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Ignoring missing values can lead to biased estimates of the covariance. Lounici (2012) gives an unbiased estimator when the data has missing values.
CovarianceWithMissing(x)
matrix, unbiased estimate of the covariance.
matrix or data.frame, data with each row an observation and each column a variable.
Stephen R. Haptonstahl srh@haptonstahl.org
High-dimensional covariance matrix estimation with missing observations. Karim Lounici. 2012.