approximations. In this work we explain the methods of producing mock datasets used in LyaCoLoRe, and then measure correlation functions on a suite of realisations of such data. We demonstrate that we are able to recover the correct BAO signal, as well as large-scale bias parameters similar to literature values. Finally, we briefly describe methods to add further astrophysical effects to our skewers - high column density systems and metal absorbers - which act as potential complications for BAO analyses., Comment: 29 pages, 7 figures

In this paper we study the universality of the results of SQUEzE, a software package to classify quasar spectra and estimate their redshifts. The code is presented in \cite{Perez-Rafols+2019}. We test the results against changes on signal-to-noise, spectral resolution, wavelength coverage, and quasar brightness. We find that SQUEzE levels of performance (quantified with purity and completeness) are stable to spectra that have a noise dispersion 4 times that of our standard test sample, BOSS. We also find that the performance remains unchanged if pixels of width 25\AA are considered, and decreases by $\sim2\%$ for pixels of width 100\AA. We see no effect when analyzing subsets of different quasar brightness, and we establish that the blue part (up to 7000\AA) of the spectra is sufficient for the classification. Finally, we compare our suite of tests with samples of spectra expected from WEAVE-QSO and DESI, and narrow-band imaging from J-PAS. We conclude that SQUEzE will perform similarly when confronted with the demands of these future surveys as when applied to current BOSS (and eBOSS) data. {\it Keywords: cosmology: observations - quasar: emission lines - quasar: absorption lines}, Comment: 9 pages, 11 figures, 3 tables; accepted to MNRAS

We measure the imprint of primordial baryon acoustic oscillations (BAO) in the correlation function of Ly$\alpha$ absorption in quasar spectra from the Baryon Oscillation Spectroscopic Survey (BOSS) and the extended BOSS (eBOSS) in Data Release 14 (DR14) of the Sloan Digital Sky Survey (SDSS)-IV. In addition to 179,965 spectra with absorption in the Lyman-$\alpha$ (Ly$\alpha$) region, we use, for the first time, Ly$\alpha$ absorption in the Lyman-$\beta$ region of 56,154 spectra. We measure the Hubble distance, $D_H$, and the comoving angular diameter distance, $D_M$, relative to the sound horizon at the drag epoch $r_d$ at an effective redshift $z=2.34$. Using a physical model of the correlation function outside the BAO peak, we find $D_H(2.34)/r_d=8.86\pm 0.29$ and $D_M(2.34)/r_d=37.41\pm 1.86$, within 1$\sigma$ from the flat-$\Lambda$CDM model consistent with CMB anisotropy measurements. With the addition of polynomial "broadband" terms, the results remain within one standard deviation of the CMB-inspired model. Combined with the quasar-Ly$\alpha$ cross-correlation measurement presented in a companion paper Blomqvist19, the BAO measurements at $z=2.35$ are within 1.7$\sigma$ of the predictions of this model., Comment: accepted by A&A

We present a measurement of the baryon acoustic oscillation (BAO) scale at redshift $z=2.35$ from the three-dimensional correlation of Lyman-$\alpha$ (Ly$\alpha$) forest absorption and quasars. The study uses 266,590 quasars in the redshift range $1.77

We present SQUEzE, a software package to classify quasar spectra and estimate their redshifts. SQUEzE is a random forest classifier operating on the parameters of candidate emission peaks identified in the spectra. We test the performance of the algorithm using visually inspected data from BOSS as a truth table. Only 4\% of the sample ($\sim$6,800 quasars and $\sim$11,520 contaminants) is needed for converged training in recommended choices of the confidence threshold ($0.2

