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Local soil conditions influence the characteristics of earthquake ground shaking and these effects must be taken into account when specifying ground shaking levels for seismic design. These effects are quantified via site response analysis, which involves the propagation of earthquake motions from the base rock through the overlying soil layers to the ground surface. Site response analysis provides surface acceleration-time series, surface acceleration response spectra, and/or spectral amplification factors based on the dynamic response of the local soil conditions. This dissertation investigates and compares the results from different site response methods. Specifically, equivalent-linear time series analysis, equivalent-linear random vibration theory analysis, and nonlinear time series analysis are considered. In the first portion of this study, hypothetical sites and events are used to compare the various site response methods. The use of hypothetical events at hypothetical sites allowed for the seismic evaluation process used in engineering practice to be mimicked. The hypothetical sites were modeled after sites with characteristics that are representative of sites in the Eastern and Western United States. The input motions selected to represent the hypothetical events were developed using the following methods: stochastically-simulated time series, linearly-scaled recorded time series, and spectrally-matched time series. The random vibration theory input motions were defined using: seismological source theory, averaging of the Fourier amplitude spectra computed from scaled time series, and a response spectrum compatible motion. All of the different input motions were then scaled to varying intensity levels and propagated through the sites to evaluate the relative differences between the methods and explain the differences. Data recorded from borehole arrays, which consist of instrumentation at surface and at depth within the soil deposit, are used to evaluate the absolute bias of the site response methods in the second portion of this study. Borehole array data is extremely useful as it captures both the input motion and the surface motion, and can be used to study solely the wave propagation process within the soil deposit. However, comparisons using the borehole data are complicated by the assumed wavefield at the base of the array. In this study, sites are selected based on site conditions and the availability of high intensity input motions. The site characteristics are then developed based on site specific information and data from laboratory soil testing. Comparisons between the observed and computed response are used to first assess the wavefield at the base of the array, and then to evaluate the accuracy of the site response methods. / text