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Blind cleaning methods are currently the preferred strategy for handling foreground contamination in single-dish HI intensity mapping surveys. Despite the increasing sophistication of blind techniques, some signal loss will be inevitable across all scales. Constructing a corrective transfer function using mock signal injection into the contaminated data has been a practice relied on for HI intensity mapping experiments. However, assessing whether this approach is viable for future intensity mapping surveys where precision cosmology is the aim, remains unexplored. In this work, using simulations, we validate for the first time the use of a foreground transfer function to reconstruct power spectra of foreground-cleaned low-redshift intensity maps and look to expose any limitations. We reveal that even when aggressive foreground cleaning is required, which causes ${>}\,50\%$ negative bias on the largest scales, the power spectrum can be reconstructed using a transfer function to within sub-percent accuracy. We specifically outline the recipe for constructing an unbiased transfer function, highlighting the pitfalls if one deviates from this recipe, and also correctly identify how a transfer function should be applied in an auto-correlation power spectrum. We validate a method that utilises the transfer function variance for error estimation in foreground-cleaned power spectra. Finally, we demonstrate how incorrect fiducial parameter assumptions (up to ${\pm}100\%$ bias) in the generation of mocks, used in the construction of the transfer function, do not significantly bias signal reconstruction or parameter inference (inducing ${<}\,5\%$ bias in recovered values)., Comment: 25 pages, 20 figures. See Figure 4 for the main demonstration of the transfer function's performance for reconstructing signal loss from foreground cleaning. Accepted for publication in MNRAS

We present and compare several methods to mitigate time-correlated (1/f) noise within the HI intensity mapping component of the MeerKAT Large Area Synoptic Survey (MeerKLASS). By simulating scan strategies, the HI signal, foreground emissions, white and correlated noise, we assess the ability of various data processing pipelines to recover the power spectrum of HI brightness temperature fluctuations. We use MeerKAT pilot data to assess the level of 1/f noise expected for the MeerKLASS survey and use these measurements to create realistic levels of time-correlated noise for our simulations. We find the time-correlated noise component within the pilot data to be between 10 and 20 times higher than the white noise level at the scale of k = 0.04 Mpc^-1. Having determined that the MeerKAT 1/f noise is partially correlated across all the frequency channels, we employ Singular Value Decomposition (SVD) as a technique to remove both the 1/f noise and Galactic foregrounds but find that over-cleaning results in the removal of HI power at large (angular and radial) scales; a power loss of 40 per cent is seen for a 3-mode SVD clean at the scale of k = 0.04 Mpc^-1. We compare the impact of map-making using weighting by the full noise covariance (i.e. including a 1/f component), as opposed to just a simple unweighted binning, finding that including the time-correlated noise information reduces the excess power added by 1/f noise by up to 30 per cent., Comment: 14 pages, 12 figures, accepted by MNRAS. This replacement features updated simulations which now include foreground emissions, telescope slew time and a receiver and elevation-dependant temperature contribution to each receiver which changes over frequency

Estimators for $n$-point clustering statistics in Fourier-space demand that modern surveys of large-scale structure be transformed to Cartesian coordinates to perform Fast Fourier Transforms (FFTs). In this work, we explore this transformation in the context of pixelised line intensity maps (LIM), highlighting potential biasing effects on power spectrum measurements. Current analyses often avoid a complete resampling of the data by approximating survey geometry as rectangular in Cartesian space, an increasingly inaccurate assumption for modern wide-sky surveys. Our simulations of a $20\,{\times}\,20\,\text{deg}^2$ 21cm LIM survey at $0.34\,{<}\,z\,{<}\,0.54$ show this assumption biases power spectrum measurements by ${>}\,20\%$ across all scales. We therefore present a more robust framework for regridding the voxel intensities onto a 3D FFT field by coordinate transforming large numbers of Monte-Carlo sampling particles. Whilst this unbiases power spectrum measurements on large scales, smaller-scale discrepancies remain, caused by structure smoothing and aliasing from separations unresolved by the grid. To correct these effects, we introduce modelling techniques, higher-order particle assignments, and interlaced FFT grids to suppress the aliased power. Using a Piecewise Cubic Spline (PCS) particle assignment and an interlaced FFT field, we achieve sub-percent accuracy up to 80% of the Nyquist frequency for our 21cm LIM simulations. We find a more subtle hierarchical improvement in results for higher-order assignment schemes, relative to the gains made for galaxy surveys, which we attribute to the extra complexity in LIM from additional discretising steps. Python code accompanying this paper is available at github.com/stevecunnington/gridimp., Comment: 15 pages, 11 figures. See Fig.9 for headline result showing sub-percent accurate power spectrum estimation. Accepted for publication in MNRAS

A goal for pathfinder intensity mapping (IM) surveys will be detecting features in the neutral hydrogen (HI) power spectrum, which serve as conclusive evidence of cosmological signals. Observing such features at the expected scales in HI IM auto-correlations, where contribution from systematics is uncertain, will provide a more convincing cosmological detection. We demonstrate how the turnover, i.e. the peak of the power spectrum at ultra-large scales, can be detected with HI IM. We find that a MeerKAT 4,000$\,{\rm deg}^2$ survey using the UHF-band is capable of a $3.1\sigma$ detection of the turnover, relative to a null model power spectrum with no turnover. This should exceed what is capable by current galaxy surveys in optical and near-infrared. The detection significance falls to ${\sim}1\sigma$ in MeerKAT's L-band but can reach ${\sim}13\sigma$ with the SKAO, which should easily surpass the constraints from future Stage-IV-like spectroscopic galaxy surveys. We also propose a new model-independent methodology for constraining the precise turnover scale ($k_0$) and our tests on UHF-band simulated data achieved a precision of 10%. This improved to 2.4% when using the full SKAO. We demonstrate how the results are robust to foreground contamination by using transfer functions, even when an incorrect cosmology has been assumed in their construction. Given that the turnover is related to the horizon scale at matter-radiation equality, a sufficiently precise constraint of $k_0$ presents the possibility for a novel probe of cosmology. We therefore present a potential methodology for constructing a standard-ruler-based distance measurement, independent of the sound horizon, using the turnover location in the HI power spectrum., Comment: 18 pages, 10 figures. See Fig 4 for main forecast of turnover detection for different HI IM surveys. See Fig 7 for constraints possible on turnover scale and Fig 8 for demo of how this can be used for cosmology. Accepted for publication in MNRAS. Minor grammatical edits made for V2 in response to editors' final proofs

