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However, the multivariate case is challenging due to the need to account for correlations across space, time and disease in both the count and zero-inflated components of the model. We are interested in comparing the transmission dynamics of several co-circulating infectious diseases across space and time, where some of the diseases can be absent for long periods. We first assume there is a baseline disease that is well-established and always present in the region. The other diseases switch between periods of presence and absence in each area through a series of coupled Markov chains, which account for long periods of disease absence, disease interactions and disease spread from neighboring areas. Since we are mainly interested in comparing the diseases, we assume the cases of the present diseases in an area jointly follow an autoregressive multinomial model. We use the multinomial model to investigate whether there are associations between certain factors, such as temperature, and differences in the transmission intensity of the diseases. Inference is performed using efficient Bayesian Markov chain Monte Carlo methods based on jointly sampling all unknown presence indicators. We apply the model to spatio-temporal counts of dengue, Zika, and chikungunya cases in Rio de Janeiro, during the first triple epidemic there.<\/jats:p>","DOI":"10.1093\/biostatistics\/kxaf034","type":"journal-article","created":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T18:41:26Z","timestamp":1762713686000},"source":"Crossref","is-referenced-by-count":1,"title":["Markov switching zero-inflated space-time multinomial models for comparing multiple infectious diseases"],"prefix":"10.1093","volume":"26","author":[{"given":"Dirk","family":"Douwes-Schultz","sequence":"first","affiliation":[{"name":"Department of Epidemiology, Biostatistics and Occupational Health, McGill University , 2001 McGill College Avenue, Suite 1200 , Montreal, QC H3A 1G1,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6448-6367","authenticated-orcid":false,"given":"Alexandra M","family":"Schmidt","sequence":"additional","affiliation":[{"name":"Department of Epidemiology, Biostatistics and Occupational Health, McGill University , 2001 McGill College Avenue, Suite 1200 , Montreal, QC H3A 1G1,","place":["Canada"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"La\u00eds Picinini","family":"Freitas","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Quantitative Methods in Health, Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation , Rua Leopoldo Bulh\u00f5es, 1480 , Rio de Janeiro, RJ 21041-210,","place":["Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marilia S\u00e1","family":"Carvalho","sequence":"additional","affiliation":[{"name":"Scientific Computing Program, Oswaldo Cruz Foundation , Av. 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