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We predict the 21-cm global signal and power spectra during the Epoch of Reionisation using the MERAXES semi-analytic galaxy formation and reionisation model, updated to include X-ray heating and thermal evolution of the intergalactic medium. Studying the formation and evolution of galaxies together with the reionisation of cosmic hydrogen using semi-analytic models (such as MERAXES) requires N-body simulations within large volumes and high mass resolutions. For this, we use a simulation of side-length $210~h^{-1}$ Mpc with $4320^3$ particles resolving dark matter haloes to masses of $5\times10^8~h^{-1}~M_\odot$. To reach the mass resolution of atomically cooled galaxies, thought to be the dominant population contributing to reionisation, at $z=20$ of $\sim 2\times10^7~h^{-1}~M_\odot$, we augment this simulation using the DARKFOREST Monte-Carlo merger tree algorithm (achieving an effective particle count of $\sim10^{12}$). Using this augmented simulation we explore the impact of mass resolution on the predicted reionisation history as well as the impact of X-ray heating on the 21-cm global signal and the 21-cm power spectra. We also explore the cosmic variance of 21-cm statistics within $70^{3}$ $h^{-3}$ Mpc$^3$ sub-volumes. We find that the midpoint of reionisation varies by $\Delta z\sim0.8$ and that the cosmic variance on the power spectrum is underestimated by a factor of $2-4$ at $k\sim 0.1-0.4$ Mpc$^{-1}$ due to the non-Gaussian nature of the 21-cm signal. To our knowledge, this work represents the first model of both reionisation and galaxy formation which resolves low-mass atomically cooled galaxies while simultaneously sampling sufficiently large scales necessary for exploring the effects of X-rays in the early Universe., Comment: 17 pages, 13 figures, revised and MNRAS accepted version

Detecting the 21-cm hyperfine transition from neutral hydrogen in the intergalactic medium is our best probe for understanding the astrophysical processes driving the Epoch of Reionisation (EoR). The primary means for a detection of this 21-cm signal is through a statistical measurement of the spatial fluctuations using the 21-cm power spectrum (PS). However, the 21-cm signal is non-Gaussian meaning the PS, which only measures the Gaussian fluctuations, is sub-optimal for characterising all of the available information. The upcoming Square Kilometre Array (SKA) will perform a deep, 1000 hr observation over 100 deg$.^{2}$ specifically designed to recover direct images of the 21-cm signal. In this work, we use the Wavelet Scattering Transform (WST) to extract the non-Gaussian information directly from these two-dimensional images of the 21-cm signal. The key advantage of the WST is its stability with respect to statistical noise for measuring non-Gaussian information, unlike the bispectrum whose statistical noise diverges. We introduce a novel method to isolate this non-Gaussian information from mock 21-cm images and demonstrate its detection at 150 (177)~MHz ($z\sim8.5$ and $\sim7$) for a fiducial model with signal-to-noise of $\sim$5~(8) assuming perfect foreground removal and $\sim2$~(3) assuming foreground wedge avoidance., 17 pages, 10 figures and 1 table. Submitted to MNRAS, comments welcome

Proximity zones of high-redshift quasars are unique probes of their central supermassive black holes as well as the intergalactic medium in the last stages of reionization. We present 22 new measurements of proximity zones of quasars with redshifts between 5.8 and 6.6, using the enlarged XQR-30 sample of high-resolution, high-SNR quasar spectra. The quasars in our sample have UV magnitudes of $M_{1450}\sim -27$ and black hole masses of $10^9$$\unicode{x2013}$$10^{10}$ M$_\odot$. Our inferred proximity zone sizes are 2$\unicode{x2013}$7 physical Mpc, with a typical uncertainty of less than 0.5 physical Mpc, which, for the first time, also includes uncertainty in the quasar continuum. We find that the correlation between proximity zone sizes and the quasar redshift, luminosity, or black hole mass, indicates a large diversity of quasar lifetimes. Two of our proximity zone sizes are exceptionally small. The spectrum of one of these quasars, with $z=6.02$, displays, unusually for this redshift, damping wing absorption without any detectable metal lines, which could potentially originate from the IGM. The other quasar has a high-ionization absorber $\sim$0.5 pMpc from the edge of the proximity zone. This work increases the number of proximity zone measurements available in the last stages of cosmic reionization to 87. This data will lead to better constraints on quasar lifetimes and obscuration fractions at high redshift, which in turn will help probe the seed mass and formation redshift of supermassive black holes., Comment: 16 pages, 9 figures, Accepted in MNRAS

The locations of Ly-$\alpha$ emitting galaxies (LAEs) at the end of the Epoch of Reionisation (EoR) are expected to correlate with regions of ionised hydrogen, traced by the redshifted 21~cm hyperfine line. Mapping the neutral hydrogen around regions with detected and localised LAEs offers an avenue to constrain the brightness temperature of the Universe within the EoR by providing an expectation for the spatial distribution of the gas, thereby providing prior information unavailable to power spectrum measurements. We use a test set of 12 hours of observations from the Murchison Widefield Array (MWA) in extended array configuration, to constrain the neutral hydrogen signature of 58 LAEs, detected with the Subaru Hypersuprime Cam in the \textit{Silverrush} survey, centred on $z$=6.58. We assume that detectable emitters reside in the centre of ionised HII bubbles during the end of reionization, and predict the redshifted neutral hydrogen signal corresponding to the remaining neutral regions using a set of different ionised bubble radii. A prewhitening matched filter detector is introduced to assess detectability. We demonstrate the ability to detect, or place limits upon, the amplitude of brightness temperature fluctuations, and the characteristic HII bubble size. With our limited data, we constrain the brightness temperature of neutral hydrogen to $\Delta{\rm T}_B, Comment: 9 pages, 6 figures, accepted for publication in MNRAS

We present a Bayesian jackknife test for assessing the probability that a data set contains biased subsets, and, if so, which of the subsets are likely to be biased. The test can be used to assess the presence and likely source of statistical tension between different measurements of the same quantities in an automated manner. Under certain broadly applicable assumptions, the test is analytically tractable. We also provide an open-source code, chiborg, that performs both analytic and numerical computations of the test on general Gaussian-distributed data. After exploring the information theoretical aspects of the test and its performance with an array of simulations, we apply it to data from the Hydrogen Epoch of Reionization Array (HERA) to assess whether different sub-seasons of observing can justifiably be combined to produce a deeper 21 cm power spectrum upper limit. We find that, with a handful of exceptions, the HERA data in question are statistically consistent and this decision is justified. We conclude by pointing out the wide applicability of this test, including to CMB experiments and the H0 tension.

Precision calibration poses challenges to experiments probing the redshifted 21-cm signal of neutral hydrogen from the Cosmic Dawn and Epoch of Reionization (z~30-6). In both interferometric and global signal experiments, systematic calibration is the leading source of error. Though many aspects of calibration have been studied, the overlap between the two types of instruments has received less attention. We investigate the sky based calibration of total power measurements with a HERA dish and an EDGES style antenna to understand the role of auto-correlations in the calibration of an interferometer and the role of sky in calibrating a total power instrument. Using simulations we study various scenarios such as time variable gain, incomplete sky calibration model, and primary beam model. We find that temporal gain drifts, sky model incompleteness, and beam inaccuracies cause biases in the receiver gain amplitude and the receiver temperature estimates. In some cases, these biases mix spectral structure between beam and sky resulting in spectrally variable gain errors. Applying the calibration method to the HERA and EDGES data, we find good agreement with calibration via the more standard methods. Although instrumental gains are consistent with beam and sky errors similar in scale to those simulated, the receiver temperatures show significant deviations from expected values. While we show that it is possible to partially mitigate biases due to model inaccuracies by incorporating a time-dependent gain model in calibration, the resulting errors on calibration products are larger and more correlated. Completely addressing these biases will require more accurate sky and primary beam models., Comment: 16 pages, 13 figures, 1 table; accepted for publication in MNRAS main journal