ABSTRACT We present the joint analysis of Neutral Hydrogen (H i) Intensity Mapping observations with three galaxy samples: the Luminous Red Galaxy (LRG) and Emission Line Galaxy (ELG) samples from the eBOSS survey, and the WiggleZ Dark Energy Survey sample. The H i intensity maps are Green Bank Telescope observations of the redshifted $21\rm cm$ emission on $100 \, {\rm deg}^2$ covering the redshift range 0.6 < z < 1.0. We process the data by separating and removing the foregrounds present in the radio frequencies with FastI ICA. We verify the quality of the foreground separation with mock realizations, and construct a transfer function to correct for the effects of foreground removal on the H i signal. We cross-correlate the cleaned H i data with the galaxy samples and study the overall amplitude as well as the scale dependence of the power spectrum. We also qualitatively compare our findings with the predictions by a semianalytical galaxy evolution simulation. The cross-correlations constrain the quantity $\Omega _{\rm {H\,\small {I}}} b_{\rm {H\,\small {I}}} r_{\rm {H\,\small {I}},{\rm opt}}$ at an effective scale keff, where $\Omega _\rm {H\,\small {I}}$ is the H i density fraction, $b_\rm {H\,\small {I}}$ is the H i bias, and $r_{\rm {H\,\small {I}},{\rm opt}}$ the galaxy–hydrogen correlation coefficient, which is dependent on the H i content of the optical galaxy sample. At $k_{\rm eff}=0.31 \, h\,{\rm Mpc^{-1}}$ we find $\Omega _{\rm {H\,\small {I}}} b_{\rm {H\,\small {I}}} r_{\rm {H\,\small {I}},{\rm Wig}} = [0.58 \pm 0.09 \, {\rm (stat) \pm 0.05 \, {\rm (sys)}}] \times 10^{-3}$ for GBT-WiggleZ, $\Omega _{\rm {H\,\small {I}}} b_{\rm {H\,\small {I}}} r_{\rm {H\,\small {I}},{\rm ELG}} = [0.40 \pm 0.09 \, {\rm (stat) \pm 0.04 \, {\rm (sys)}}] \times 10^{-3}$ for GBT-ELG, and $\Omega _{\rm {H\,\small {I}}} b_{\rm {H\,\small {I}}} r_{\rm {H\,\small {I}},{\rm LRG}} = [0.35 \pm 0.08 \, {\rm (stat) \pm 0.03 \, {\rm (s

We present a detection of correlated clustering between MeerKAT radio intensity maps and galaxies from the WiggleZ Dark Energy Survey. We find a $7.7\sigma$ detection of the cross-correlation power spectrum, the amplitude of which is proportional to the product of the HI density fraction ($\Omega_{\rm HI}$), HI bias ($b_{\rm HI}$) and the cross-correlation coefficient ($r$). We therefore obtain the constraint $\Omega_{\rm HI} b_{\rm HI} r\,{=}\,[0.86\,{\pm}\,0.10\,({\rm stat})\,{\pm}\,0.12\,({\rm sys})]\,{\times}\,10^{-3}$, at an effective scale of $k_{\rm eff}\,{\sim}\,0.13\,h\,{\rm Mpc}^{-1}$. The intensity maps were obtained from a pilot survey with the MeerKAT telescope, a 64-dish pathfinder array to the SKA Observatory (SKAO). The data were collected from 10.5 hours of observations using MeerKAT's L-band receivers over six nights covering the 11hr field of WiggleZ, in the frequency range $1015-973\,{\rm MHz}$ (0.400$\,{<}\,z\,{<}\,$0.459 in redshift). This detection is the first practical demonstration of the multi-dish auto-correlation intensity mapping technique for cosmology. This marks an important milestone in the roadmap for the cosmology science case with the full SKAO., Comment: 11 pages, 7 figures. See Fig.5 for the main result, showing the cross-power spectrum between MeerKAT and WiggleZ, revealing the 7.7\sigma detection. v2 is the version accepted for publication by MNRAS. The main changes from v1 were in introducing the radio intensity mapping data

A goal for pathfinder intensity mapping (IM) surveys will be detecting features in the neutral hydrogen (HI) power spectrum, which serve as conclusive evidence of cosmological signals. Observing such features at the expected scales in HI IM auto-correlations, where contribution from systematics is uncertain, will provide a more convincing cosmological detection. We demonstrate how the turnover, i.e. the peak of the power spectrum at ultra-large scales, can be detected with HI IM. We find that a MeerKAT 4,000$\,{\rm deg}^2$ survey using the UHF-band is capable of a $3.1\sigma$ detection of the turnover, relative to a null model power spectrum with no turnover. This should exceed what is capable by current galaxy surveys in optical and near-infrared. The detection significance falls to ${\sim}1\sigma$ in MeerKAT's L-band but can reach ${\sim}13\sigma$ with the SKAO, which should easily surpass the constraints from future Stage-IV-like spectroscopic galaxy surveys. We also propose a new model-independent methodology for constraining the precise turnover scale ($k_0$) and our tests on UHF-band simulated data achieved a precision of 10%. This improved to 2.4% when using the full SKAO. We demonstrate how the results are robust to foreground contamination by using transfer functions, even when an incorrect cosmology has been assumed in their construction. Given that the turnover is related to the horizon scale at matter-radiation equality, a sufficiently precise constraint of $k_0$ presents the possibility for a novel probe of cosmology. We therefore present a potential methodology for constructing a standard-ruler-based distance measurement, independent of the sound horizon, using the turnover location in the HI power spectrum., Comment: 18 pages, 10 figures. See Fig 4 for main forecast of turnover detection for different HI IM surveys. See Fig 7 for constraints possible on turnover scale and Fig 8 for demo of how this can be used for cosmology. Accepted for publication in MNRAS. Minor grammatical edits made for V2 in response to editors' final proofs

