A local space–time kriging approach applied to a national outpatient malaria data set

Increases in the availability of reliable health data are widely recognised as essential for efforts to strengthen health-care systems in resource-poor settings worldwide. Effective health-system planning requires comprehensive and up-to-date information on a range of health metrics and this requirement is generally addressed by a Health Management Information System (HMIS) that coordinates the routine collection of data at individual health facilities and their compilation into national databases. In many resource-poor settings, these systems are inadequate and national databases often contain only a small proportion of the expected records. In this paper, we take an important health metric in Kenya (the proportion of outpatient treatments for malaria (MP)) from the national HMIS database and predict the values of MP at facilities where monthly records are missing. The available MP data were densely distributed across a spatiotemporal domain and displayed second-order heterogeneity. We used three different kriging methodologies to make cross-validation predictions of MP in order to test the effect on prediction accuracy of (a) the extension of a spatial-only to a space–time prediction approach, and (b) the replacement of a globally stationary with a locally varying random function model. Space–time kriging was found to produce predictions with 98.4% less mean bias and 14.8% smaller mean imprecision than conventional spatial-only kriging. A modification of space–time kriging that allowed space–time variograms to be recalculated for every prediction location within a spatially local neighbourhood resulted in a larger decrease in mean imprecision over ordinary kriging (18.3%) although the mean bias was reduced less (87.5%)

Spatio-temporal modelling of malaria incidence for evaluation of public health policy interventions in Ghana, West Africa

Malaria is a major challenge to both the public health and the socio-economic development of Ghana. Major factors which account for this situation include poor environmental conditions and the lack of prevention services. In spite of the numerous intervention measures, the disease continues to be the most prevalent health problem in the country. The risk assessment reports for Ghana were based on household surveys which provide inadequate data for accurate analysis of incidence cases. This poses a serious threat to planning and management for the health care delivery system in Ghana. Malaria transmission varies with geographical location and time (or season). Spatio-temporal modelling coupled with adequate data has shown to better define the public burden of the disease, providing risk maps to describe the incidence variation in space and time and also identifying high risk areas for health policy implementation. Geostatistics contributes immensely to the prediction of the random processes distributed in space or time in epidemiological studies. In this study, we conduct spatial statistical analysis of malaria incidence to produce evidence-based monthly maps of Ghana illustrating the patterns of malaria risk over space and time. This is achieved using monthly morbidity cases reported on the disease from public health facilities at district level and population data over the period 1998-2010 to compute the malaria incidence rates, being the number of reported cases per unit resident population of 10,000. Lognormal ordinary kriging is used to model the spatial and temporal correlations, and then back-transformed to estimate the monthly malaria risk at local level. The space-time experimental variogram describing the correlations structure is modelled with nested spherical and exponential-cosine functions coupled with nugget effect. The modelled variogram indicate both short and long spatial and temporal dependence of the malaria incidence rates at local level with the temporal component exhibiting an increasing seasonal pattern of period of 12 months. The results also indicate varied spatial distribution of malaria incidence across the country, the highest risk being observed in the northern most and several locations in central and western parts of the country, and lowest in some areas in the north and south along the coast. This statistical-based model approach of malaria epidemiology will be useful for short-term prediction and also provide a basis for resource allocation for the disease’s control in the country

Space-time statistical analysis of malaria morbidity incidence cases in Ghana: A geostatistical modelling approach