We present the first attempt at measuring the baryonic acoustic oscillations (BAO) in the large scale cross-correlation between the magnesium-II doublet (MgII) flux transmission field and the position of quasar and galaxy tracers. The MgII flux transmission continuous field at $0.3 < z < 1.6$ is measured from 500,589 quasar spectra obtained in the Baryonic Oscillation Spectroscopic Survey (BOSS) and the extended BOSS (eBOSS). The position of 246,697 quasar tracers and 1,346,776 galaxy tracers are extracted from the Sloan Digital Sky Survey (SDSS) I, II, BOSS and eBOSS catalogs. In addition to measuring the cosmological BAO scale and the biased matter density correlation, this study allows tests and improvements to cosmological Lyman-$\alpha$ analyses. A feature consistent with that of the BAO is detected at a significance of $\Delta \chi^{2} = 7.25$. The measured MgII linear transmission bias parameters are $b_{\mathrm{MgII(2796)}} (z = 0.59) = (-6.82 \pm 0.54) \, \times 10^{-4}$ and $b_{\mathrm{MgII(2804)}} (z = 0.59) = (-5.55 \pm 0.46) \, \times 10^{-4}$, and the MgI bias is $b_{\mathrm{MgI(2853)}} (z = 0.59) = (-1.48 \pm 0.24) \, \times 10^{-4}$. Their redshift evolution is characterized by the power-law index: $\gamma_{\mathrm{Mg}} = 3.36 \pm 0.46$. These measurements open a new window towards using BAO from flux transmission at $z < 1$ in the final eBOSS sample and in the upcoming sample from the Dark Energy Spectroscopic Instrument., Comment: 16 pages, 9 figures, matches the published version by ApJ

We measure the cosmological bias factor of DLAs from their cross-correlation with the Ly$\alpha$ forest absorption, as a function of the DLA metal strength, defined from an average of equivalent widths of the strongest detectable low-ionization metal lines. A clear increase of the bias factor with metal strength is detected, as expected from a relation of metallicity and velocity dispersion with host halo mass. The relation is stronger after the metal strength is corrected for the HI column density, to make it more related to metallicity instead of metal column density. After correcting for the effects of measurement errors of the metal strength parameter, we find that the bias factor of DLAs with the weakest metal lines is close to unity, consistent with an origin in dwarf galaxies with host halo masses $\sim10^{10} M_{\odot}$, whereas the most metal rich DLAs have a bias factor as large as $b_{\rm DLA} \sim 3$, indicative of massive galaxies or galaxy groups in host halos with masses $\sim 10^{12} M_{\odot}$. Our result confirms the physical origin of the relation of bias factors measured from cross-correlation studies to the host halos of the absorbers., Comment: 18 pages, 5 figures, 2 tables, accepted to MNRAS

We present the first paper of the series Origin of Metals around Galaxies (OMG) aimed to study the origin of the metals observed in the circumgalactic and intergalactic media. In this work we extract and build the catalogs of metal absorbers that will be used in future analyses, and make our results publicly available to the community. We design a fully automatic algorithm to search for absorption metal-line doublets of the species CIV, NV, SiIV and MgII in high-resolution ($R\gtrsim30\,000$) quasar spectra without human intervention, and apply it to the high-resolution and signal-to-noise ratio spectra of 690 quasars, observed with the UVES and HIRES instruments. We obtain $5\,656$ CIV doublets, $7\,919$ doublets of MgII, $2\,258$ of SiIV, and 239 of NV, constituting the largest high-resolution metal-doublet samples to date, and estimate the dependence of their completeness and purity on various doublet parameters such as equivalent width and redshift, using real and artificial quasar spectra. The catalogs include doublets with rest-frame line equivalent widths down to a few ${\rm m\AA}$, all detected at a significance above 3$\sigma$, and covering the redshifts between $1

The Baryon Oscillation Spectroscopic Survey of SDSS-III has provided an unprecedentedly large sample of Damped \lya systems (DLAs), the largest repositories of neutral hydrogen in the Universe. This DLA sample has been used to determine the DLA bias factor from their cross-correlation with the \lya forest absorption in \cite{FontRibera2012,Perez2018}, showing that DLAs are associated with relatively massive halos. However, the low resolution and signal-to-noise of BOSS spectra do not allow precise measurements of the DLA metal lines. We define a metal strength parameter, $S$, based on combining equivalent widths of 17 metal lines, that can be measured with an optimal signal-to-noise ratio for individual DLAs in BOSS spectra, allowing for the classification of the DLA population into subgroups of different $S$. We present the distribution of this DLA metal strength and the dependence of its mean value on $N_{\rm HI}$ and redshift. We search for systematic effects and variations in the catalogue purity by examining the dependence of the $S$ distribution on the spectral signal-to-noise and the estimated error on $S$. A catalogue of DLAs with measured equivalent widths for the selected 17 metal lines and the value of $S$ is made publicly available, which will be used to measure the dependence of the DLA bias factor on the $S$ parameter. The relation of the metal strength on the gas metal abundances and velocity dispersion can be constrained by studying the stacked metal absorption spectra of DLAs as a function of $S$, allowing for future determinations of the dependence of the bias factor on the metallicity and velocity dispersion of DLAs., Comment: 12 pages, 10 figures, link to online catalogue (https://github.com/andreuandreu/Catalogue_Metal_Strength_DLAs_SDSS-BOSS_DR12)