Cosmological parameter estimation in the post-reionisation era via the radio emission of neutral hydrogen (HI), is one of the key science goals of the forthcoming SKA Observatory (SKAO). In this paper, we explore detection capability for baryon acoustic oscillations (BAO) with a SKAO-like experimental set up, using a suite of 100 simulations inclusive of the main limitations from foreground contamination and poor angular resolution caused by the radio telescope beam. The latter represents a serious challenge for BAO detection with HI intensity mapping, hence we investigate adopting a multipole expansion approach as a means for mitigating the BAO detection limitations caused by the broad single-dish beam. We also showcase the gains made from cross-correlating the HI intensity mapping data with an overlapping spectroscopic galaxy survey, aiming to test the potential synergies between the SKA Project and other future cosmological experiments at optical/near-infrared wavelengths, like the Euclid satellite or the Dark Energy Spectroscopic Instrument. Whilst we were still able to achieve a ~4.5 sigma detection of BAO features in auto-correlation despite the dominant beam effect, a cross-correlation can increase this to a ~6 sigma detection. Furthermore, by adopting the widely studied multipole expansion formalism, we show that including the power spectrum quadrupole besides the monopole in a joint fit can approximately double the BAO detection significance. Despite not implementing a radial-only power spectrum analysis in favour of the three-dimensional power spectrum and its multipoles, we were still able to obtain robust constraints on the radial Alcock-Paczynski parameter, but found that perpendicular parameter remains unconstrained and prior dominated due to beam effects., Comment: 18 pages, 13 figures; fixed formatting and references

21cm intensity mapping experiments are bringing an influx of high spectral resolution observational data in the $\sim100$ MHz $- 1$ GHz regime. We use pilot $971-1075$ MHz data from MeerKAT in single-dish mode, recently used to test the calibration and data reduction scheme of the upcoming MeerKLASS survey, to probe the spectral index of diffuse synchrotron emission below 1 GHz within $145^{\circ} < \alpha < 180^{\circ}$, $-1^{\circ} < \delta < 8^{\circ}$. Through comparisons with data from the OVRO Long Wavelength Array and the Maipu and MU surveys, we find an average spectral index of $-2.75 < \beta < -2.71$ between 45 and 1055 MHz. By fitting for spectral curvature with a spectral index of the form $\beta + c \, {\rm{ln}}(\nu / 73~{\rm MHz})$, we measure $\beta = -2.55 \pm 0.13$ and $c = -0.12 \pm 0.05$ within our target field. Our results are in good agreement (within $1\sigma$) with existing measurements from experiments such as ARCADE2 and EDGES. These results show the calibration accuracy of current data and demonstrate that MeerKLASS will also be capable of achieving a secondary science goal of probing the interstellar medium., Comment: 17 pages, 13 figures, accepted for publication in MNRAS. Updated to match published paper (additional references and acknowledgements)

Neutral Hydrogen Intensity Mapping (HI IM) surveys will be a powerful new probe of cosmology. However, strong astrophysical foregrounds contaminate the signal and their coupling with instrumental systematics further increases the data cleaning complexity. In this work, we simulate a realistic single-dish HI IM survey of a $5000$~deg$^2$ patch in the $950 - 1400$ MHz range, with both the MID telescope of the SKA Observatory (SKAO) and MeerKAT, its precursor. We include a state-of-the-art HI simulations and explore different foreground models and instrumental effects such as non-homogeneous thermal noise and beam side-lobes. We perform the first Blind Foreground Subtraction Challenge for HI IM on these synthetic data-cubes, aiming to characterise the performance of available foreground cleaning methods with no prior knowledge of the sky components and noise level. Nine foreground cleaning pipelines joined the Challenge, based on statistical source separation algorithms, blind polynomial fitting, and an astrophysical-informed parametric fit to foregrounds. We devise metrics to compare the pipeline performances quantitatively. In general, they can recover the input maps' 2-point statistics within 20 per cent in the range of scales least affected by the telescope beam. However, spurious artefacts appear in the cleaned maps due to interactions between the foreground structure and the beam side-lobes. We conclude that it is fundamental to develop accurate beam deconvolution algorithms and test data post-processing steps carefully before cleaning. This study was performed as part of SKAO preparatory work by the HI IM Focus Group of the SKA Cosmology Science Working Group., Comment: Accepted version for publication in MNRAS

We apply for the first time Gaussian Process Regression (GPR) as a foreground removal technique in the context of single-dish, low redshift HI intensity mapping, and present an open-source Python toolkit for doing so. We use MeerKAT and SKA1-MID-like simulations of 21cm foregrounds (including polarisation leakage), HI cosmological signal and instrumental noise. We find that it is possible to use GPR as a foreground removal technique in this context, and that it is better suited in some cases to recover the HI power spectrum than Principal Component Analysis (PCA), especially on small scales. GPR is especially good at recovering the radial power spectrum, outperforming PCA when considering the full bandwidth of our data. Both methods are worse at recovering the transverse power spectrum, since they rely on frequency-only covariance information. When halving our data along frequency, we find that GPR performs better in the low frequency range, where foregrounds are brighter. It performs worse than PCA when frequency channels are missing, to emulate RFI flagging. We conclude that GPR is an excellent foreground removal option for the case of single-dish, low redshift HI intensity mapping in the absence of missing frequency channels. Our Python toolkit gpr4im and the data used in this analysis are publicly available on GitHub., Comment: 19 pages, 1 table, 13 figures, main results in figures 6 and 9, code and data available at https://github.com/paulassoares/gpr4im. Version accepted by MNRAS

