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Abstract BackgroundFactors influencing the health of populations are subjects of interdisciplinary study. However, datasets relevant to public health often lack interdisciplinary breath. It is difficult to combine data on health outcomes with datasets on potentially important contextual factors, like political violence or development, due to incompatible levels of geographic support; differing data formats and structures; differences in sampling procedures and wording; and the stability of temporal trends. We present a computational package to combine spatially misaligned datasets, and provide an illustrative analysis of multi-dimensional factors in health outcomes. MethodsWe rely on a new software toolkit, Sub-National Geospatial Data Archive (SUNGEO), to combine data across disciplinary domains and demonstrate a use case on vaccine hesitancy in Low and Middle-Income Countries (LMICs). We use data from the World Bank’s High Frequency Phone Surveys (HFPS) from Kenya, Indonesia, and Malawi. We curate and combine these surveys with data on political violence, elections, economic development, and other contextual factors, using SUNGEO. We then develop a stochastic model to analyze the integrated data and evaluate 1) the stability of vaccination preferences in all three countries over time, and 2) the association between local contextual factors and vaccination preferences. ResultsIn all three countries, vaccine-acceptance is more persistent than vaccine-hesitancy from round to round: the long-run probability of staying vaccine-acceptant (hesitant) was 0.96 (0.65) in Indonesia, 0.89 (0.21) in Kenya, and 0.76 (0.40) in Malawi. However, vaccine acceptance was significantly less durable in areas exposed to political violence, with percentage point differences (ppd) in vaccine acceptance of -10 (Indonesia), -5 (Kenya), and -64 (Malawi). In Indonesia and Kenya, although not Malawi, vaccine acceptance was also significantly less durable in locations without competitive elections (-19 and -6 ppd, respectively) and in locations with more limited transportation infrastructure (-11 and -8 ppd). ConclusionWith SUNGEO, researchers can combine spatially misaligned and incompatible datasets. As an illustrative example, we find that vaccination hesitancy is correlated with political violence, electoral uncompetitiveness and limited access to public goods, consistent with past results that vaccination hesitancy is associated with government distrust.