Malaria is one of the most prevalent and devastating health problems worldwide. It is a highly endemic disease in Ghana, which poses a major challenge to both the public health and socio-economic development of the country. Major factors accounting for this situation include variability in environmental conditions and lack of prevention services coupled with host of other socio-economic factors. Ghana’s National Malaria Control Programme (NMCP) risk assessment measures have been largely based on household surveys which provided inadequate data for accurate prediction of new incidence cases coupled with frequent incomplete monthly case reports. These raise concerns about annual estimates on the disease burden and also pose serious threats to efficient public health planning including the country’s quest of reducing malaria morbidity and mortality cases by 75% by 2015. In this thesis, both geostatistical space-time models and time series seasonal autoregressive integrated moving average (SARIMA) predictive models have been studied and applied to the monthly malaria morbidity cases from both district and regional health facilities in Ghana. The study sought to explore the spatio-temporal distributions of the malaria morbidity incidence and to account for the potential influence of climate variability, with particular focus on producing monthly spatial maps, delimiting areas with high risk of morbidity. This was achieved by modelling the morbidity cases as incidence rates, being the number of new reported cases per 100,000 residents, which together with the climatic covariates were considered as realisations of random processes occurring in space and/or time. The SARIMA models indicated an upward trend of morbidity incidence in the regions with strong seasonal variation which can be explained primarily by the effects of rainfall, temperature and relative humidity in the month preceding incidence of the disease as well as the morbidity incidence in the previous months. The various spacetime ordinary kriging (STOK) models showed varied spatial and temporal distributions of the morbidity incidence rates, which have increased and expanded across the country over the years. The space-time semivariogram models characterising the spatio-temporal continuity of the incidence rates indicated that the occurrence of the malaria morbidity was spatially and temporally correlated within spatial and temporal ranges varying between 30 and 250 km and 6 and 100 months, respectively. The predicted incidence rates were found to be heterogeneous with highly elevated risk at locations near the borders with neighbouring countries in the north and west as well as the central parts towards the east. The spatial maps showed transition of high risk areas from the north-west to the north-east parts with climatic variables contributing to the variations in the number of morbidity cases across the country. The morbidity incidence estimates were found to be higher during the wet season when temperatures were relatively low whilst low incidence rates were observed in the warm weather period during the dry seasons. In conclusion, the study quantified the malaria morbidity burden in Ghana to produce evidence-based monthly morbidity maps, illustrating the risk patterns of the morbidity of the disease. Increased morbidity risk, delimiting the highest risk areas was also established. This statistical-based modelling approach is important as it allows shortterm prediction of the malaria morbidity incidence in specific regions and districts and also helps support efficient public health planning in the country

Information for decision making from imperfect national data: tracking major changes in health care use in Kenya using geostatistics

Background: most Ministries of Health across Africa invest substantial resources in some form of health management information system (HMIS) to coordinate the routine acquisition and compilation of monthly treatment and attendance records from health facilities nationwide. Despite the expense of these systems, poor data coverage means they are rarely, if ever, used to generate reliable evidence for decision makers. One critical weakness across Africa is the current lack of capacity to effectively monitor patterns of service use through time so that the impacts ofchanges in policy or service delivery can be evaluated. Here, we present a new approach that, for the first time, allows national changes in health service use during a time of major health policy change to be tracked reliably using imperfect data from a national HMIS.Methods: monthly attendance records were obtained from the Kenyan HMIS for 1 271 government-run and 402 faith-based outpatient facilities nationwide between 1996 and 2004. Aspace-time geostatistical model was used to compensate for the large proportion of missing records caused by non-reporting health facilities, allowing robust estimation of monthly and annualuse of services by outpatients during this period.Results: we were able to reconstruct robust time series of mean levels of outpatient utilisation of health facilities at the national level and for all six major provinces in Kenya. These plots revealed reliably for the first time a period of steady nationwide decline in the use of health facilities in Kenyabetween 1996 and 2002, followed by a dramatic increase from 2003. This pattern was consistent across different causes of attendance and was observed independently in each province.Conclusion: the methodological approach presented can compensate for missing records in health information systems to provide robust estimates of national patterns of outpatient service use. This represents the first such use of HMIS data and contributes to the resurrection of these hugely expensive but underused systems as national monitoring tools. Applying this approach to Kenya has yielded output with immediate potential to enhance the capacity of decision makers in monitoring nationwide patterns of service use and assessing the impact of changes in health policy and service deliver

Modeling malaria cases associated with environmental risk factors in Ethiopia using geographically weighted regression

Dissertation submitted in partial fulfilment of the requirements for the degree of Master of Science in Geospatial TechnologiesIn Ethiopia, still, malaria is killing and affecting a lot of people of any age group somewhere in the country at any time. However, due to limited research, little is known about the spatial patterns and correlated risk factors on the wards scale. In this research, we explored spatial patterns and evaluated related potential environmental risk factors in the distribution of malaria cases in Ethiopia in 2015 and 2016. Hot Spot Analysis (Getis-Ord Gi* statistic) was used to assess the clustering patterns of the disease. The ordinary least square (OLS), geographically weighted regression (GWR), and semiparametric geographically weighted regression (s-GWR) models were compared to describe the spatial association of potential environmental risk factors with malaria cases. Our results revealed a heterogeneous and highly clustered distribution of malaria cases in Ethiopia during the study period. The s-GWR model best explained the spatial correlation of potential risk factors with malaria cases and was used to produce predictive maps. The GWR model revealed that the relationship between malaria cases and elevation, temperature, precipitation, relative humidity, and normalized difference vegetation index (NDVI) varied significantly among the wards. During the study period, the s-GWR model provided a similar conclusion, except in the case of NDVI in 2015, and elevation and temperature in 2016, which were found to have a global relationship with malaria cases. Hence, precipitation and relative humidity exhibited a varying relationship with malaria cases among the wards in both years. This finding could be used in the formulation and execution of evidence-based malaria control and management program to allocate scare resources locally at the wards level. Moreover, these study results provide a scientific basis for malaria researchers in the country

Climatic, environmental and socio-economic factors for malaria transmission modelling in KwaZulu-Natal, South Africa.