We study the clustering of HI intensity maps produced from simulations with a focus on baryonic acoustic oscillations (BAO) and the effects induced by telescope beam smoothing and foreground cleaning. We start by creating a HI catalogue at $z=1.321$ based on the Semi-Analytic Galaxy Evolution (SAGE) model applied to the UNIT simulations. With this catalogue we investigate the relation between model HI and the dark matter haloes and we also study the abundance of HI, $\Omega_{\rm HI}$, predicted by this model. We then create synthetic HI intensity maps with a Nearest-Grid-Point approach. In order to simulate the telescope beam effect, a Gaussian smoothing is applied on the plane perpendicular to the line of sight. The effect of foreground removal methods is simulated by exponentially damping the largest wavelength Fourier modes on the radial direction. We study the anisotropic 2-point correlation function (2PCF) $\xi(r_\perp,r_\parallel)$ and how it is affected by the aforementioned observational effects. In order to better isolate the BAO signal, we study several 2PCF $\mu$-wedges (with a restricted range of orientations $\mu$) tailored to address the systematics effects and we compare them with different definitions of radial 2PCFs. Finally, we discuss our findings in the context of an SKA-like survey, finding a clear BAO signal in most of the estimators here proposed., Comment: published in MNRAS; 18 pages, 10 figures

Cosmological parameter estimation in the post-reionisation era via neutral hydrogen radio emission ($\text{\hi}$), is among the key science goals of the forthcoming SKA Observatory (SKAO). This paper explores detection capability for baryon acoustic oscillations (BAO) with a suite of \(100\) simulations introducing the main limitations from foreground contamination and poor angular resolution caused by the radio telescope beam. Such broad single-dish beam representing a serious challenge for BAO detection with \hi\ intensity mapping, we investigate a multipole expansion approach as a means for mitigating such limitations. We also showcase the gains made from cross-correlating the \hi\ intensity mapping data with an overlapping spectroscopic galaxy survey, aiming to test potential synergies between the SKA Project and other future cosmological experiments at optical/near-infrared wavelengths. For our ${\sim}\,4\,000\,\mathrm{deg}^2$ data set at $z\,{=}\,0.9$, replicating the essential features of an SKAO \hi\ intensity mapping survey, we were able to achieve a ${\sim}\,4.5\sigma$ detection of BAO features in auto-correlation despite the dominant beam effect. Cross-correlation with an overlapping galaxy survey can increase this to a ${\sim}\,6\sigma$ detection. Furthermore, including the power spectrum quadrupole besides the monopole in a joint fit can approximately double the BAO detection significance. Despite not implementing a radial-only $P(k_\parallel)$ analysis in favour of the three-dimensional $P(\bm{k})$ and its multipoles, we were still able to obtain robust constraints on the radial Alcock-Paczynski parameter, whereas the perpendicular parameter remains unconstrained and prior dominated due to beam effects., Comment: 18 pages, 13 figures; fixed formatting and references

21cm intensity mapping experiments are bringing an influx of high spectral resolution observational data in the $\sim100$ MHz $- 1$ GHz regime. We use pilot $971-1075$ MHz data from MeerKAT in single-dish mode, recently used to test the calibration and data reduction scheme of the upcoming MeerKLASS survey, to probe the spectral index of diffuse synchrotron emission below 1 GHz within $145^{\circ} < \alpha < 180^{\circ}$, $-1^{\circ} < \delta < 8^{\circ}$. Through comparisons with data from the OVRO Long Wavelength Array and the Maipu and MU surveys, we find an average spectral index of $-2.75 < \beta < -2.71$ between 45 and 1055 MHz. By fitting for spectral curvature with a spectral index of the form $\beta + c \, {\rm{ln}}(\nu / 73~{\rm MHz})$, we measure $\beta = -2.55 \pm 0.13$ and $c = -0.12 \pm 0.05$ within our target field. Our results are in good agreement (within $1\sigma$) with existing measurements from experiments such as ARCADE2 and EDGES. These results show the calibration accuracy of current data and demonstrate that MeerKLASS will also be capable of achieving a secondary science goal of probing the interstellar medium., Comment: 17 pages, 13 figures, accepted for publication in MNRAS. Updated to match published paper (additional references and acknowledgements)

Neutral Hydrogen Intensity Mapping (HI IM) surveys will be a powerful new probe of cosmology. However, strong astrophysical foregrounds contaminate the signal and their coupling with instrumental systematics further increases the data cleaning complexity. In this work, we simulate a realistic single-dish HI IM survey of a $5000$~deg$^2$ patch in the $950 - 1400$ MHz range, with both the MID telescope of the SKA Observatory (SKAO) and MeerKAT, its precursor. We include a state-of-the-art HI simulations and explore different foreground models and instrumental effects such as non-homogeneous thermal noise and beam side-lobes. We perform the first Blind Foreground Subtraction Challenge for HI IM on these synthetic data-cubes, aiming to characterise the performance of available foreground cleaning methods with no prior knowledge of the sky components and noise level. Nine foreground cleaning pipelines joined the Challenge, based on statistical source separation algorithms, blind polynomial fitting, and an astrophysical-informed parametric fit to foregrounds. We devise metrics to compare the pipeline performances quantitatively. In general, they can recover the input maps' 2-point statistics within 20 per cent in the range of scales least affected by the telescope beam. However, spurious artefacts appear in the cleaned maps due to interactions between the foreground structure and the beam side-lobes. We conclude that it is fundamental to develop accurate beam deconvolution algorithms and test data post-processing steps carefully before cleaning. This study was performed as part of SKAO preparatory work by the HI IM Focus Group of the SKA Cosmology Science Working Group., Comment: Accepted version for publication in MNRAS

We study the clustering of HI intensity maps produced from simulations with a focus on baryonic acoustic oscillations (BAO) and the effects induced by telescope beam smoothing and foreground cleaning. We start by creating a HI catalogue at $z=1.321$ based on the Semi-Analytic Galaxy Evolution (SAGE) model applied to the UNIT simulations. With this catalogue we investigate the relation between model HI and the dark matter haloes and we also study the abundance of HI, $\Omega_{\rm HI}$, predicted by this model. We then create synthetic HI intensity maps with a Nearest-Grid-Point approach. In order to simulate the telescope beam effect, a Gaussian smoothing is applied on the plane perpendicular to the line of sight. The effect of foreground removal methods is simulated by exponentially damping the largest wavelength Fourier modes on the radial direction. We study the anisotropic 2-point correlation function (2PCF) $\xi(r_\perp,r_\parallel)$ and how it is affected by the aforementioned observational effects. In order to better isolate the BAO signal, we study several 2PCF $\mu$-wedges (with a restricted range of orientations $\mu$) tailored to address the systematics effects and we compare them with different definitions of radial 2PCFs. Finally, we discuss our findings in the context of an SKA-like survey, finding a clear BAO signal in most of the estimators here proposed., Comment: published in MNRAS; 18 pages, 10 figures

