We build a physical model for high-redshift Lyman Alpha emitters (LAEs) by coupling state of the art cosmological simulations (GADGET-2) with a dust model and a radiative transfer code (pCRASH). We post-process the cosmological simulation with pCRASH using five different values of the escape fraction of hydrogen ionizing photons (f_esc=0.05,0.25,0.5,0.75,0.95) until reionization is complete, i.e. the average neutral hydrogen fraction drops to <X_HI>~10^-4. Then, the only free-parameter left to match model results to the observed Lya and UV luminosity functions of LAEs at z~6.6 is the relative escape of Lyman Alpha (Lya) and continuum photons from the galactic environment (f_alpha/f_c). We find a three-dimensional degeneracy such that the theoretical model can be reconciled with observations for an IGM Lya transmission <T_alpha>_LAE~38-50% (which translates to <X_HI>~0.5-10^-4 for Gaussian emission lines), f_esc~0.05-0.50 and f_alpha/f_c~0.6-1.8.
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