We present measurements of the cross-correlation of the triply-ionized carbon (CIV) forest with quasars using Sloan Digital Sky Survey Data Release 14. The study exploits a large sample of new quasars from the first two years of observations by the Extended Baryon Oscillation Spectroscopic Survey (eBOSS). The CIV forest is a weaker tracer of large-scale structure than the Ly$\alpha$ forest, but benefits from being accessible at redshifts $z<2$ where the quasar number density from eBOSS is high. Our data sample consists of 287,651 CIV forest quasars in the redshift range $1.4

We present a measurement of the DLA mean bias from the cross-correlation of DLA and the Ly$\alpha$ forest, updating earlier results of Font-Ribera et al. 2012 with the final BOSS Data Release and an improved method to address continuum fitting corrections. Our cross-correlation is well fitted by linear theory with the standard $\Lambda CDM$ model, with a DLA bias of $b_{\rm DLA} = 1.99\pm 0.11$; a more conservative analysis, which removes DLA in the Ly$\beta$ forest and uses only the cross-correlation at $r> 10{\rm h^{-1}\,Mpc}$, yields $b_{\rm DLA} = 2.00\pm 0.19$. This assumes the cosmological model from \cite{Planck2015} and the Ly$\alpha$ forest bias factors of Bautista et al. 2017, and includes only statistical errors obtained from bootstrap analysis. The main systematic errors arise from possible impurities and selection effects in the DLA catalogue, and from uncertainties in the determination of the Ly$\alpha$ forest bias factors and a correction for effects of high column density absorbers. We find no dependence of the DLA bias on column density or redshift. The measured bias value corresponds to a host halo mass $\sim 4\cdot10^{11} {\rm M_{\odot}}$ if all DLA were hosted in halos of a similar mass. In a realistic model where host halos over a broad mass range have a DLA cross section $\Sigma(M_h) \propto M_h^{\alpha}$ down to $M_h > M_{\rm min} =10^{8.5} {\rm M_{\odot}}$, we find that $\alpha > 1$ is required to have $b_{\rm DLA}> 1.7$, implying a steeper relation or higher value of $M_{\rm min}$ than is generally predicted in numerical simulations of galaxy formation., Comment: accepted to MNRAS, 23 pages, 8 figures, 4 tables

We present a measurement of baryon acoustic oscillations (BAO) in the cross-correlation of quasars with the Ly$\alpha$-forest flux-transmission at a mean redshift $z=2.40$. The measurement uses the complete SDSS-III data sample: 168,889 forests and 234,367 quasars from the SDSS Data Release DR12. In addition to the statistical improvement on our previous study using DR11, we have implemented numerous improvements at the analysis level allowing a more accurate measurement of this cross-correlation. We also developed the first simulations of the cross-correlation allowing us to test different aspects of our data analysis and to search for potential systematic errors in the determination of the BAO peak position. We measure the two ratios $D_{H}(z=2.40)/r_{d} = 9.01 \pm 0.36$ and $D_{M}(z=2.40)/r_{d} = 35.7 \pm 1.7$, where the errors include marginalization over the non-linear velocity of quasars and the metal - quasar cross-correlation contribution, among other effects. These results are within $1.8\sigma$ of the prediction of the flat-$\Lambda$CDM model describing the observed CMB anisotropies. We combine this study with the Ly$\alpha$-forest auto-correlation function [2017A&A...603A..12B], yielding $D_{H}(z=2.40)/r_{d} = 8.94 \pm 0.22$ and $D_{M}(z=2.40)/r_{d} = 36.6 \pm 1.2$, within $2.3\sigma$ of the same flat-$\Lambda$CDM model., Comment: accepted by A&A