We apply for the first time Gaussian Process Regression (GPR) as a foreground removal technique in the context of single-dish, low redshift HI intensity mapping, and present an open-source Python toolkit for doing so. We use MeerKAT and SKA1-MID-like simulations of 21cm foregrounds (including polarisation leakage), HI cosmological signal and instrumental noise. We find that it is possible to use GPR as a foreground removal technique in this context, and that it is better suited in some cases to recover the HI power spectrum than Principal Component Analysis (PCA), especially on small scales. GPR is especially good at recovering the radial power spectrum, outperforming PCA when considering the full bandwidth of our data. Both methods are worse at recovering the transverse power spectrum, since they rely on frequency-only covariance information. When halving our data along frequency, we find that GPR performs better in the low frequency range, where foregrounds are brighter. It performs worse than PCA when frequency channels are missing, to emulate RFI flagging. We conclude that GPR is an excellent foreground removal option for the case of single-dish, low redshift HI intensity mapping in the absence of missing frequency channels. Our Python toolkit gpr4im and the data used in this analysis are publicly available on GitHub., Comment: 19 pages, 1 table, 13 figures, main results in figures 6 and 9, code and data available at https://github.com/paulassoares/gpr4im. Version accepted by MNRAS

The bispectrum is a 3-point statistic with the potential to provide additional information beyond power spectra analyses of survey datasets. Radio telescopes which broadly survey the 21cm emission from neutral hydrogen (HI) are a promising way to probe LSS and in this work we present an investigation into the HI intensity mapping (IM) bispectrum using simulations. We present a model of the redshift space HI IM bispectrum including observational effects from the radio telescope beam and 21cm foreground contamination. We validate our modelling prescriptions with measurements from robust IM simulations, inclusive of these observational effects. Our foreground simulations include polarisation leakage, on which we use a Principal Component Analysis cleaning method. We also investigate the effects from a non-Gaussian beam including side-lobes. For a MeerKAT-like single-dish IM survey at $z=0.39$, we find that foreground removal causes a 8% reduction in the equilateral bispectrum's signal-to-noise ratio $S/N$, whereas the beam reduces it by 62%. We find our models perform well, generally providing $\chi^2_\text{dof}\sim 1$, indicating a good fit to the data. Whilst our focus is on post-reionisation, single-dish IM, our modelling of observational effects, especially foreground removal, can also be relevant to interferometers and reionisation studies., Comment: 19 pages, 14 figures. The main results for telescope beam and foreground effects on the bispectrum can be found in Sec 3.2 and 3.3. Minor changes to text in Version 2 in response to referee report and an amendment to Fig 12 to include more information. Version 2 accepted for publication in MNRAS

We present the joint analysis of Neutral Hydrogen (HI) Intensity Mapping observations with three galaxy samples: the Luminous Red Galaxy (LRG) and Emission Line Galaxy (ELG) samples from the eBOSS survey, and the WiggleZ Dark Energy Survey sample. The HI intensity maps are Green Bank Telescope observations of the redshifted 21cm emission on 100deg2 covering the redshift range $0.6

We present a detailed overview of the cosmological surveys that we aim to carry out with Phase 1 of the Square Kilometre Array (SKA1) and the science that they will enable. We highlight three main surveys: a medium-deep continuum weak lensing and low-redshift spectroscopic HI galaxy survey over 5 000 deg2; a wide and deep continuum galaxy and HI intensity mapping (IM) survey over 20 000 deg2 from z = 0.35 to 3; and a deep, high-redshift HI IM survey over 100 deg2 from z = 3 to 6. Taken together, these surveys will achieve an array of important scientific goals: measuring the equation of state of dark energy out to z = 3 with percent-level precision measurements of the cosmic expansion rate; constraining possible deviations from General Relativity on cosmological scales by measuring the growth rate of structure through multiple independent methods; mapping the structure of the Universe on the largest accessible scales, thus constraining fundamental properties such as isotropy, homogeneity, and non-Gaussianity; and measuring the HI density and bias out to z = 6. These surveys will also provide highly complementary clustering and weak lensing measurements that have independent systematic uncertainties to those of optical and near-infrared (NIR) surveys like Euclid, LSST, and WFIRST leading to a multitude of synergies that can improve constraints significantly beyond what optical or radio surveys can achieve on their own. This document, the 2018 Red Book, provides reference technical specifications, cosmological parameter forecasts, and an overview of relevant systematic effects for the three key surveys and will be regularly updated by the Cosmology Science Working Group in the run up to start of operations and the Key Science Programme of SKA1.

We present a framework and an open-source python toolkit to analyse the 2-point statistics of 3D fluctuations in the context of HI intensity maps using the multipole expansion formalism. We include simulations of the cosmological HI signal using N-body and log-normal methods, foregrounds and their removal, as well as instrumental effects. Using these simulations and analytical modelling, we investigate the impact of foreground cleaning and the instrumental beam on the power spectrum multipoles as well as on the Fourier space clustering wedges. We find that both the instrumental beam and the foreground removal can produce a quadrupole (and a hexadecapole) signal, and demonstrate the importance of controlling and accurately modelling these effects for precision radio cosmology. We conclude that these effects can be modelled with reasonable accuracy using our multipole expansion technique. We also perform an MCMC analysis to showcase the effect of foreground cleaning on the estimation of the HI abundance and bias parameters. The accompanying python toolkit is available at https://github.com/IntensityTools/MultipoleExpansion, and includes an interactive suite of examples to aid new users., Comment: 21 pages, 14 figures

While most purpose-built 21cm intensity mapping experiments are close-packed interferometer arrays, general-purpose dish arrays should also be capable of measuring the cosmological 21cm signal. This can be achieved most efficiently if the array is used as a collection of scanning autocorrelation dishes rather than as an interferometer. As a first step towards demonstrating the feasibility of this observing strategy, we show that we are able to successfully calibrate dual-polarisation autocorrelation data from 64 MeerKAT dishes in the L-band (856-1712 MHz, 4096 channels), with 10.5 hours of data retained from six nights of observing. We describe our calibration pipeline, which is based on multi-level RFI flagging, periodic noise diode injection to stabilise gain drifts and an absolute calibration based on a multi-component sky model. We show that it is sufficiently accurate to recover maps of diffuse celestial emission and point sources over a 10 deg x 30 deg patch of the sky overlapping with the WiggleZ 11hr field. The reconstructed maps have a good level of consistency between per-dish maps and external datasets, with the estimated thermal noise limited to 1.4 x the theoretical noise level (~ 2 mK). The residual maps have rms amplitudes below 0.1 K, corresponding to <1% of the model temperature. The reconstructed Galactic HI intensity map shows excellent agreement with the Effelsberg-Bonn HI Survey, and the flux of the radio galaxy 4C+03.18 is recovered to within 3.6%, which demonstrates that the autocorrelation can be successfully calibrated to give the zero-spacing flux and potentially help in the imaging of MeerKAT interferometric data. Our results provide a positive indication towards the feasibility of using MeerKAT and the future SKA to measure the HI intensity mapping signal and probe cosmology on degree scales and above., Comment: 24 pages, 34 figures, accepted for publication in MNRAS

The success of HI intensity mapping is largely dependent on how well 21cm foreground contamination can be controlled. In order to progress our understanding further, we present a range of simulated foreground data from four different $\sim3000$\,deg$^2$ sky regions, with and without effects from polarization leakage. Combining these with underlying cosmological HI simulations creates a range of single-dish intensity mapping test cases that require different foreground treatments. This allows us to conduct the most generalized study to date into 21cm foregrounds and their cleaning techniques for the post-reionization era. We first provide a pedagogical review of the most commonly used blind foreground removal techniques (PCA/SVD, FASTICA, GMCA). We also trial a non-blind parametric fitting technique and discuss potential hybridization of methods. We highlight the similarities and differences in these techniques finding that the blind methods produce near equivalent results, and we explain the fundamental reasons for this. The simulations allow an exact decomposition of the resulting cleaned data and we analyse the contribution from foreground residuals. Our results demonstrate that polarized foreground residuals should be generally subdominant to HI on small scales ($k\gtrsim0.1\,h\,\text{Mpc}^{-1}$). However, on larger scales, results are more region dependent. In some cases, aggressive cleans severely damp HI power but still leave dominant foreground residuals. We also demonstrate the gain from cross-correlations with optical galaxy surveys, where extreme levels of residual foregrounds can be circumvented. However, these residuals still contribute to errors and we discuss the optimal balance between over- and under-cleaning., Comment: 21 pages, 16 figures. Changes made in response to reviewer report. Noted changes from V1: analysis now only performed on two foreground regions (excluding Galactic Plane and Barnard's loop since these were very high emission regions). General results and conclusions unchanged though. Version 2 accepted for publication in MNRAS

We assess the performance of the multipole expansion formalism in the case of single-dish HI intensity mapping, including instrumental and foreground removal effects. This formalism is used to provide MCMC forecasts for a range of HI and cosmological parameters, including redshift space distortions and the Alcock-Paczynski effect. We first determine the range of validity of our power spectrum modelling by fitting to simulation data, concentrating on the monopole, quadrupole, and hexadecapole contributions. We then show that foreground subtraction effects can lead to severe biases in the determination of cosmological parameters, in particular the parameters relating to the transverse BAO rescaling, the growth rate and the HI bias ($\alpha_\perp$, $\overline{T}_\text{HI} f\sigma_8$, and $\overline{T}_\text{HI} b_\text{HI} \sigma_8$, respectively). We attempt to account for these biases by constructing a 2-parameter foreground modelling prescription, and find that our prescription leads to unbiased parameter estimation at the expense of increasing the estimated uncertainties on cosmological parameters. In addition, we confirm that instrumental and foreground removal effects significantly impact the theoretical covariance matrix, and cause the covariance between different multipoles to become non-negligible. Finally, we show the effect of including higher-order multipoles in our analysis, and how these can be used to investigate the presence of instrumental and systematic effects in HI intensity mapping data., Comment: 18 pages, 12 figures, 5 tables, main concepts in figures 2 and 3, main results in figures 5 and 10

Potential evidence for primordial non-Gaussianity (PNG) is expected to lie in the largest scales mapped by cosmological surveys. Forthcoming 21cm intensity mapping experiments will aim to probe these scales by surveying neutral hydrogen (HI) within galaxies. However, foreground signals dominate the faint 21cm emission, meaning foreground cleaning is required to recover the cosmological signal. The effect this has is to damp the HI power spectrum on the largest scales, especially along the line-of-sight. Whilst there is agreement that this contamination is potentially problematic for probing PNG, it is yet to be fully explored and quantified. In this work we carry out the first forecasts on $f_\text{NL}$ that incorporate simulated foreground maps that are removed using techniques employed in real data. Using an MCMC analysis, we demonstrate that foreground cleaned data recovers hugely biased values ($f_\text{NL} = -102.1_{-7.96}^{+8.39}$ [68% CL]) on our $f_\text{NL}=0$ fiducial input. Introducing a model with fixed parameters for the foreground contamination allows us to recover unbiased results ($f_\text{NL} = -2.94_{-11.9}^{+11.4}$). However, it is not clear that we will have sufficient understanding of foreground contamination to allow for such rigid models. Treating the main parameter $k_\parallel^\text{FG}$ in our foreground model as a nuisance parameter and marginalizing over it, still recovers unbiased results but at the expense of much larger errors ($f_\text{NL} = 0.75^{+40.2}_{-44.5}$), that can only be reduced by imposing the Planck 2018 prior. Our results show that significant progress on understanding and controlling foreground removal effects is necessary in order to study PNG with HI intensity mapping., Comment: 15 pages, 8 figures. The busy reader should study Fig 8 which demonstrates the degeneracy between f_NL and k_FG the main parameter in our model to account for foreground removal effects. Accepted by MNRAS

