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We use the Sherwood-Relics suite of hybrid hydrodynamical and radiative transfer simulations to model the effect of inhomogeneous reionisation on the 1D power spectrum of the Lyman-$alpha$ forest transmitted flux at redshifts $4.2leq z leq 5$. Relative to models that assume a homogeneous UV background, reionisation suppresses the power spectrum at small scales, $k sim 0.1rm,km^{-1},s$, by $sim 10$ per cent because of spatial variations in the thermal broadening kernel and the divergent peculiar velocity field associated with over-pressurised intergalactic gas. On larger scales, $k<0.03rm,km^{-1},s$, the power spectrum is instead enhanced by $10$-$50$ per cent by large scale spatial variations in the neutral hydrogen fraction. The effect of inhomogeneous reionisation must therefore be accounted for in analyses of forthcoming high precision measurements. We provide a correction for the Lyman-$alpha$ forest power spectrum at $4.1leq z leq 5.4$ in a form that can be easily applied within other parameter inference frameworks. We perform a Bayesian analysis of mock data to assess the extent of systematic biases that may arise in measurements of the intergalactic medium if ignoring this correction. At the scales probed by current high resolution Lyman-$alpha$ forest data at $z>4$, $0.006 rm ,km^{-1},sleq k leq 0.2 rm, km^{-1},s$, we find inhomogeneous reionisation does not introduce any significant bias in thermal parameter recovery for the current measurement uncertainties of $sim 10$ per cent. However, for $5$ per cent uncertainties, $sim 1sigma$ shifts between the estimated and true parameters occur.
Our understanding of the intergalactic medium at redshifts $z=5$-$6$ has improved considerably in the last few years due to the discovery of quasars with $z>6$ that enable Lyman-$alpha$ forest studies at these redshifts. A realisation from this has b
The lya forest at high redshifts is a powerful probe of reionization. Modeling and observing this imprint comes with significant technical challenges: inhomogeneous reionization must be taken into account while simultaneously being able to resolve th
We present the Lyman-$alpha$ flux power spectrum measurements of the XQ-100 sample of quasar spectra obtained in the context of the European Southern Observatory Large Programme Quasars and their absorption lines: a legacy survey of the high redshift
We present constraints on neutrino masses, the primordial fluctuation spectrum from inflation, and other parameters of the $Lambda$CDM model, using the one-dimensional Ly$alpha$-forest power spectrum measured by Palanque-Delabrouille et al. (2013) fr
The latest measurements of CMB electron scattering optical depth reported by Planck significantly reduces the allowed space of HI reionization models, pointing toward a later ending and/or less extended phase transition than previously believed. Reio