We study the mean absorption spectrum of the Damped Lyman alpha population at $z\sim 2.6$ by stacking normalized, rest-frame shifted spectra of $\sim 27\,000$ DLAs from the DR12 of BOSS/SDSS-III. We measure the equivalent widths of 50 individual metal absorption lines in 5 intervals of DLA hydrogen column density, 5 intervals of DLA redshift, and overall mean equivalent widths for an additional 13 absorption features from groups of strongly blended lines. The mean equivalent width of low-ionization lines increases with $N_{\rm HI}$, whereas for high-ionization lines the increase is much weaker. The mean metal line equivalent widths decrease by a factor $\sim 1.1-1.5$ from $z\sim2.1$ to $z \sim 3.5$, with small or no differences between low- and high-ionization species. We develop a theoretical model, inspired by the presence of multiple absorption components observed in high-resolution spectra, to infer mean metal column densities from the equivalent widths of partially saturated metal lines. We apply this model to 14 low-ionization species and to AlIII, SIII, SiIII, CIV, SiIV, NV and OVI. We use an approximate derivation for separating the equivalent width contributions of several lines to blended absorption features, and infer mean equivalent widths and column densities from lines of the additional species NI, ZnII, CII${}^{*}$, FeIII, and SIV. Several of these mean column densities of metal lines in DLAs are obtained for the first time; their values generally agree with measurements of individual DLAs from high-resolution, high signal-to-noise ratio spectra when they are available., Comment: Resubmitted after referee revision. Added evolution of metal-line equivalent widths with redshift (Section 5). Added assessment of result dependencies on sample and methodology. Comparison of relative abundances of DLAs vs Milky Way ISM and halo (Figure 16). Publicly available videos of composite quasar and DLA spectra realizations here: https://github.com/lluism/

The third generation of the Sloan Digital Sky Survey (SDSS-III) took data from 2008 to 2014 using the original SDSS wide-field imager, the original and an upgraded multi-object fiber-fed optical spectrograph, a new near-infrared high-resolution spectrograph, and a novel optical interferometer. All the data from SDSS-III are now made public. In particular, this paper describes Data Release 11 (DR11) including all data acquired through 2013 July, and Data Release 12 (DR12) adding data acquired through 2014 July (including all data included in previous data releases), marking the end of SDSS-III observing. Relative to our previous public release (DR10), DR12 adds one million new spectra of galaxies and quasars from the Baryon Oscillation Spectroscopic Survey (BOSS) over an additional 3000 sq. deg of sky, more than triples the number of H-band spectra of stars as part of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE), and includes repeated accurate radial velocity measurements of 5500 stars from the Multi-Object APO Radial Velocity Exoplanet Large-area Survey (MARVELS). The APOGEE outputs now include measured abundances of 15 different elements for each star. In total, SDSS-III added 2350 sq. deg of ugriz imaging; 155,520 spectra of 138,099 stars as part of the Sloan Exploration of Galactic Understanding and Evolution 2 (SEGUE-2) survey; 2,497,484 BOSS spectra of 1,372,737 galaxies, 294,512 quasars, and 247,216 stars over 9376 sq. deg; 618,080 APOGEE spectra of 156,593 stars; and 197,040 MARVELS spectra of 5,513 stars. Since its first light in 1998, SDSS has imaged over 1/3 of the Celestial sphere in five bands and obtained over five million astronomical spectra., Comment: DR12 data are available at http://www.sdss3.org/dr12. 30 pages. 11 figures. Accepted to ApJS