We present a framework and an open-source python toolkit to analyse the 2-point statistics of 3D fluctuations in the context of HI intensity maps using the multipole expansion formalism. We include simulations of the cosmological HI signal using N-body and log-normal methods, foregrounds and their removal, as well as instrumental effects. Using these simulations and analytical modelling, we investigate the impact of foreground cleaning and the instrumental beam on the power spectrum multipoles as well as on the Fourier space clustering wedges. We find that both the instrumental beam and the foreground removal can produce a quadrupole (and a hexadecapole) signal, and demonstrate the importance of controlling and accurately modelling these effects for precision radio cosmology. We conclude that these effects can be modelled with reasonable accuracy using our multipole expansion technique. We also perform an MCMC analysis to showcase the effect of foreground cleaning on the estimation of the HI abundance and bias parameters. The accompanying python toolkit is available at https://github.com/IntensityTools/MultipoleExpansion, and includes an interactive suite of examples to aid new users., Comment: 21 pages, 14 figures

The future of precision cosmology could benefit from cross-correlations between intensity maps of unresolved neutral hydrogen (HI) and more conventional optical galaxy surveys. A major challenge that needs to be overcome is removing the 21cm foreground emission that contaminates the cosmological HI signal. Using N-body simulations we simulate HI intensity maps and optical catalogues which share the same underlying cosmology. Adding simulated foreground contamination and using state-of-the-art reconstruction techniques we investigate the impacts that 21cm foregrounds and other systematics have on these cross-correlations. We find that the impact a FASTICA 21cm foreground clean has on the cross-correlations with spectroscopic optical surveys with well-constrained redshifts is minimal. However, problems arise when photometric surveys are considered: we find that a redshift uncertainty {\sigma}_z {\geq} 0.04 causes significant degradation in the cross power spectrum signal. We diagnose the main root of these problems, which relates to arbitrary amplitude changes along the line-of-sight in the intensity maps caused by the foreground clean and suggest solutions which should be applicable to real data. These solutions involve a reconstruction of the line-of-sight temperature means using the available overlapping optical data along with an artificial extension to the HI data through redshift to address edge effects. We then put these solutions through a further test in a mock experiment that uses a clustering-based redshift estimation technique to constrain the photometric redshifts of the optical sample. We find that with our suggested reconstruction, cross-correlations can be utilized to make an accurate prediction of the optical redshift distribution., Comment: Version 2 - accepted for publication on 5th July 2019 in Monthly Notices of the Royal Astronomical Society Main Journal

The future of precision cosmology could benefit from cross-correlations between intensity maps of unresolved neutral hydrogen (HI) and more conventional optical galaxy surveys. A major challenge that needs to be overcome is removing the 21cm foreground emission that contaminates the cosmological HI signal. Using N-body simulations we simulate HI intensity maps and optical catalogues which share the same underlying cosmology. Adding simulated foreground contamination and using state-of-the-art reconstruction techniques we investigate the impacts that 21cm foregrounds and other systematics have on these cross-correlations. We find that the impact a FASTICA 21cm foreground clean has on the cross-correlations with spectroscopic optical surveys with well-constrained redshifts is minimal. However, problems arise when photometric surveys are considered: we find that a redshift uncertainty {\sigma}_z {\geq} 0.04 causes significant degradation in the cross power spectrum signal. We diagnose the main root of these problems, which relates to arbitrary amplitude changes along the line-of-sight in the intensity maps caused by the foreground clean and suggest solutions which should be applicable to real data. These solutions involve a reconstruction of the line-of-sight temperature means using the available overlapping optical data along with an artificial extension to the HI data through redshift to address edge effects. We then put these solutions through a further test in a mock experiment that uses a clustering-based redshift estimation technique to constrain the photometric redshifts of the optical sample. We find that with our suggested reconstruction, cross-correlations can be utilized to make an accurate prediction of the optical redshift distribution., Comment: Version 2 - accepted for publication on 5th July 2019 in Monthly Notices of the Royal Astronomical Society Main Journal

We present a detailed overview of the cosmological surveys that will be carried out with Phase 1 of the Square Kilometre Array (SKA1), and the science that they will enable. We highlight three main surveys: a medium-deep continuum weak lensing and low-redshift spectroscopic HI galaxy survey over 5,000 sqdeg; a wide and deep continuum galaxy and HI intensity mapping survey over 20,000 sqdeg from z = 0.35 - 3; and a deep, high-redshift HI intensity mapping survey over 100 sqdeg from z = 3 - 6. Taken together, these surveys will achieve an array of important scientific goals: measuring the equation of state of dark energy out to z ~ 3 with percent-level precision measurements of the cosmic expansion rate; constraining possible deviations from General Relativity on cosmological scales by measuring the growth rate of structure through multiple independent methods; mapping the structure of the Universe on the largest accessible scales, thus constraining fundamental properties such as isotropy, homogeneity, and non-Gaussianity; and measuring the HI density and bias out to z = 6. These surveys will also provide highly complementary clustering and weak lensing measurements that have independent systematic uncertainties to those of optical surveys like LSST and Euclid, leading to a multitude of synergies that can improve constraints significantly beyond what optical or radio surveys can achieve on their own. This document, the 2018 Red Book, provides reference technical specifications, cosmological parameter forecasts, and an overview of relevant systematic effects for the three key surveys, and will be regularly updated by the Cosmology Science Working Group in the run up to start of operations and the Key Science Programme of SKA1., Comment: Red Book 2018 of the Square Kilometre Array Cosmology Science Working Group; 35 pages, 27 figures; To be submitted to PASA

Precision cosmology requires accurate galaxy redshifts, but next generation optical surveys will observe unprecedented numbers of resolved galaxies, placing strain on the amount of spectroscopic follow-up required. We show how useful information can be gained on the redshift distributions of optical galaxy samples from spatial cross-correlations with intensity maps of unresolved HI (21cm) spectral line emission. We construct a redshift distribution estimator, which we test using simulations. We utilise the S3-SAX catalogue which includes HI emission information for each galaxy, which we use to construct HI intensity maps. We also make use of simulated LSST and Euclid-like photometry enabling us to apply the HI clustering calibration to realistic simulated photometric redshifts. While taking into account important limitations to HI intensity mapping such as lost k-modes from foreground cleaning and poor angular resolution due to large receiver beams, we show that excellent constraints on redshift distributions can be provided for an optical photometric sample.

We present a detailed overview of the cosmological surveys that will be carried out with Phase 1 of the Square Kilometre Array (SKA1), and the science that they will enable. We highlight three main surveys: a medium-deep continuum weak lensing and low-redshift spectroscopic HI galaxy survey over 5,000 sqdeg; a wide and deep continuum galaxy and HI intensity mapping survey over 20,000 sqdeg from z = 0.35 - 3; and a deep, high-redshift HI intensity mapping survey over 100 sqdeg from z = 3 - 6. Taken together, these surveys will achieve an array of important scientific goals: measuring the equation of state of dark energy out to z ~ 3 with percent-level precision measurements of the cosmic expansion rate; constraining possible deviations from General Relativity on cosmological scales by measuring the growth rate of structure through multiple independent methods; mapping the structure of the Universe on the largest accessible scales, thus constraining fundamental properties such as isotropy, homogeneity, and non-Gaussianity; and measuring the HI density and bias out to z = 6. These surveys will also provide highly complementary clustering and weak lensing measurements that have independent systematic uncertainties to those of optical surveys like LSST and Euclid, leading to a multitude of synergies that can improve constraints significantly beyond what optical or radio surveys can achieve on their own. This document, the 2018 Red Book, provides reference technical specifications, cosmological parameter forecasts, and an overview of relevant systematic effects for the three key surveys, and will be regularly updated by the Cosmology Science Working Group in the run up to start of operations and the Key Science Programme of SKA1., Comment: Red Book 2018 of the Square Kilometre Array Cosmology Science Working Group; 35 pages, 27 figures; To be submitted to PASA

Precision cosmology requires accurate galaxy redshifts, but next generation optical surveys will observe unprecedented numbers of resolved galaxies, placing strain on the amount of spectroscopic follow-up required. We show how useful information can be gained on the redshift distributions of optical galaxy samples from spatial cross-correlations with intensity maps of unresolved HI (21cm) spectral line emission. We construct a redshift distribution estimator, which we test using simulations. We utilise the S3-SAX catalogue which includes HI emission information for each galaxy, which we use to construct HI intensity maps. We also make use of simulated LSST and Euclid-like photometry enabling us to apply the HI clustering calibration to realistic simulated photometric redshifts. While taking into account important limitations to HI intensity mapping such as lost k-modes from foreground cleaning and poor angular resolution due to large receiver beams, we show that excellent constraints on redshift distributions can be provided for an optical photometric sample.

Inferring cosmological parameters from time-delay strong lenses requires a significant investment of telescope time; it is therefore tempting to focus on the systems with the brightest sources, the highest image multiplicities and the widest image separations. We investigate if this selection bias can influence the properties of the lenses studied and the cosmological parameters that are inferred. Using a population of lenses with ellipsoidal powerlaw density profiles, we build a sample of double and quadruple image systems. Assuming reasonable thresholds on image separation and flux, based on current lens monitoring campaigns, we find that the typical density profile slopes of monitorable lenses are significantly shallower than the input ensemble. From a sample of quadruple image lenses we find that this selection function can introduce a 3.5% bias on the inferred time-delay distances if the ensemble of deflector properties is used as a prior for a cosmographical analysis. This bias remains at the 2.4% level when high resolution imaging of the quasar host is used to precisely infer the density profiles of individual lenses. We also investigate if the lines-of-sight for monitorable strong lenses are biased. After adding external convergence, $\kappa$, and shear to our lens population we find that the expectation value for $\kappa$ is increased by 0.004 and 0.009 for doubles and quads respectively. $\kappa$ is degenerate with the value of $H_0$ inferred from time delays; fortunately the shift in $\kappa$ only induces a 0.9 (0.4) percent bias on $H_0$ for quads (doubles). We therefore conclude that whilst the properties of typical quasar lenses and their lines-of-sight do deviate from the global population, the total magnitude of this effect is likely a subdominant effect for current analyses, but has the potential to be a major systematic for samples of $\sim$25 or more lenses., Comment: 10 Pages. Submitted to MNRAS. Revised after comments from referee

Inferring cosmological parameters from time-delay strong lenses requires a significant investment of telescope time; it is therefore tempting to focus on the systems with the brightest sources, the highest image multiplicities and the widest image separations. We investigate if this selection bias can influence the properties of the lenses studied and the cosmological parameters that are inferred. Using a population of lenses with ellipsoidal powerlaw density profiles, we build a sample of double and quadruple image systems. Assuming reasonable thresholds on image separation and flux, based on current lens monitoring campaigns, we find that the typical density profile slopes of monitorable lenses are significantly shallower than the input ensemble. From a sample of quadruple image lenses we find that this selection function can introduce a 3.5% bias on the inferred time-delay distances if the ensemble of deflector properties is used as a prior for a cosmographical analysis. This bias remains at the 2.4% level when high resolution imaging of the quasar host is used to precisely infer the density profiles of individual lenses. We also investigate if the lines-of-sight for monitorable strong lenses are biased. After adding external convergence, $\kappa$, and shear to our lens population we find that the expectation value for $\kappa$ is increased by 0.004 and 0.009 for doubles and quads respectively. $\kappa$ is degenerate with the value of $H_0$ inferred from time delays; fortunately the shift in $\kappa$ only induces a 0.9 (0.4) percent bias on $H_0$ for quads (doubles). We therefore conclude that whilst the properties of typical quasar lenses and their lines-of-sight do deviate from the global population, the total magnitude of this effect is likely a subdominant effect for current analyses, but has the potential to be a major systematic for samples of $\sim$25 or more lenses., Comment: 10 Pages. Submitted to MNRAS. Revised after comments from referee