The Multi-frequency Angular Power Spectrum (MAPS) is an alternative to spherically-averaged power spectra, and computes local fluctuations in the angular power spectrum without need for line-of-sight spectral transform. To test different approaches to MAPS and treatment of the foreground contamination, and compare with the spherically-averaged power spectrum, and the single-frequency angular power spectrum. We apply the MAPS to 110~hours of data in $z=6.2-7.5$ obtained for the Murchison Widefield Array Epoch of Reionisation experiment to compute the statistical power of 21~cm brightness temperature fluctuations. In the presence of bright foregrounds, a filter is applied to remove large-scale modes prior to MAPS application, significantly reducing MAPS power due to systematics. The MAPS shows a contrast of 10$^2$--10$^3$ to a simulated 21~cm cosmological signal for spectral separations of 0--4~MHz after application of the filter, reflecting results for the spherically-averaged power spectrum. The single-frequency angular power spectrum is also computed. At $z=7.5$ and $l=200$, we find an angular power of 53~mK$^2$, exceeding a simulated cosmological signal power by a factor of one thousand. Residual spectral structure, inherent to the calibrated data, and not spectral leakage from large-scale modes, is the dominant source of systematic power bias. The single-frequency angular power spectrum yields slightly poorer results compared with the spherically-averaged power spectrum, having applied a spectral filter to reduce foregrounds. Exploration of other filters may improve this result, along with consideration of wider bandwidths., 9 pages, 9 figures; accepted for publication in Astronomy & Astrophysics

Using the latest upper limits on the 21-cm power spectrum at $z\approx9.1$ from the Low Frequency Array (LOFAR), we explore regions of parameter space which are inconsistent with the data. We use 21CMMC, a Monte Carlo Markov Chain sampler of 21cmFAST which directly forward models the 3D cosmic 21-cm signal in a fully Bayesian framework. We use the astrophysical parameterisation from 21cmFAST, which includes mass-dependent star formation rates and ionising escape fractions as well as soft-band X-ray luminosities to place limits on the properties of the high-$z$ galaxies. Further, we connect the disfavoured regions of parameter space with existing observational constraints on the Epoch of Reionisation such as ultra-violet (UV) luminosity functions, background UV photoionisation rate, intergalactic medium (IGM) neutral fraction and the electron scattering optical depth. We find that all models exceeding the 21-cm signal limits set by LOFAR at $z\approx9.1$ are excluded at $\gtrsim2\sigma$ by other probes. Finally, we place limits on the IGM spin temperature from LOFAR, disfavouring at 95 per cent confidence spin temperatures below $\sim2.6$ K across an IGM neutral fraction range of $0.15 \lesssim \bar{x}_{H{\scriptscriptstyle I}} \lesssim 0.6$. Note, these limits are only obtained from 141 hrs of data in a single redshift bin. With tighter upper limits, across multiple redshift bins expected in the near future from LOFAR, more viable models will be ruled out. Our approach demonstrates the potential of forward modelling tools such as 21CMMC in combining 21-cm observations with other high-$z$ probes to constrain the astrophysics of galaxies., Comment: 12 pages, 4 pages, 1 table. Submitted to MNRAS, comments welcome

Interferometry of the cosmic 21-cm signal is set to revolutionise our understanding of the Epoch of Reionisation (EoR) and the Cosmic Dawn (CD). The culmination of ongoing efforts will be the upcoming Square Kilometre Array (SKA), which will provide tomography of the 21-cm signal from the first billion years of our Universe. Using a galaxy formation model informed by high-$z$ luminosity functions, here we forecast the accuracy with which the first phase of SKA-low (SKA1-low) can constrain the properties of the unseen galaxies driving the astrophysics of the EoR and CD. We consider three observing strategies: (i) deep (1000h on a single field); (ii) medium-deep (100hr on 10 independent fields); and (iii) shallow (10hr on 100 independent fields). Using the 21-cm power spectrum as a summary statistic, and conservatively only using the 21-cm signal above the foreground wedge, we predict that all three observing strategies should recover astrophysical parameters to a fractional precision of $\sim 0.1$ -- 10 per cent. The reionisation history is recovered to an uncertainty of $\Delta z \lesssim 0.1$ (1$\sigma$) for the bulk of its duration. The medium-deep strategy, balancing thermal noise against cosmic variance, results in the tightest constraints, slightly outperforming the deep strategy. The shallow observational strategy performs the worst, with up to a $\sim 10$ -- 60 per cent increase in the recovered uncertainty. We note, however, that non-Gaussian summary statistics, tomography, as well as unbiased foreground removal would likely favour the deep strategy., Comment: 10 pages, 2 figures, submitted to MNRAS, comments welcome

The key challenge in the observation of the redshifted 21-cm signal from cosmic reionization is its separation from the much brighter foreground emission. Such separation relies on the different spectral properties of the two components, although, in real life, the foreground intrinsic spectrum is often corrupted by the instrumental response, inducing systematic effects that can further jeopardize the measurement of the 21-cm signal. In this paper, we use Gaussian Process Regression to model both foreground emission and instrumental systematics in $\sim 2$ hours of data from the Hydrogen Epoch of Reionization Array. We find that a simple co-variance model with three components matches the data well, giving a residual power spectrum with white noise properties. These consist of an "intrinsic" and instrumentally corrupted component with a coherence-scale of 20 MHz and 2.4 MHz respectively (dominating the line of sight power spectrum over scales $k_{\parallel} \le 0.2$ h cMpc$^{-1}$) and a baseline dependent periodic signal with a period of $\sim 1$ MHz (dominating over $k_{\parallel} \sim 0.4 - 0.8$h cMpc$^{-1}$) which should be distinguishable from the 21-cm EoR signal whose typical coherence-scales is $\sim 0.8$ MHz., 15 pages, 15 figures, 1 table, Accepted to MNRAS

We present the first application of the isosceles bispectrum to MCMC parameter inference from the cosmic 21-cm signal. We extend the MCMC sampler 21cmMC to use the fast bispectrum code, BiFFT, when computing the likelihood. We create mock 1000h observations with SKA1-low, using PyObs21 to account for uv-sampling and thermal noise. Assuming the spin temperature is much higher than that of the CMB, we consider two different reionization histories for our mock observations: fiducial and late-reionization. For both models we find that bias on the inferred parameter means and 1-$\sigma$ credible intervals can be substantially reduced by using the isosceles bispectrum (calculated for a wide range of scales and triangle shapes) together with the power spectrum (as opposed to just using one of the statistics). We find that making the simplifying assumption of a Gaussian likelihood with a diagonal covariance matrix does not notably bias parameter constraints for the three-parameter reionization model and basic instrumental effects considered here. This is true even if we use extreme (unlikely) initial conditions which would be expected to amplify biases. We also find that using the cosmic variance error calculated with Monte-Carlo simulations using the fiducial model parameters whilst assuming the late-reionization model for the simulated data also does not strongly bias the inference. This implies we may be able to sparsely sample and interpolate the cosmic variance error over the parameter space, substantially reducing computational costs. All codes used in this work are publicly-available., Comment: 12 pages, 11 figures (submitted to MNRAS)

The light-cone effect breaks the periodicity and statistical homogeneity (ergodicity) along the line-of-sight direction of cosmological emission/absorption line surveys. The spherically averaged power spectrum (SAPS), which by definition assumes ergodicity and periodicity in all directions, can only quantify some of the second-order statistical information in the 3D light-cone signals and therefore gives a biased estimate of the true statistics. The multi-frequency angular power spectrum (MAPS), by extracting more information from the data, does not rely on these assumptions. It is therefore better aligned with the properties of the signal. We have compared the performance of the MAPS and SAPS metrics for parameter estimation for a mock 3D light-cone observation of the 21-cm signal from the Epoch of Reionization. Our investigation is based on a simplified 3-parameter 21cmFAST model. We find that the MAPS produces parameter constraints which are a factor of $\sim 2$ more stringent than when the SAPS is used. The significance of this result does not change much even in the presence of instrumental noise expected for 128 hours of SKA-Low observations. Our results therefore suggest that a parameter estimation framework based on the MAPS metric would yield superior results over one using the SAPS metric., Comment: Published in MNRAS Letters

Detecting the cosmic 21-cm signal during the Epoch of Reionisation and Cosmic Dawn will reveal insights into the properties of the first galaxies and advance cosmological parameter estimation. Until recently, the primary focus for astrophysical parameter inference from the 21-cm signal centred on the power spectrum (PS). However, the cosmic 21-cm signal is highly non-Gaussian rendering the PS sub-optimal for characterising the cosmic signal. In this work, we introduce a new technique to analyse the non-Gaussian information in images of the 21-cm signal called the Wavelet Scattering Transform (WST). This approach closely mirrors that of convolutional neural networks with the added advantage of not requiring tuning or training of a neural network. Instead, it compresses the 2D spatial information into a set of coefficients making it easier to interpret while also providing a robust statistical description of the non-Gaussian information contained in the cosmic 21-cm signal. First, we explore the application of the WST to mock 21-cm images to gain valuable physical insights by comparing to the known behaviour from the 21-cm PS. Then we quantitatively explore the WST applied to the 21-cm signal by extracting astrophysical parameter constraints using Fisher Matrices from a realistic 1000 hr mock observation with the Square Kilometre Array. We find that: (i) the WST applied only to 2D images can outperform the 3D spherically averaged 21-cm PS, (ii) the excision of foreground contaminated modes can degrade the constraining power by a factor of ~1.5-2 with the WST and (iii) higher cadences between the 21-cm images can further improve the constraining power., Comment: 25 pages, 16 figures and 2 tables. Accepted for publication in MNRAS