The existence of a cosmic neutrino background can be probed indirectly by CMB experiments, not only by measuring the background density of radiation in the universe, but also by searching for the typical signatures of the fluctuations of free-streaming species in the temperature and polarisation power spectrum. Previous studies have already proposed a rather generic parametrisation of these fluctuations, that could help to discriminate between the signature of ordinary free-streaming neutrinos, or of more exotic dark radiation models. Current data are compatible with standard values of these parameters, which seems to bring further evidence for the existence of a cosmic neutrino background. In this work, we investigate the robustness of this conclusion under various assumptions. We generalise the definition of an effective sound speed and viscosity speed to the case of massive neutrinos or other dark radiation components experiencing a non-relativistic transition. We show that current bounds on these effective parameters do not vary significantly when considering an arbitrary value of the particle mass, or extended cosmological models with a free effective neutrino number, dynamical dark energy or a running of the primordial spectrum tilt. We conclude that it is possible to make a robust statement about the detection of the cosmic neutrino background by CMB experiments., Comment: version accepted for publication in JCAP. 19 pages, 7 figures, 3 tables. Minor changes. References added

We present a measurement of the cross-correlation of MgII absorption and massive galaxies, using the DR11 main galaxy sample of the Baryon Oscillation Spectroscopic Survey of SDSS-III (CMASS galaxies), and the DR7 quasar spectra of SDSS-II. The cross-correlation is measured by stacking quasar absorption spectra shifted to the redshift of galaxies that are within a certain impact parameter bin of the quasar, after dividing by a quasar continuum model. This results in an average MgII equivalent width as a function of impact parameter from a galaxy, ranging from 50 kpc to more than 10 Mpc in proper units, which includes all MgII absorbers. We show that special care needs to be taken to use an unbiased quasar continuum estimator, to avoid systematic errors in the measurement of the mean stacked MgII equivalent width. The measured cross-correlation follows the expected shape of the galaxy correlation function, although measurement errors are large. We use the cross-correlation amplitude to derive the bias factor of MgII absorbers, finding bMgII = 2.33 \pm? 0.19, where the error accounts only for the statistical uncertainty in measuring the mean equivalent width. This bias factor is larger than that obtained in previous studies and may be affected by modeling uncertainties that we discuss, but if correct it suggests that MgII absorbers at redshift z \simeq 0:5 are spatially distributed on large scales similarly to the CMASS galaxies in BOSS. Keywords: galaxies: haloes, galaxies: formation, quasars: absorption lines, large-scale structure of universe, Comment: Accepted for publication to MNRAS. Accepted 2014 December 12. Received 2014 November 29; in original form 2014 February 6

The Sloan Digital Sky Survey (SDSS) has been in operation since 2000 April. This paper presents the tenth public data release (DR10) from its current incarnation, SDSS-III. This data release includes the first spectroscopic data from the Apache Point Observatory Galaxy Evolution Experiment (APOGEE), along with spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS) taken through 2012 July. The APOGEE instrument is a near-infrared R~22,500 300-fiber spectrograph covering 1.514--1.696 microns. The APOGEE survey is studying the chemical abundances and radial velocities of roughly 100,000 red giant star candidates in the bulge, bar, disk, and halo of the Milky Way. DR10 includes 178,397 spectra of 57,454 stars, each typically observed three or more times, from APOGEE. Derived quantities from these spectra (radial velocities, effective temperatures, surface gravities, and metallicities) are also included.DR10 also roughly doubles the number of BOSS spectra over those included in the ninth data release. DR10 includes a total of 1,507,954 BOSS spectra, comprising 927,844 galaxy spectra; 182,009 quasar spectra; and 159,327 stellar spectra, selected over 6373.2 square degrees., Comment: 15 figures; 1 table. Accepted to ApJS. DR10 is available at http://www.sdss3.org/dr10 v3 fixed 3 diacritic markings in the arXiv HTML listing of the author names

The Baryon Oscillation Spectroscopic Survey (BOSS) is designed to measure the scale of baryon acoustic oscillations (BAO) in the clustering of matter over a larger volume than the combined efforts of all previous spectroscopic surveys of large scale structure. BOSS uses 1.5 million luminous galaxies as faint as i=19.9 over 10,000 square degrees to measure BAO to redshifts z<0.7. Observations of neutral hydrogen in the Lyman alpha forest in more than 150,000 quasar spectra (g<22) will constrain BAO over the redshift range 2.15

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014., Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr9