Calibration in a Data Sparse Environment: How Many Cases Did We Miss?

Reported case numbers in the COVID-19 pandemic are assumed in many countries to have underestimated the true prevalence of the disease. Deficits in reporting may have been particularly great in countries with limited testing capability and restrictive testing policies. Simultaneously, some models have been accused of over-reporting the scale of the pandemic. At a time when modeling consortia around the world are turning to the lessons learnt from pandemic modelling, we present an example of simulating testing as well as the spread of disease. In particular, we factor in the amount and nature of testing that was carried out in the first wave of the COVID-19 pandemic (March - September 2020), calibrating our spatial Agent Based Model (ABM) model to the reported case numbers in Zimbabwe

Scale matters: Variations in spatial and temporal patterns of epidemic outbreaks in agent-based models

Agent-based modellers frequently make use of techniques to render simulated populations more computationally tractable on actionable timescales. Many generate a relatively small number of “representative” agents, each of which is “scaled up” to represent some larger number of individuals involved in the system being studied. The degree to which this “scaling” has implications for model forecasts is an underdeveloped field of study; in particular, there has been little known research on the spatial implications of such techniques. This work presents a case study of the impact of the simulated population size, using a model of the spread of COVID-19 among districts in Zimbabwe for the underlying system being studied. The impact of the relative scale of the population is explored in conjunction with the spatial setup, and crucial model parameters are varied to highlight where scaled down populations can be safely used and where modellers should be cautious. The results imply that in particular, different geographical dynamics of the spread of disease are associated with varying population sizes, with implications for researchers seeking to use scaled populations in their research. This article is an extension on work previously presented as part of the International Conference on Computational Science 2022 (Wise et al., 2022)[1]

The effect of choice interventions on retention-related, behavioural and mood outcomes: a systematic review with meta-analysis

The provision of choice within interventions has been associated with increased motivation, engagement and interest, as well as improved clinical outcomes. Existing reviews are limited by their wide inclusion criteria or by not assessing behaviour change and mood outcomes. This review examines whether participant-driven choice-based interventions specifically are more likely to be enjoyed and accepted by participants compared to no-choice interventions, and whether this impacts on intervention outcomes in terms of behaviour change or mood. Forty-four randomised controlled trials were identified for inclusion. Random effects meta-analyses were performed for retention-related outcomes (drop-out, adherence and satisfaction), and aggregate behaviour change and mood outcomes. Choice-based interventions resulted in significantly less participant drop-out and increased adherence compared to interventions not offering choice. Results for the behaviour change and mood analyses were mixed. This meta-analytic review demonstrates that choice-based interventions may enhance participant retention and adherence, thus researchers and clinicians alike should consider the provision of choice when designing research and interventions. The evidence for the role of choice in behaviour change and mood is less convincing, and there is a need for more, higher quality research in this area

Calibration in a Data Sparse Environment: How Many Cases Did We Miss? (Short Paper)

Reported case numbers in the COVID-19 pandemic are assumed in many countries to have underestimated the true prevalence of the disease. Deficits in reporting may have been particularly great in countries with limited testing capability and restrictive testing policies. Simultaneously, some models have been accused of over-reporting the scale of the pandemic. At a time when modeling consortia around the world are turning to the lessons learnt from pandemic modelling, we present an example of simulating testing as well as the spread of disease. In particular, we factor in the amount and nature of testing that was carried out in the first wave of the COVID-19 pandemic (March - September 2020), calibrating our spatial Agent Based Model (ABM) model to the reported case numbers in Zimbabwe

A stitch in time: The importance of water and sanitation services (WSS) infrastructure maintenance for cholera risk. A geospatial analysis in Harare, Zimbabwe.