The Square Kilometre Array (SKA) is a planned radio interferometer of unprecedented scale that will revolutionize low-frequency radio astronomy when completed. In particular, one of its core science drivers is the systematic mapping of the Cosmic Dawn and Epoch of Reionization, which mark the birth of the first stars and galaxies in the Universe and their subsequent ionization of primordial intergalactic hydrogen, respectively. The SKA will offer the most sensitive view of these poorly understood epochs using the redshifted 21 cm hyperfine signal from intergalactic hydrogen. However, significant technical challenges stand in the way of realizing this scientific promise. These mainly involve the mitigation of systematics coming from astrophysical foregrounds, terrestrial radio interference, and the instrumental response. The Low Frequency Array, the Murchison Widefield Array and the Hydrogen Epoch of Reionization Array are SKA pathfinder experiments that have developed a variety of strategies for addressing these challenges, each with unique characteristics that stem largely from their different instrumental designs. We outline these various directions, highlighting key differences and synergies, and discuss how these relate to the future of low-frequency intensity mapping with the SKA. We also briefly summarize the challenges associated with modeling the 21 cm signal and discuss the methodologies being proposed for inferring constraints on astrophysical models., Comment: Version accepted to JATIS

Radio Frequency Interference (RFI) is one of the systematic challenges preventing 21cm interferometric instruments from detecting the Epoch of Reionization. To mitigate the effects of RFI on data analysis pipelines, numerous inpaint techniques have been developed to restore RFI corrupted data. We examine the qualitative and quantitative errors introduced into the visibilities and power spectrum due to inpainting. We perform our analysis on simulated data as well as real data from the Hydrogen Epoch of Reionization Array (HERA) Phase 1 upper limits. We also introduce a convolutional neural network that capable of inpainting RFI corrupted data in interferometric instruments. We train our network on simulated data and show that our network is capable at inpainting real data without requiring to be retrained. We find that techniques that incorporate high wavenumbers in delay space in their modeling are best suited for inpainting over narrowband RFI. We also show that with our fiducial parameters Discrete Prolate Spheroidal Sequences (DPSS) and CLEAN provide the best performance for intermittent ``narrowband'' RFI while Gaussian Progress Regression (GPR) and Least Squares Spectral Analysis (LSSA) provide the best performance for larger RFI gaps. However we caution that these qualitative conclusions are sensitive to the chosen hyperparameters of each inpainting technique. We find these results to be consistent in both simulated and real visibilities. We show that all inpainting techniques reliably reproduce foreground dominated modes in the power spectrum. Since the inpainting techniques should not be capable of reproducing noise realizations, we find that the largest errors occur in the noise dominated delay modes. We show that in the future, as the noise level of the data comes down, CLEAN and DPSS are most capable of reproducing the fine frequency structure in the visibilities of HERA data., Comment: 21 pages, 13 figures

The excursion set reionization framework is widely used, due to its speed and accuracy in reproducing the 3D topology of reionization. However, it is known that it does not conserve photon number. Here, we introduce an efficient, on-the-fly recipe to approximately account for photon conservation. Using a flexible galaxy model shown to reproduce current high-$z$ observables, we quantify the bias in the inferred reionization history and galaxy properties resulting from the non-conservation of ionizing photons. Using a mock 21-cm observation, we perform inference with and without correcting for ionizing photon conservation. We find that ignoring photon conservation results in very modest biases in the inferred galaxy properties, for our fiducial model. The notable exception is in the power-law scaling of the ionizing escape fraction with halo mass, which can be biased from the true value by $\sim2.4\sigma$ (corresponding to $\sim0.2$ in the power-law index). Our scheme is implemented in the public code ${\tt 21cmFAST}$., Comment: 9 pages, 4 figures, 1 table, accepted for publication in MNRAS

We present a framework for identifying and flagging malfunctioning antennas in large radio interferometers. We outline two distinct categories of metrics designed to detect outliers along known failure modes of large arrays: cross-correlation metrics, based on all antenna pairs, and auto-correlation metrics, based solely on individual antennas. We define and motivate the statistical framework for all metrics used, and present tailored visualizations that aid us in clearly identifying new and existing systematics. We implement these techniques using data from 105 antennas in the Hydrogen Epoch of Reionization Array (HERA) as a case study. Finally, we provide a detailed algorithm for implementing these metrics as flagging tools on real data sets., Comment: 31 pages, 17 figures

Observations in the lowest MWA band between $75-100$ MHz have the potential to constrain the distribution of neutral hydrogen in the intergalactic medium at redshift $\sim 13-17$. Using 15 hours of MWA data, we analyse systematics in this band such as radio-frequency interference (RFI), ionospheric and wide field effects. By updating the position of point sources, we mitigate the direction independent calibration error due to ionospheric offsets. Our calibration strategy is optimized for the lowest frequency bands by reducing the number of direction dependent calibrators and taking into account radio sources within a wider field of view. We remove data polluted by systematics based on the RFI occupancy and ionospheric conditions, finally selecting 5.5 hours of the cleanest data. Using these data, we obtain two sigma upper limits on the 21 cm power spectrum in the range of $0.1\lessapprox k \lessapprox 1 ~\rm ~h~Mpc^{-1}$ and at $z$=14.2, 15.2 and 16.5, with the lowest limit being $6.3\times 10^6 ~\rm mK^2$ at $\rm k=0.14 \rm ~h~Mpc^{-1}$ and at $z=15.2$ with a possibility of a few \% of signal loss due to direction independent calibration., Comment: 17 pages, 18 figures, accepted to MNRAS

Current attempts to measure the 21cm Power Spectrum of neutral hydrogen during the Epoch of Reionization are limited by systematics which produce measured upper limits above both the thermal noise and the expected cosmological signal. These systematics arise from a combination of observational, instrumental, and analysis effects. In order to further understand and mitigate these effects, it is instructive to explore different aspects of existing datasets. One such aspect is the choice of observing field. To date, MWA EoR observations have largely focused on the EoR0 field. In this work, we present a new detailed analysis of the EoR1 field. The EoR1 field is one of the coldest regions of the Southern radio sky, but contains the very bright radio galaxy Fornax-A. The presence of this bright extended source in the primary beam of the interferometer makes the calibration and analysis of EoR1 particularly challenging. We demonstrate the effectiveness of a recently developed shapelet model of Fornax-A in improving the results from this field. We also describe and apply a series of data quality metrics which identify and remove systematically contaminated data. With substantially improved source models, upgraded analysis algorithms and enhanced data quality metrics, we determine EoR power spectrum upper limits based on analysis of the best $\sim$14-hours data observed during 2015 and 2014 at redshifts 6.5, 6.8 and 7.1, with the lowest $2\sigma$ upper limit at z=6.5 of $\Delta^2 \leq (73.78 ~\mathrm{mK)^2}$ at $k=0.13~\mathrm{h~ Mpc^{-1}}$, improving on previous EoR1 measurement results., Comment: 18 pages, 17 figures, Accepted for publication in MNRAS

Precise measurements of the 21 cm power spectrum are crucial for understanding the physical processes of hydrogen reionization. Currently, this probe is being pursued by low-frequency radio interferometer arrays. As these experiments come closer to making a first detection of the signal, error estimation will play an increasingly important role in setting robust measurements. Using the delay power spectrum approach, we have produced a critical examination of different ways that one can estimate error bars on the power spectrum. We do this through a synthesis of analytic work, simulations of toy models, and tests on small amounts of real data. We find that, although computed independently, the different error bar methodologies are in good agreement with each other in the noise-dominated regime of the power spectrum. For our preferred methodology, the predicted probability distribution function is consistent with the empirical noise power distributions from both simulated and real data. This diagnosis is mainly in support of the forthcoming HERA upper limit, and also is expected to be more generally applicable., Comment: 35 Pages, 9 Figures, 4 Tables. Replaced with accepted ApJ version; some clarifying text added in response to referee comments with no changes to results

