Large scale genetic datasets often aggregate the total allele counts of distinct genetic markers. Inferring haplotype frequencies (i.e.\ the frequency of multimarker alleles) from these pooled data is a challenge. Previous spatio-temporal modelling in this context has been limited to 3 markers due to the computational cost. In this work, we propose a nearest neighbor Gaussian process (NNGP) model to improve scaling with the number of markers and observations. To infer the parameters of our model, we develop a novel sequential Monte Carlo squared algorithm, which uses particle Gibbs with ancestor sampling to mutate the NNGP function values. The latter has a linear cost in the number of observations and the number of NNGPs, and can be applied to a broad range of NNGP models. As a case study, we analyse genetic data relating to antimalarial drug resistance in Africa, and show our scaling results empirically on a 3 and 6 genetic marker dataset.

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