  Making use of the Rydberg blockade, we generate entanglement between two
atoms individually trapped in two optical tweezers. In this paper we detail the
analysis of the data and show that we can determine the amount of entanglement
between the atoms in the presence of atom losses during the entangling
sequence. Our model takes into account states outside the qubit basis and
allows us to perform a partial reconstruction of the density matrix describing
the two atom state. With this method we extract the amount of entanglement
between pairs of atoms still trapped after the entangling sequence and measure
the fidelity with respect to the expected Bell state. We find a fidelity
$F_{\rm pairs} =0.74(7)$ for the 62% of atom pairs remaining in the traps at
the end of the entangling sequence.
