Radio astronomy is entering a new era with new and future radio observatories such as the Low Frequency Array and the Square Kilometer Array. We describe in detail an automated flagging pipeline and evaluate its performance. With only a fraction of the computational cost of correlation and its use of the previously introduced SumThreshold method, it is found to be both fast and unrivalled in its high accuracy. The LOFAR radio environment is analysed with the help of this pipeline. The high time and spectral resolution of LOFAR have resulted in an observatory where only a few percent of the data is lost due to RFI.
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