Malaria and anemia are significant public health concerns that contribute to child mortality in African. Despite global efforts to control the two diseases, their prevalence in high-risk regions like Nigeria remains high. Understanding socioeconomic, demographic, and geographical factors associated with malaria and anemia, is critical for effective intervention strategies. The study aims to assess the risk factors for malaria and anemia in children under 5 years using the joint generalized linear mixed model (JGLMM). The Nigeria Malaria Indicator Survey (NMIS) 2021 dataset was used, with a sample of 10,120 children aged 6-59 months. A two-stage sampling method was applied. Descriptive statistics and chi-square tests examined factors associated with malaria and anemia prevalence. Missing data were handled using multiple imputations with chained equations (MICE). Lastly, the adjusted odds ratio was interpreted for the current study. SAS was used in analyzing the data and statistical significance was set at 5% significance level. The prevalence of malaria and anemia was 36.81 and 67.66%, respectively, in children between 6 and 59 months old in Nigeria. The JGLMM was used to examine malaria RDT and anemia findings in conjunction with demographic, geographic, and socioeconomic covariates. The following underlying risk factors for malaria and anemia in children were discovered in the study: region, altitude, age of child in months, toilet facility of the household, main wall material used for the house, main roof material used for the house, children under five who slept under a mosquito net, whether the child had fever in last 2 weeks before the survey took place, place of residence where the child resides, household wealth index, sex of child, and mother's education level. However, whether the mother knew of ways to prevent malaria was not statistically significant regarding anemia. This study highlights the importance of addressing fever as a key factor for anemia and improving housing conditions to reduce malaria and anemia prevalence. Policymakers should prioritize mosquito net distribution and healthcare access, particularly in rural areas. The study's novelty lies in its handling of missing data through imputation techniques, enhancing the reliability of findings.
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