The formation of the first galaxies during cosmic dawn and reionization (at redshifts $z=5-30$), triggered the last major phase transition of our universe, as hydrogen evolved from cold and neutral to hot and ionized. The 21-cm line of neutral hydrogen will soon allow us to map these cosmic milestones and study the galaxies that drove them. To aid in interpreting these observations, we upgrade the publicly available code {\tt 21cmFAST}. We introduce a new, flexible parametrization of the additive feedback from: an inhomogeneous, $H_2$-dissociating (Lyman-Werner; LW) background; and dark matter -- baryon relative velocities; which recovers results from recent, small-scale hydrodynamical simulations with both effects. We perform a large, "best-guess" simulation as the 2021 installment of the Evolution of 21-cm Structure (EOS) project. This improves the previous release with a galaxy model that reproduces the observed UV luminosity functions (UVLFs), and by including a population of molecular-cooling galaxies. The resulting 21-cm global signal and power spectrum are significantly weaker, primarily due to a more rapid evolution of the star-formation rate density required to match the UVLFs. Nevertheless, we forecast high signal-to-noise detections for both HERA and the SKA. We demonstrate how the stellar-to-halo mass relation of the unseen, first galaxies can be inferred from the 21-cm evolution. Finally, we show that the spatial modulation of X-ray heating due to relative velocities provides a unique acoustic signature that is detectable at $z \approx 10-15$ in our fiducial model. Ours are the first public simulations with joint inhomogeneous LW and relative-velocity feedback across the entire cosmic dawn and reionization., Comment: 23+3 pages, 23+3 figures. Matches accepted version. Simulation output available at https://www.dropbox.com/sh/dqh9r6wb0s68jfo/AACc9ZCqsN0SQ_JJN7GRVuqDa?dl=0

As current- and next-generation astronomical instruments come online, they will generate an unprecedented deluge of data. Analyzing these data in real time presents unique conceptual and computational challenges, and their long-term storage and archiving is scientifically essential for generating reliable, reproducible results. We present here the real-time processing (RTP) system for the Hydrogen Epoch of Reionization Array (HERA), a radio interferometer endeavoring to provide the first detection of the highly redshifted 21 cm signal from Cosmic Dawn and the Epoch of Reionization by an interferometer. The RTP system consists of analysis routines run on raw data shortly after they are acquired, such as calibration and detection of radio-frequency interference (RFI) events. RTP works closely with the Librarian, the HERA data storage and transfer manager which automatically ingests data and transfers copies to other clusters for post-processing analysis. Both the RTP system and the Librarian are public and open source software, which allows for them to be modified for use in other scientific collaborations. When fully constructed, HERA is projected to generate over 50 terabytes (TB) of data each night, and the RTP system enables the successful scientific analysis of these data., Comment: 15 pages, 3 figures, published in Astronomy and Computing

The first generation of galaxies is expected to form in minihalos, accreting gas through ${\rm H}_2$ cooling, and possessing unique properties. Although unlikely to be directly detected in UV/infrared surveys, the radiation from these molecular-cooling galaxies (MCGs) could leave an imprint in the 21-cm signal from the Cosmic Dawn. Here we quantify their detectability with upcoming radio interferometers. We generate mock 21-cm power spectra using a model for both MCGs as well as more massive, atomic-cooling galaxies (AGCs), allowing both populations to have different properties and scaling relations. The galaxy parameters are chosen so as to be consistent with: (i) high-redshift UV luminosity functions; (ii) the upper limit on the neutral fraction from QSO spectra; (iii) the Thomson scattering optical depth to the CMB; and (iv) the timing of the recent putative EDGES detection. The latter implies a significant contribution of MCGs to the Cosmic Dawn, if confirmed to be cosmological. We then perform Bayesian inference on two models including and ignoring MCG contributions. Comparing their Bayesian evidences, we find a strong preference for the model including MCGs, despite the fact that it has more free parameters. This suggests that if MCGs indeed play a significant role in the Cosmic Dawn, it should be possible to infer their properties from upcoming 21-cm power spectra. Our study illustrates how these observations can discriminate among uncertain galaxy formation models with varying complexities, by maximizing the Bayesian evidence., 12 pages, 3 figures, submitted to MNRAS, comments are welcome

Bright, high redshift ($z>6$) QSOs are powerful probes of the ionisation state of the intervening intergalactic medium (IGM). The detection of Ly$\alpha$ damping wing absorption imprinted in the spectrum of high-z QSOs can provide strong constraints on the epoch of reionisation (EoR). In this work, we perform an independent Ly$\alpha$ damping wing analysis of two known $z>7$ QSOs; DESJ0252-0503 at $z=7.00$ (Wang et al.) and J1007+2115 at $z=7.51$ (Yang et al.). For this, we utilise our existing Bayesian framework which simultaneously accounts for uncertainties in: (i) the intrinsic Ly$\alpha$ emission profile (reconstructed from a covariance matrix of measured emission lines; extended in this work to include NV) and (ii) the distribution of ionised (H\,{\scriptsize II}) regions within the IGM using a $1.6^3$ Gpc$^3$ reionisation simulation. This approach is complementary to that used in the aforementioned works as it focuses solely redward of Ly$\alpha$ ($1218 < \lambda < 1230$\AA) making it more robust to modelling uncertainties while also using a different methodology for (i) and (ii). We find, for a fiducial EoR morphology, $\bar{x}_{\rm HI} = 0.64\substack{+0.19 \\ -0.23}$ (68 per cent) at $z=7$ and $\bar{x}_{\rm HI} = 0.27\substack{+0.21 \\ -0.17}$ at $z=7.51$ consistent within $1\sigma$ to the previous works above, though both are slightly lower in amplitude. Following the inclusion of NV into our reconstruction pipeline, we perform a reanalysis of ULASJ1120+0641 at $z=7.09$ (Mortlock et al.) and ULASJ1342+0928 at $z=7.54$ (Ba\~nados et al.) finding $\bar{x}_{\rm HI} = 0.44\substack{+0.23 \\ -0.24}$ at $z=7.09$ and $\bar{x}_{\rm HI} = 0.31\substack{+0.18 \\ -0.19}$ at $z=7.54$. Finally, we combine the QSO damping wing constraints for all four $z\gtrsim7$ QSOs to obtain a single, unified constraint of $\bar{x}_{\rm HI} = 0.49\substack{+0.11 \\ -0.11}$ at $z=7.29$., Comment: 15 pages, 9 figures. Submitted to MNRAS, comments welcome

In 21 cm cosmology, precision calibration is key to the separation of the neutral hydrogen signal from very bright but spectrally-smooth astrophysical foregrounds. The Hydrogen Epoch of Reionization Array (HERA), an interferometer specialized for 21 cm cosmology and now under construction in South Africa, was designed to be largely calibrated using the self-consistency of repeated measurements of the same interferometric modes. This technique, known as "redundant-baseline calibration" resolves most of the internal degrees of freedom in the calibration problem. It assumes, however, on antenna elements with identical primary beams placed precisely on a redundant grid. In this work, we review the detailed implementation of the algorithms enabling redundant-baseline calibration and report results with HERA data. We quantify the effects of real-world non-redundancy and how they compare to the idealized scenario in which redundant measurements differ only in their noise realizations. Finally, we study how non-redundancy can produce spurious temporal structure in our calibration solutions--both in data and in simulations--and present strategies for mitigating that structure., Comment: 24 Pages, 19 Figures. Updated to match the accepted MNRAS version

The very first galaxies that started the cosmic dawn likely resided in so-called "minihaloes", with masses of $\sim10^5$-$10^8\mathrm{M}_\odot$, accreting their gas from the intergalactic medium through H$_2$ cooling. Such molecularly cooled galaxies (MCGs) mostly formed in pristine environments, hosted massive, metal-free stars, and were eventually sterilized by the build-up of a disassociating (Lyman-Werner; LW) background. Therefore, their properties might be very different from the galaxies we see in the later Universe. Although MCGs are probably too faint to be observed directly, we could nevertheless infer their properties from the imprint they leave in the cosmic 21-cm signal. Here we quantify this imprint by extending the public simulation code 21cmFAST to allow for a distinct population of MCGs. We allow MCGs to have different properties from other galaxies, including unique scaling relations for their stellar-to-halo mass ratios, ionizing escape fractions, and spectral energy distributions. We track inhomogeneous recombinations, disassociative LW feedback, and photoheating from reionization. After demonstrating how MCGs can shape the 21-cm signal, we explore to what extent current observations can already place constraints on their properties. The cosmic microwave background optical depth from Planck sets an upper limit on the product of the ionizing escape fraction and the stellar mass in MCGs. When including also the timing of the putative EDGES absorption signal, we find an additional strong degeneracy between the stellar mass and the X-ray luminosity of MCGs. If proven to be of cosmic origin, the timing of the EDGES signal would have been set by MCGs., 19 pages, 8 figures, 1 table; Updated to match the published version. Only minor changes

A number of current and future experiments aim to detect the reionization of neutral hydrogen by the first stars and galaxies in the Universe via the redshifted 21cm line. Using the \textsc{BlueTides} simulation, we investigate the measurement of an \textit{average} ionised region towards the beginning of reionization by stacking redshifted 21cm images around optically identified bright galaxies using mock observations. We find that with an SKA 1000 hour observation, assuming perfect foreground subtraction, a $5\sigma$ detection of a stacked HII region can be made with 30 images around some of the brightest galaxies in \textsc{bluetides} (brighter than $M_{UV} < -22.75$) at $z=9$ (corresponding to a neutral fraction of 90.1 \% in our model). We present simulated relationships between the UV magnitude of galaxies, the sizes of the ionised regions they reside in, and the shape of the stacked profiles. These mock observations can also distinguish between scenarios where the IGM is in net emission or absorption of 21cm photons. Once 21cm foreground contamination is included, we find that even with up to 200 images around these rare, bright galaxies, only a tentative $> 1\sigma$ detection will be possible. However, partial foreground subtraction substantially improves signal-to-noise. For example, we predict that reducing the area of Fourier space dominated by foregrounds by 50 (80) percent will allow $> 3\sigma$ ($> 5\sigma$) detections of ionised regions at $z=9$., Comment: 12 pages, 17 figures, Accepted for publication in MNRAS

Characterizing the epoch of reionization (EoR) at $z\gtrsim 6$ via the redshifted 21 cm line of neutral Hydrogen (HI) is critical to modern astrophysics and cosmology, and thus a key science goal of many current and planned low-frequency radio telescopes. The primary challenge to detecting this signal is the overwhelmingly bright foreground emission at these frequencies, placing stringent requirements on the knowledge of the instruments and inaccuracies in analyses. Results from these experiments have largely been limited not by thermal sensitivity but by systematics, particularly caused by the inability to calibrate the instrument to high accuracy. The interferometric bispectrum phase is immune to antenna-based calibration and errors therein, and presents an independent alternative to detect the EoR HI fluctuations while largely avoiding calibration systematics. Here, we provide a demonstration of this technique on a subset of data from the Hydrogen Epoch of Reionization Array (HERA) to place approximate constraints on the brightness temperature of the intergalactic medium (IGM). From this limited data, at $z=7.7$ we infer "$1\sigma$" upper limits on the IGM brightness temperature to be $\le 316$ "pseudo" mK at $\kappa_\parallel=0.33$ "pseudo" $h$ Mpc$^{-1}$ (data-limited) and $\le 1000$ "pseudo" mK at $\kappa_\parallel=0.875$ "pseudo" $h$ Mpc$^{-1}$ (noise-limited). The "pseudo" units denote only an approximate and not an exact correspondence to the actual distance scales and brightness temperatures. By propagating models in parallel to the data analysis, we confirm that the dynamic range required to separate the cosmic HI signal from the foregrounds is similar to that in standard approaches, and the power spectrum of the bispectrum phase is still data-limited (at $\gtrsim 10^6$ dynamic range) indicating scope for further improvement in sensitivity as the array build-out continues., Comment: 22 pages, 12 figures (including sub-figures). Published in PhRvD. Abstract may be slightly abridged compared to the actual manuscript due to length limitations on arXiv

Next generation observatories will enable us to study the first billion years of our Universe in unprecedented detail. Foremost among these are 21-cm interferometry with the HERA and the SKA, and high-$z$ galaxy observations with the James Webb Space Telescope (JWST). Taking a basic galaxy model, in which we allow the star formation rates and ionizing escape fractions to have a power-law dependence on halo mass with an exponential turnover below some threshold, we quantify how observations from these instruments can be used to constrain the astrophysics of high-$z$ galaxies. For this purpose, we generate mock JWST LFs, based on two different hydrodynamical cosmological simulations; these have intrinsic luminosity functions (LFs) which turn over at different scales and yet are fully consistent with present-day observations. We also generate mock 21-cm power spectrum observations, using 1000h observations with SKA1 and a moderate foreground model. Using only JWST data, we predict up to a factor of 2-3 improvement (compared with HST) in the fractional uncertainty of the star formation rate to halo mass relation and the scales at which the LFs peak (i.e. turnover). Most parameters regulating the UV galaxy properties can be constrained at the level of $\sim 10$% or better, if either (i) we are able to better characterize systematic lensing uncertainties than currently possible; or (ii) the intrinsic LFs peak at magnitudes brighter than $M_{\rm UV} \lesssim -13$. Otherwise, improvement over HST-based inference is modest. When combining with upcoming 21-cm observations, we are able to significantly mitigate degeneracies, and constrain all of our astrophysical parameters, even for our most pessimistic assumptions about upcoming JWST LFs. The 21-cm observations also result in an order of magnitude improvement in constraints on the EoR history., 10 pages, 6 figures, 1 table, submitted to MNRAS

The Epoch of Reionization (EoR) depends on the complex astrophysics governing the birth and evolution of the first galaxies and structures in the intergalactic medium. EoR models rely on cosmic microwave background (CMB) observations, and in particular the large-scale E-mode polarization power spectra (EE PS), to help constrain their highly uncertain parameters. However, rather than directly forward-modelling the EE PS, most EoR models are constrained using a summary statistic -- the Thompson scattering optical depth, $\tau_e$. Compressing CMB observations to $\tau_e$ requires adopting a basis set for the EoR history. The common choice is the unphysical, redshift-symmetric hyperbolic tangent (Tanh) function, which differs in shape from physical EoR models based on hierarchical structure formation. Combining public EoR and CMB codes, 21cmFAST and CLASS, here we quantify how inference using the $\tau_e$ summary statistic impacts the resulting constraints on galaxy properties and EoR histories. Using the last Planck 2018 data release, we show that the marginalized constraints on the EoR history are more sensitive to the choice of the basis set (Tanh vs physical model) than to the CMB likelihood statistic ($\tau_e$ vs PS). For example, EoR histories implied by the growth of structure show a small tail of partial reionization extending to higher redshifts. However, biases in inference using $\tau_e$ are negligible for the Planck 2018 data. Using EoR constraints from high-redshift observations including the quasar dark fraction, galaxy UV luminosity functions and CMB EE PS, our physical model recovers $\tau_e=0.0569^{+0.0081}_{-0.0066}$., Comment: 11 pages, 5 figures, Updated to match the published version. Added Gamma evolution; Only minor changes

This brief code paper presents a new Python-wrapped version of the popular 21cm cosmology simulator, 21cmFAST. The new version, v3+, maintains the same core functionality of previous versions of 21cmFAST, but features a simple and intuitive interface, and a great deal more flexibility. This evolution represents the work of a formalized collaboration, and the new version, available publicly on GitHub, provides a single point-of-reference for all future upgrades and community-added features. In this paper, we describe simple usage of 21cmFAST, some of its new features, and provide a simple performance benchmark., Comment: 6 pages, 3 figures, published in JOSS

We analyze data from the Hydrogen Epoch of Reionization Array. This is the third in a series of papers on the closure phase delay-spectrum technique designed to detect the HI 21cm emission from cosmic reionization. We present the details of the data and models employed in the power spectral analysis, and discuss limitations to the process. We compare images and visibility spectra made with HERA data, to parallel quantities generated from sky models based on the GLEAM survey, incorporating the HERA telescope model. We find reasonable agreement between images made from HERA data, with those generated from the models, down to the confusion level. For the visibility spectra, there is broad agreement between model and data across the full band of $\sim 80$MHz. However, models with only GLEAM sources do not reproduce a roughly sinusoidal spectral structure at the tens of percent level seen in the observed visibility spectra on scales $\sim 10$ MHz on 29 m baselines. We find that this structure is likely due to diffuse Galactic emission, predominantly the Galactic plane, filling the far sidelobes of the antenna primary beam. We show that our current knowledge of the frequency dependence of the diffuse sky radio emission, and the primary beam at large zenith angles, is inadequate to provide an accurate reproduction of the diffuse structure in the models. We discuss implications due to this missing structure in the models, including calibration, and in the search for the HI 21cm signal, as well as possible mitigation techniques., Comment: 17 pages, 10 figures, accepted for the ApJ Supplement

