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This paper presents the design and deployment of the Hydrogen Epoch of Reionization Array (HERA) phase II system. HERA is designed as a staged experiment targeting 21 cm emission measurements of the Epoch of Reionization. First results from the phase I array are published as of early 2022, and deployment of the phase II system is nearing completion. We describe the design of the phase II system and discuss progress on commissioning and future upgrades. As HERA is a designated Square Kilometre Array pathfinder instrument, we also show a number of “case studies” that investigate systematics seen while commissioning the phase II system, which may be of use in the design and operation of future arrays. Common pathologies are likely to manifest in similar ways across instruments, and many of these sources of contamination can be mitigated once the source is identified.

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. Monitoring the performance of a many‐element system is essential to acquiring science‐quality data and requires an automated approachWe define metrics based on cross‐correlations that assess the health of the whole array and its component subsystems in an automated wayWe outline metrics based on autocorrelations that identify systematics and provide a generalizable approach to automated antenna flagging Monitoring the performance of a many‐element system is essential to acquiring science‐quality data and requires an automated approach We define metrics based on cross‐correlations that assess the health of the whole array and its component subsystems in an automated way We outline metrics based on autocorrelations that identify systematics and provide a generalizable approach to automated antenna flagging

We introduce a new pipeline for analyzing and mitigating radio frequency interference (RFI), which we call Sky-Subtracted Incoherent Noise Spectra (ssins). ssinsis designed to identify and remove faint RFI below the single baseline thermal noise by employing a frequency-matched detection algorithm on baseline-averaged amplitudes of time-differenced visibilities. We demonstrate the capabilities of ssinsusing the Murchison Widefield Array (MWA) in Western Australia. We successfully image aircraft flying over the array via digital television reflection detected using ssinsand summarize an RFI occupancy survey of MWA Epoch of Reionization data. We describe how to use ssinswith new data using a documented, publicly available implementation with comprehensive usage tutorials.

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? 30). 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.