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The Real Time Kinematics Global Positioning System (RTK-GPS) has been proved to be a feasible tool for structure health monitoring. However, there are some limitations using the traditional RTK method under the long baseline conditions, and annoying ionospheric delay.To eliminate this delay, in this paper we present an improved Extended Kalman Filter with Triple-Differenced Ionospheric-Free (EKF-TDIF) method by introducing a triple-differenced operator and an independent white noise. The proposed method is tested for the deformation monitoring of Donghai Bridge especially under the ionospheric active, temperature variation, and typhoon conditions. Experimental results and comparisons with GAMIT show that our proposed method is accurate and feasible for the long-baseline bridge deformation monitoring.