We use the latest multi-redshift ($z=6.5-8.7$) upper limits on the 21-cm signal from the Murchison Widefield Array (MWA) to explore astrophysical models which are inconsistent with the data. These upper limits are achieved using 298 h of carefully excised data over four observing seasons. To explore these upper limits in the context of reionisation astrophysics, we use 21CMMC. We then connect the disfavoured regions of parameter space to existing observational constraints on reionisation such as high-$z$ galaxy ultra-violet (UV) luminosity functions, background UV photoionisation rate, intergalactic medium (IGM) neutral fraction, the electron scattering optical depth and the soft-band X-ray emissivity. We find the vast majority of models disfavoured by the MWA limits are already inconsistent with existing observational constraints. These inconsistent models arise from two classes of models: (i) `cold' reionisation and (ii) pure matter density fluctuations (i.e. no reionisation). However, a small subsample of models are consistent implying the existing MWA limits provide unique information in disfavouring models of reionisation, albeit extremely weakly. We also provide the first limits on the soft-band X-ray emissivity from galaxies at high redshifts, finding $1\sigma$ lower limits of $\epsilon_{{\rm X},0.5-2~{\rm keV}}\gtrsim10^{34.5}$ erg s$^{-1}$ Mpc$^{-3}$. Finally, we recover 95 per cent disfavoured limits on the IGM spin temperature of $\bar{T}_{\rm S}\lesssim$ 1.3, 1.4, 1.5, 1.8, 2.1, 2.4 K at $z=6.5, 6.8, 7.1, 7.8, 8.2, 8.7$. With this we infer the IGM must have undergone, at the very least, a small amount of X-ray heating. Note, the limits on $\epsilon_{{\rm X},0.5-2~{\rm keV}}$ and $\bar{T}_{\rm S}$ are conditional on the IGM neutral fraction., Comment: 14 pages, 7 figures, 1 table. Submitted to MNRAS, comments welcome. arXiv admin note: text overlap with arXiv:2006.03203

The experimental efforts to detect the redshifted 21 cm signal from the Epoch of Reionization (EoR) are limited predominantly by the chromatic instrumental systematic effect. The delay spectrum methodology for 21 cm power spectrum measurements brought new attention to the critical impact of an antenna's chromaticity on the viability of making this measurement. This methodology established a straightforward relationship between time-domain response of an instrument and the power spectrum modes accessible to a 21 cm EoR experiment. We examine the performance of a prototype of the Hydrogen Epoch of Reionization Array (HERA) array element that is currently observing in Karoo desert, South Africa. We present a mathematical framework to derive the beam integrated frequency response of a HERA prototype element in reception from the return loss measurements between 100-200 MHz and determined the extent of additional foreground contamination in the delay space. The measurement reveals excess spectral structures in comparison to the simulation studies of the HERA element. Combined with the HERA data analysis pipeline that incorporates inverse covariance weighting in optimal quadratic estimation of power spectrum, we find that in spite of its departure from the simulated response, HERA prototype element satisfies the necessary criteria posed by the foreground attenuation limits and potentially can measure the power spectrum at spatial modes as low as $k_{\parallel} > 0.1h$~Mpc$^{-1}$. The work highlights a straightforward method for directly measuring an instrument response and assessing its impact on 21 cm EoR power spectrum measurements for future experiments that will use reflector-type antenna., 13 pages, 10 figures, Submitted to APJ

Radio Frequency Interference (RFI) is an ever-present limiting factor among radio telescopes even in the most remote observing locations. When looking to retain the maximum amount of sensitivity and reduce contamination for Epoch of Reionization studies, the identification and removal of RFI is especially important. In addition to improved RFI identification, we must also take into account computational efficiency of the RFI-Identification algorithm as radio interferometer arrays such as the Hydrogen Epoch of Reionization Array grow larger in number of receivers. To address this, we present a Deep Fully Convolutional Neural Network (DFCN) that is comprehensive in its use of interferometric data, where both amplitude and phase information are used jointly for identifying RFI. We train the network using simulated HERA visibilities containing mock RFI, yielding a known "ground truth" dataset for evaluating the accuracy of various RFI algorithms. Evaluation of the DFCN model is performed on observations from the 67 dish build-out, HERA-67, and achieves a data throughput of 1.6$\times 10^{5}$ HERA time-ordered 1024 channeled visibilities per hour per GPU. We determine that relative to an amplitude only network including visibility phase adds important adjacent time-frequency context which increases discrimination between RFI and Non-RFI. The inclusion of phase when predicting achieves a Recall of 0.81, Precision of 0.58, and $F_{2}$ score of 0.75 as applied to our HERA-67 observations., Comment: 11 pages, 7 figures

The 21-cm power spectrum (PS) has been shown to be a powerful discriminant of reionization and cosmic dawn astrophysical parameters. However, the 21-cm tomographic signal is highly non-Gaussian. Therefore there is additional information which is wasted if only the PS is used for parameter recovery. Here we showcase astrophysical parameter recovery directly from 21-cm images, using deep learning with convolutional neural networks (CNN). Using a data base of 2D images taken from 10 000 21-cm light-cones (each generated from different cosmological initial conditions), we show that a CNN is able to recover parameters describing the first galaxies: (i) T-vir, their minimum host halo virial temperatures (or masses) capable of hosting efficient star formation; (ii) zeta, their typical ionizing efficiencies; (iii) L-X/SFR, their typical soft-band X-ray luminosity to star formation rate; and (iv) E-0, the minimum X-ray energy capable of escaping the galaxy into the IGM. For most of their allowed ranges, log T-vir and log L-X/SFR are recovered with < 1 per cent uncertainty, while zeta and E-0 are recovered with similar to 10 per cent uncertainty. Our results are roughly comparable to the accuracy obtained from Monte Carlo Markov Chain sampling of the PS with 21CMMC for the two mock observations analysed previously, although we caution that we do not yet include noise and foreground contaminants in this proof-of-concept study.

The detection of the Epoch of Reionization (EoR) delay power spectrum using a "foreground avoidance method" highly depends on the instrument chromaticity. The systematic effects induced by the radio-telescope spread the foreground signal in the delay domain, which contaminates the EoR window theoretically observable. Applied to the Hydrogen Epoch of Reionization Array (HERA), this paper combines detailed electromagnetic and electrical simulations in order to model the chromatic effects of the instrument, and quantify its frequency and time responses. In particular, the effects of the analogue receiver, transmission cables, and mutual coupling are included. These simulations are able to accurately predict the intensity of the reflections occurring in the 150-m cable which links the antenna to the back-end. They also show that electromagnetic waves can propagate from one dish to another one through large sections of the array due to mutual coupling. The simulated system time response is attenuated by a factor $10^{4}$ after a characteristic delay which depends on the size of the array and on the antenna position. Ultimately, the system response is attenuated by a factor $10^{5}$ after 1400 ns because of the reflections in the cable, which corresponds to characterizable ${k_\parallel}$-modes above 0.7 $h\;\rm{Mpc}^{-1}$ at 150 MHz. Thus, this new study shows that the detection of the EoR signal with HERA Phase I will be more challenging than expected. On the other hand, it improves our understanding of the telescope, which is essential to mitigate the instrument chromaticity., Comment: 13 pages, 17 figures - Submitted to MNRAS - 2nd revision

We compute robust lower limits on the spin temperature, $T_{\rm S}$, of the $z=8.4$ intergalactic medium (IGM), implied by the upper limits on the 21-cm power spectrum recently measured by PAPER-64. Unlike previous studies which used a single epoch of reionization (EoR) model, our approach samples a large parameter space of EoR models: the dominant uncertainty when estimating constraints on $T_{\rm S}$. Allowing $T_{\rm S}$ to be a free parameter and marginalizing over EoR parameters in our Markov Chain Monte Carlo code 21CMMC, we infer $T_{\rm S}\ge3 {\rm K}$ (corresponding approximately to $1\sigma$) for a mean IGM neutral fraction of $\bar{x}_{\rm H{\scriptsize I}}\gtrsim0.1$. We further improve on these limits by folding-in additional EoR constraints based on: (i) the dark fraction in QSO spectra, which implies a strict upper limit of $\bar{x}_{\rm H{\scriptsize I}}[z=5.9]\leq 0.06+0.05 \,(1\sigma)$; and (ii) the electron scattering optical depth, $\tau_{\rm e}=0.066\pm0.016\,(1\sigma)$ measured by the Planck satellite. By restricting the allowed EoR models, these additional observations tighten the approximate $1\sigma$ lower limits on the spin temperature to $T_{\rm S} \ge 6$ K. Thus, even such preliminary 21-cm observations begin to rule out extreme scenarios such as `cold reionization', implying at least some prior heating of the IGM. The analysis framework developed here can be applied to upcoming 21-cm observations, thereby providing unique insights into the sources which heated and subsequently reionized the very early Universe., Comment: 7 pages, 1 figure, accepted to MNRAS (matches online version)

