  We model the high redshift (z > 5) Lyman-$\alpha$ emitting (LAE) galaxy
population using the empirical rest-frame equivalent width distribution. We
calibrate to the observed luminosity function and angular correlation function
at z = 5.7 as measured by the SILVERRUSH survey. This allows us to populate the
high-dynamic-range Sherwood simulation suite with LAEs, and to calculate the
transmission of their Ly $\alpha$ emission through the inter-galactic medium
(IGM). We use this simulated population to explore the effect of the IGM on
high-redshift observations of LAEs, and make predictions for the narrowband
filter redshifts at z = 6.6, 7.0 and 7.3. Comparing our model with existing
observations, we find a late reionization is suggested, consistent with the
recent low optical depth derived from the cosmic microwave background (CMB) by
the Planck collaboration and the opacity fluctuations in the Ly $\alpha$
forest. We also explore the role of the circum-galactic medium (CGM) and the
larger volume of gas which is infalling onto the host halo versus the IGM in
attenuating the Ly $\alpha$ signal, finding that a significant fraction of the
attenuation is due to the CGM and infalling gas, which increases towards the
end of reionization, albeit with a large scatter across the mock LAE
population.