Doctoral Degree. University of KwaZulu-Natal, Durban.Sub-Saharan Africa (SSA) largely bears the burden of the global malaria disease, with the transmission and intensity influenced by the interaction of a variety of climatic, environmental, socio-economic, and human factors. Other factors include parasitic and vectoral factors. In South Africa (SA) in general and KwaZulu-Natal (KZN) in particular, the change of the malaria control intervention policy in 2000, may be responsible for the significant progress over the past two decades in reducing malaria case report to near zero. Currently, malaria incidence in KZN is less than 1 case per 1000 persons at risk placing the province in the malaria elimination stage. To meeting the elimination target, it is necessary to study the dynamics of malaria transmission in KZN employing various analytical/statistical models. Thus, the aim of this study was to explore the factors that influence malaria transmission by employing different analytical models and approaches in a setting with low malaria endemicity and transmission. This involves a sound appraisal of the existing literature on the contribution of remote sensing technology in understanding malaria transmission, evaluation of existing malaria control intervention; delineation of empirical map of malaria risk; provide information on the climatic, environmental and socio-economic factors that influences malaria risk and transmission; and formulation of a relevant malaria forecast and surveillance models. The investigator started with a systemic review of studies in chapter two. The studies were aimed at identifying significant remotely-sensed climatic and environmental determinants of malaria transmission for modelling malaria transmission and risk in SSA via a variety of statistical approaches. Normalised difference vegetation index (NDVI) was identified as the most significant remotely-sensed climatic/environmental determinants of malaria transmission in SSA. Majority of the studies employed the generalised linear modelling approach compared to the Bayesian modelling approach. In the third chapter, malaria cases from the endemic areas of KZN with remotely-sensed climatic and environmental data were used to model the climatic and environmental determinants of malaria transmission and develop a malaria risk map in KZN. The spatiotemporal zero inflated Poisson model formulated indicates that at 95% Bayesian credible interval (BCI) NDVI (0.91; 95% BCI = 0.71, -1.12), precipitation (0.11; 95% BCI = 0.08, 0.14), elevation (0.05; 95% BCI = 0.032, 0.07) and night temperature (0.04; 95% BCI = 0.03, 0.04) are significantly related to malaria transmission in KZN, SA. The area with the highest risk of malaria morbidity in KZN was identified as the north-eastern part of the province. The fourth chapter was to establish the socio-economic status (SES) that influence malaria transmission in the endemic areas of KZN, by employing a Bayesian inference approach. The obtained posterior samples revealed that, significant association existed between malaria disease and low SES such as illiteracy, unemployment, no toilet facilities and no electricity at 95% BCI Lack of toilet facilities (odds ration (OR) =12.54; 95% BCI = 0.63, 24.38) exhibited the strongest association with malaria and highest risk of malaria disease. This was followed by no education (OR =11.83; 95% BCI = 0.54, 24.27) and lack of electricity supply (OR =10.56; 95% BCI = 0.43, 23.92) respectively. In the fifth chapter, the seasonal autoregressive integrated moving average (SARIMA) intervention time series analysis (ITSA) was employed to model the effect of the malaria control intervention, dichlorodiphenyltrichloroethane (DDT) on confirmed monthly malaria cases. The result is an abrupt and permanent decline of monthly malaria cases (w0= −1174.781, p-value = 0.003) following the implementation of the intervention policy. Finally, the sixth chapter employed a SARIMA modelling approach to predict malaria cases in the endemic areas of KZN. Three plausible models were identified, and based on the goodness of fit statistics and parameter estimation, the SARIMA (0,1,1) (0,1,1)12 model was identified as the best fit model. The SARIMA (0,1,1)(0,1,1)12 model was used to forecast malaria cases during 2014, and it was observed to fit closely with the reported malaria cases during January to December 2014. The models generated in this study demonstrated the need for the KZN malaria program, relevant policy makers and stakeholders to further strengthen the KZN malaria elimination efforts. The required malaria elimination fortification are not limited to the implementation of additional sustainable developmental approach that combines both improved malaria intervention resources and socio-economic conditions, strengthening of existing community health workers, and strengthening of the already existing cross-border collaborations. However, more studies in the area of statistical modelling as well as practical applications of the generated models are encouraged. These can be accomplished by exploring new avenues via cross-sectional survey to understand the impact of community and social related structures in malaria burden; strengthening of existing community health workers; knowledge, attitude and practices in malaria control and intervention; and the likely effects of temporal/seasonal and spatial variations of malaria incidence in neighbouring endemic countries should be explored

Development of a new model for evaluating malaria risk In Chimoio, Mozambique

Dissertation presented as the partial requirement for obtaining a Master's degree in Information Management, specialization in Knowledge Management and Business IntelligenceMalaria is a life-threatening disease that continues to pose serious economic, social and health burdens. Climate plays an important role in the dynamics and distribution of malaria. In particular, temperature and precipitation appear to be critical in perpetuating malaria transmission. In the last decades, there has been an increased interest in the use of weather forecasts for predicting malaria epidemics and setting up early warning systems. In 2017, there have been almost 9 million reported cases of malaria in Mozambique. Malaria is considered one of the deadliest diseases in the country. Previous studies have established that temperature, rainfall and humidity were determinant for malaria transmission and intensity in this region. The purpose of this study is to apply time series analysis and regression modelling to analyse the relationship between malaria incidence and these climatic variables in Chimoio, a municipality located in central Mozambique, and possibly develop a model that can accurately predict the occurrence of malaria outbreaks across this region. With a combination of two (15-week lagged maximum temperature and 3-week lagged precipitation) to three (15-week lagged maximum temperature, 12-week lagged relative humidity and 3-week lagged precipitation) climatic variables, added to the number of malaria cases reported in the previous week, we were able to explain more than 70% of the variability in weekly malaria incidence. These models also quite accurately represent the observed trends of malaria incidence in Chimoio, during the study period. This simple and economical approach, supported by meteorological and epidemiologic data that are readily available, could potentially be applied by local health authorities in order to predict malaria outbreaks. With this information, adequate preventative interventions and resource allocation could be planned and deployed within a more reasonable time frame. Further studies are required in order to determine if this methodology can be successfully applied to other regions of the globe

A Knowledge-Based Data Mining System for Diagnosing Malaria Related Cases in Healthcare Management

Data mining a process for assembling and analyzing data into useful information can be applied as rapid measures for malaria diagnosis. In this research work we implemented (knowledge-base) inference engine that will help in mining sample patient records to discover interesting relationships in malaria related cases. The computer programming language employed was the C#.NET programming language and Microsoft SQL Server 2005 served as the Relational Database Management System (RDBMS). The results obtained showed that knowledge-based data mining system was able to successfully mine out and diagnose possible diseases corresponding to the selected symptoms entered as query. With this finding, we believe the development of a Knowledge-based data mining system will not only be beneficial towards the diagnosis of malaria related cases in a more cost effective means but will assist in crucial decision making and new policy formulation in the malaria endemic regions

SPATIO-TEMPORAL DYNAMICS OF SHORT-TERM TRAFFIC

Short-term traffic forecasting and missing data imputation can benefit from the use of neighboring traffic information, in addition to temporal data alone. However, little attention has been given to quantifying the effect of upstream and downstream traffic on the traffic at current location. The knowledge about temporal and spatial propagation of traffic is still limited in the current literature. To fill this gap, this dissertation research focus on revealing the spatio-temporal correlations between neighboring traffic to develop reliable algorithms for short-term traffic forecasting and data imputation based on spatio-temporal dynamics of traffic. In the first part of this dissertation, spatio-temporal relationships of speed series from consecutive segments were studied for different traffic conditions. The analysis results show that traffic speeds of consecutive segments are highly correlated. While downstream traffic tends to replicate the upstream condition under light traffic conditions, it may also affect upstream condition during congestion and build up situations. These effects were statistically quantified and an algorithm for properly choosing the “best” or most correlated neighbor(s), for potential traffic prediction or imputation purposes was proposed. In the second part of the dissertation, a spatio-temporal kriging (ST-Kriging) model that determines the most desirable extent of spatial and temporal traffic data from neighboring locations was developed for short-term traffic forecasting. The new ST-Kriging model outperforms all benchmark models under various traffic conditions. In the final part of the dissertation, a spatio-temporal data imputation approach was proposed and its performance was evaluated under scenarios with different data missing rates. Compared against previous methods, better flexibility and stable imputation accuracy were reported for this new imputation technique