The central challenge in 21~cm cosmology is isolating the cosmological signal from bright foregrounds. Many separation techniques rely on the accurate knowledge of the sky and the instrumental response, including the antenna primary beam. For drift-scan telescopes such as the Hydrogen Epoch of Reionization Array \citep[HERA, ][]{DeBoer2017} that do not move, primary beam characterization is particularly challenging because standard beam-calibration routines do not apply \citep{Cornwell2005} and current techniques require accurate source catalogs at the telescope resolution. We present an extension of the method from \citet{Pober2012} where they use beam symmetries to create a network of overlapping source tracks that break the degeneracy between source flux density and beam response and allow their simultaneous estimation. We fit the beam response of our instrument using early HERA observations and find that our results agree well with electromagnetic simulations down to a -20~dB level in power relative to peak gain for sources with high signal-to-noise ratio. In addition, we construct a source catalog with 90 sources down to a flux density of 1.4~Jy at 151~MHz., 22 pages, 22 figures, accepted for publication in ApJ

Foreground power dominates the measurements of interferometers that seek a statistical detection of highly-redshifted HI emission from the Epoch of Reionization (EoR). The chromaticity of the instrument creates a boundary in the Fourier transform of frequency (proportional to $k_\parallel$) between spectrally smooth emission, characteristic of the strong synchrotron foreground (the "wedge"), and the spectrally structured emission from HI in the EoR (the "EoR window"). Faraday rotation can inject spectral structure into otherwise smooth polarized foreground emission, which through instrument effects or miscalibration could possibly pollute the EoR window. Using data from the HERA 19-element commissioning array, we investigate the polarization response of this new instrument in the power spectrum domain. We perform a simple image-based calibration based on the unpolarized diffuse emission of the Global Sky Model, and show that it achieves qualitative redundancy between the nominally-redundant baselines of the array and reasonable amplitude accuracy. We construct power spectra of all fully polarized coherencies in all pseudo-Stokes parameters. We compare to simulations based on an unpolarized diffuse sky model and detailed electromagnetic simulations of the dish and feed, confirming that in Stokes I, the calibration does not add significant spectral structure beyond the expected level. Further, this calibration is stable over the 8 days of observations considered. Excess power is seen in the power spectra of the linear polarization Stokes parameters which is not easily attributable to leakage via the primary beam, and results from some combination of residual calibration errors and actual polarized emission. Stokes V is found to be highly discrepant from the expectation of zero power, strongly pointing to the need for more accurate polarized calibration., Comment: 21 pages, 12 figures, submitted to ApJ

The properties of the first galaxies, expected to drive the Cosmic Dawn (CD) and the Epoch of Reionization (EoR), are encoded in the 3D structure of the cosmic 21-cm signal. Parameter inference from upcoming 21-cm observations promises to revolutionize our understanding of these unseen galaxies. However, prior inference was done using models with several simplifying assumptions. Here we introduce a flexible, physically-motivated parametrization for high-$z$ galaxy properties, implementing it in the public code 21cmFAST. In particular, we allow their star formation rates and ionizing escape fraction to scale with the masses of their host dark matter halos, and directly compute inhomogeneous, sub-grid recombinations in the intergalactic medium. Combining current Hubble observations of the rest-frame UV luminosity function (UV LFs) at high-$z$ with a mock 1000h 21-cm observation using the Hydrogen Epoch of Reionization Arrays (HERA), we constrain the parameters of our model using a Monte Carlo Markov Chain sampler of 3D simulations, 21CMMC. We show that the amplitude and scaling of the stellar mass with halo mass is strongly constrained by LF observations, while the remaining galaxy properties are constrained mainly by 21-cm observations. The two data sets compliment each other quite well, mitigating degeneracies intrinsic to each observation. All eight of our astrophysical parameters are able to be constrained at the level of $\sim 10\%$ or better. The updated versions of 21cmFAST and 21CMMC used in this work are publicly available., Comment: 16 pages, 8 figures and 2 tables. Associated movies are available at http://homepage.sns.it/mesinger/21CMMC.html. Updated to match the published version. All results and conclusions remain unchanged

We introduce 21CMMC: a parallelized, Monte Carlo Markov Chain analysis tool, incorporating the epoch of reionization (EoR) seminumerical simulation 21CMFAST. 21CMMC estimates astrophysical parameter constraints from 21 cm EoR experiments, accommodating a variety of EoR models, as well as priors on model parameters and the reionization history. To illustrate its utility, we consider two different EoR scenarios, one with a single population of galaxies (with a mass-independent ionizing efficiency) and a second, more general model with two different, feedback-regulated populations (each with mass-dependent ionizing efficiencies). As an example, combining three observations (z=8, 9 and 10) of the 21 cm power spectrum with a conservative noise estimate and uniform model priors, we find that interferometers with specifications like the Low Frequency Array/Hydrogen Epoch of Reionization Array (HERA)/Square Kilometre Array 1 (SKA1) can constrain common reionization parameters: the ionizing efficiency (or similarly the escape fraction), the mean free path of ionizing photons and the log of the minimum virial temperature of star-forming haloes to within 45.3/22.0/16.7, 33.5/18.4/17.8 and 6.3/3.3/2.4 per cent, ~$1\sigma$ fractional uncertainty, respectively. Instead, if we optimistically assume that we can perfectly characterize the EoR modelling uncertainties, we can improve on these constraints by up to a factor of ~few. Similarly, the fractional uncertainty on the average neutral fraction can be constrained to within $\lesssim10$ per cent for HERA and SKA1. By studying the resulting impact on astrophysical constraints, 21CMMC can be used to optimize (i) interferometer designs; (ii) foreground cleaning algorithms; (iii) observing strategies; (iv) alternative statistics characterizing the 21 cm signal; and (v) synergies with other observational programs., Comment: Accepted to MNRAS, matches online version. 20 pages, 4 tables, 11 colour figures

Current and upcoming radio interferometric experiments are aiming to make a statistical characterization of the high-redshift 21cm fluctuation signal spanning the hydrogen reionization and X-ray heating epochs of the universe. However, connecting 21cm statistics to underlying physical parameters is complicated by the theoretical challenge of modeling the relevant physics at computational speeds quick enough to enable exploration of the high dimensional and weakly constrained parameter space. In this work, we use machine learning algorithms to build a fast emulator that mimics expensive simulations of the 21cm signal across a wide parameter space to high precision. We embed our emulator within a Markov-Chain Monte Carlo framework, enabling it to explore the posterior distribution over a large number of model parameters, including those that govern the Epoch of Reionization, the Epoch of X-ray Heating, and cosmology. As a worked example, we use our emulator to present an updated parameter constraint forecast for the Hydrogen Epoch of Reionization Array experiment, showing that its characterization of a fiducial 21cm power spectrum will considerably narrow the allowed parameter space of reionization and heating parameters, and could help strengthen Planck's constraints on $\sigma_8$. We provide both our generalized emulator code and its implementation specifically for 21cm parameter constraints as publicly available software., Comment: 22 pages, 9 figures; accepted to ApJ

We quantify the presence of Ly\alpha\ damping wing absorption from a partially-neutral intergalactic medium (IGM) in the spectrum of the $z=7.08$ QSO, ULASJ1120+0641. Using a Bayesian framework, we simultaneously account for uncertainties in: (i) the intrinsic QSO emission spectrum; and (ii) the distribution of cosmic HI patches during the epoch of reionisation (EoR). For (i) we use a new intrinsic Ly\alpha\ emission line reconstruction method (Greig et al.), sampling a covariance matrix of emission line properties built from a large database of moderate-$z$ QSOs. For (ii), we use the Evolution of 21-cm Structure (EOS; Mesinger et al.) simulations, which span a range of physically-motivated EoR models. We find strong evidence for the presence of damping wing absorption redward of Ly\alpha\ (where there is no contamination from the Ly\alpha\ forest). Our analysis implies that the EoR is not yet complete by $z=7.1$, with the volume-weighted IGM neutral fraction constrained to $\bar{x}_{\rm H\,{\scriptsize I}} = 0.40\substack{+0.21 -0.19}$ at $1\sigma$ ($\bar{x}_{\rm H\,{\scriptsize I}} = 0.40\substack{+0.41 -0.32}$ at $2\sigma$). This result is insensitive to the EoR morphology. Our detection of significant neutral HI in the IGM at $z=7.1$ is consistent with the latest Planck 2016 measurements of the CMB Thompson scattering optical depth (Planck Collaboration XLVII)., Comment: 12 pages, 7 figures, 1 table. Accepted to MNRAS, matches online version

