High precison calibration is essential for a new generation of radio interferometers looking for Epoch of Reionization and Baryon Acoustic Oscillation signatures in neutral hydrogen. These arrays have so far been calibrated by redundant calibration, which usually assumes baselines intended to be identical are perfectly so. We present a new calibration scheme that relaxes the assumption of explicit redundancy by calculating the expected covariance of baselines. The technique also allows one to take advantage of partial knowledge of the sky, such as point sources with known positions but unknown fluxes. We describe a 2-level sparse matrix inverse to make the calibration tractable for 1,000-element class interferometers. We provide a reference implementation and use it to test the calibration of simulations of an array with imperfectly located antennas observing Euclidean-distributed point sources. Including position information for a handful of the brightest sources, we find the amplitude/phase reconstruction improves by a factor of $\sim$2/5 over redundant calibration for the noise levels/position errors adopted in the simulations. Inclusion of source positions also allows us to measure the overall phase gradient across the array, information which is lost in traditional redundant calibration.