We study the redshift evolution of the quasar UV Luminosity Function (LF) for 0.5 < z < 6.5, by collecting the most up to date observational data and, in particular, the recently discovered population of faint AGNs. We fit the QSO LF using either a double power-law or a Schechter function, finding that both forms provide good fits to the data. We derive empirical relations for the LF parameters as a function of redshift and, based on these results, predict the quasar UV LF at z=8. From the inferred LF evolution, we compute the redshift evolution of the QSO/AGN comoving ionizing emissivity and hydrogen photoionization rate. If faint AGNs are included, the contribution of quasars to reionization increases substantially. However, their level of contribution critically depends on the detailed shape of the QSO LF, which can be constrained by efficient searches of high-z quasars. To this aim, we predict the expected (i) number of z>6 quasars detectable by ongoing and future NIR surveys (as EUCLID and WFIRST), and (ii) number counts for a single radio-recombination line observation with SKA-MID (FoV = 0.49 deg^2) as a function of the Hnalpha flux density, at 0, Comment: 11 pages, 6 figures, 1 table; MNRAS accepted

The cosmic 21 cm signal is set to revolutionise our understanding of the early Universe, allowing us to probe the 3D temperature and ionisation structure of the intergalactic medium (IGM). It will open a window onto the unseen first galaxies, showing us how their UV and X-ray photons drove the cosmic milestones of the epoch of reionisation (EoR) and epoch of heating (EoH). To facilitate parameter inference from the 21 cm signal, we previously developed 21CMMC: a Monte Carlo Markov Chain sampler of 3D EoR simulations. Here we extend 21CMMC to include simultaneous modelling of the EoH, resulting in a complete Bayesian inference framework for the astrophysics dominating the observable epochs of the cosmic 21 cm signal. We demonstrate that second generation interferometers, the Hydrogen Epoch of Reionisation Array (HERA) and Square Kilometre Array (SKA) will be able to constrain ionising and X-ray source properties of the first galaxies with a fractional precision of order $\sim1$-10 per cent (1$\sigma$). The ionisation history of the Universe can be constrained to within a few percent. Using our extended framework, we quantify the bias in EoR parameter recovery incurred by the common simplification of a saturated spin temperature in the IGM. Depending on the extent of overlap between the EoR and EoH, the recovered astrophysical parameters can be biased by $\sim3-10\sigma$., Comment: 20 pages, 10 figures, 4 tables. Accepted to MNRAS (matches online version). Movies showing the imprint of the astrophysical parameters on the 21cm signal can be found at http://homepage.sns.it/mesinger/21CMMC.html

Interferometry of the cosmic 21-cm signal is set to revolutionize our understanding of the Epoch of Reionization (EoR), eventually providing 3D maps of the early Universe. Initial detections however will be low signal-to-noise, limited by systematics. To confirm a putative 21-cm detection, and check the accuracy of 21-cm data analysis pipelines, it would be very useful to cross-correlate against a genuine cosmological signal. The most promising cosmological signals are wide-field maps of Lyman alpha emitting galaxies (LAEs), expected from the Subaru Hyper-Suprime Cam (HSC) Ultra-Deep field. Here we present estimates of the correlation between LAE maps at z~7 and the 21-cm signal observed by both the Low Frequency Array (LOFAR) and the planned Square Kilometer Array Phase 1 (SKA1). We adopt a systematic approach, varying both: (i) the prescription of assigning LAEs to host halos; and (ii) the large-scale structure of neutral and ionized regions (i.e. EoR morphology). We find that the LAE-21cm cross-correlation is insensitive to (i), thus making it a robust probe of the EoR. A 1000h observation with LOFAR would be sufficient to discriminate at >1 standard deviation a fully ionized Universe from one with a mean neutral fraction of xHI~0.50, using the LAE-21cm cross-correlation function on scales of R~3-10 Mpc. Unlike LOFAR, whose detection of the LAE-21cm cross-correlation is limited by noise, SKA1 is mostly limited by ignorance of the EoR morphology. However, the planned 100h wide-field SKA1-Low survey will be sufficient to discriminate an ionized Universe from one with xHI~0.25, even with maximally pessimistic assumptions., 10 pages, 8 figures, 1 table, submitted to MNRAS

The Hydrogen Epoch of Reionization Array (HERA) is a staged experiment to measure 21 cm emission from the primordial intergalactic medium (IGM) throughout cosmic reionization ($z=6-12$), and to explore earlier epochs of our Cosmic Dawn ($z\sim30$). During these epochs, early stars and black holes heated and ionized the IGM, introducing fluctuations in 21 cm emission. HERA is designed to characterize the evolution of the 21 cm power spectrum to constrain the timing and morphology of reionization, the properties of the first galaxies, the evolution of large-scale structure, and the early sources of heating. The full HERA instrument will be a 350-element interferometer in South Africa consisting of 14-m parabolic dishes observing from 50 to 250 MHz. Currently, 19 dishes have been deployed on site and the next 18 are under construction. HERA has been designated as an SKA Precursor instrument. In this paper, we summarize HERA's scientific context and provide forecasts for its key science results. After reviewing the current state of the art in foreground mitigation, we use the delay-spectrum technique to motivate high-level performance requirements for the HERA instrument. Next, we present the HERA instrument design, along with the subsystem specifications that ensure that HERA meets its performance requirements. Finally, we summarize the schedule and status of the project. We conclude by suggesting that, given the realities of foreground contamination, current-generation 21 cm instruments are approaching their sensitivity limits. HERA is designed to bring both the sensitivity and the precision to deliver its primary science on the basis of proven foreground filtering techniques, while developing new subtraction techniques to unlock new capabilities. The result will be a major step toward realizing the widely recognized scientific potential of 21 cm cosmology., Comment: 26 pages, 24 figures, 2 tables

We present upper limits on the 21 cm power spectrum at $z = 5.9$ calculated from the model-independent limit on the neutral fraction of the intergalactic medium of $x_{\rm H{\small I }} < 0.06 + 0.05\ (1\sigma)$ derived from dark pixel statistics of quasar absorption spectra. Using 21CMMC, a Markov chain Monte Carlo Epoch of Reionization analysis code, we explore the probability distribution of 21 cm power spectra consistent with this constraint on the neutral fraction. We present 99 per cent confidence upper limits of $\Delta^2(k) < 10$ to $20\ {\rm mK}^2$ over a range of $k$ from 0.5 to $2.0\ h{\rm Mpc}^{-1}$, with the exact limit dependent on the sampled $k$ mode. This limit can be used as a null test for 21 cm experiments: a detection of power at $z=5.9$ in excess of this value is highly suggestive of residual foreground contamination or other systematic errors affecting the analysis., Comment: 5 pages, 1 figure, accepted to MNRAS letters

We extend 21CMMC, a Monte Carlo Markov Chain sampler of 3D reionisation simulations, to perform parameter estimation directly on 3D light-cones of the cosmic 21cm signal. This brings theoretical analysis closer to the tomographic 21-cm observations achievable with next generation interferometers like HERA and the SKA. Parameter recovery can therefore account for modes which evolve with redshift/frequency. Additionally, simulated data can be more easily corrupted to resemble real data. Using the light-cone version of 21CMMC, we quantify the biases in the recovered astrophysical parameters if we use the 21cm power spectrum from the co-evolution approximation to fit a 3D light-cone mock observation. While ignoring the light-cone effect under most assumptions will not significantly bias the recovered astrophysical parameters, it can lead to an underestimation of the associated uncertainty. However significant biases ($\sim$few -- 10 $\sigma$) can occur if the 21cm signal evolves rapidly (i.e. the epochs of reionisation and heating overlap significantly) and: (i) foreground removal is very efficient, allowing large physical scales ($k\lesssim0.1$~Mpc$^{-1}$) to be used in the analysis or (ii) theoretical modelling is accurate to within $\sim10$ per cent in the power spectrum amplitude., Comment: Submitted to MNRAS, comments welcome. 13 pages, 5 figures and 2 tables