Understanding the factors associated with cholera outbreaks is an integral part of designing better approaches to mitigate their impact. Using a rich set of georeferenced case data from the cholera epidemic that occurred in Harare from September 2018 to January 2019, we apply spatio-temporal modelling to better understand how the outbreak unfolded and the factors associated with higher risk of being a reported case. Using Call Detail Records (CDR) to estimate weekly population movement of the community throughout the city, results suggest that broader human movement (not limited to infected agents) helps to explain some of the spatio-temporal patterns of cases observed. In addition, results highlight a number of socio-demographic risk factors and suggest that there is a relationship between cholera risk and water infrastructure. The analysis shows that populations living close to the sewer network, with high access to piped water are associated with at higher risk. One possible explanation for this observation is that sewer bursts led to the contamination of the piped water network. This could have turned access to piped water, usually assumed to be associated with reduced cholera risk, into a risk factor itself. Such events highlight the importance of maintenance in the provision of SDG improved water and sanitation infrastructure

Developing a Combined Drought Index to Monitor Agricultural Drought in Sri Lanka

Developing an agricultural drought monitoring index through integrating multiple input variables into a single index is vital to facilitate the decision-making process. This study aims to develop an agricultural drought index (agCDI) to monitor and characterize the spatial and temporal patterns of drought in Sri Lanka. Long-term (1982 to 2020) remote sensing and model-based agroclimatic input parameters—normalized difference vegetation index (NDVI), land surface temperature (LST), 3-month precipitation z-score (stdPCP), and evaporative demand drought index (EDDI)—were used to develop agCDI. The principal component analysis (PCA) approach was employed to qualitatively determine the grid-based percentage contribution of each input parameter. The agCDI was apparently evaluated using an independent dataset, including the crop yield for the major crop growing districts and observed streamflow-based surface runoff index (SRI) for the two main crop growing seasons locally, called Yala (April to September) and Maha (October to March), using 20-years of data (from 2000 to 2020). The results illustrate the good performance of agCDI, in terms of predominantly capturing and characterizing the historic drought conditions in the main agricultural producing districts both during the Yala and Maha seasons. There is a relatively higher chance of the occurrence of moderate to extreme droughts in the Yala season, compared to the Maha season. The result further depicts that relatively good correlation coefficient values (> 0.6) were obtained when agCDI was evaluated using a rice crop yield in the selected districts. Although the agCDI correlated well with SRI in some of the stations (>0.6), its performance was somehow underestimated in some of the stations, perhaps due to the time lag of the streamflow response to drought. In general, agCDI showed its good performance in capturing the spatial and temporal patterns of the historic drought and, hence, the model can be used to develop agricultural drought monitoring and an early warning system to mitigate the adverse impacts of drought in Sri Lanka

Developing a Combined Drought Index to Monitor Agricultural Drought in Sri Lanka

Developing an agricultural drought monitoring index through integrating multiple input variables into a single index is vital to facilitate the decision-making process. This study aims to develop an agricultural drought index (agCDI) to monitor and characterize the spatial and temporal patterns of drought in Sri Lanka. Long-term (1982 to 2020) remote sensing and model-based agroclimatic input parameters—normalized difference vegetation index (NDVI), land surface temperature (LST), 3-month precipitation z-score (stdPCP), and evaporative demand drought index (EDDI)—were used to develop agCDI. The principal component analysis (PCA) approach was employed to qualitatively determine the grid-based percentage contribution of each input parameter. The agCDI was apparently evaluated using an independent dataset, including the crop yield for the major crop growing districts and observed streamflow-based surface runoff index (SRI) for the two main crop growing seasons locally, called Yala (April to September) and Maha (October to March), using 20-years of data (from 2000 to 2020). The results illustrate the good performance of agCDI, in terms of predominantly capturing and characterizing the historic drought conditions in the main agricultural producing districts both during the Yala and Maha seasons. There is a relatively higher chance of the occurrence of moderate to extreme droughts in the Yala season, compared to the Maha season. The result further depicts that relatively good correlation coefficient values (> 0.6) were obtained when agCDI was evaluated using a rice crop yield in the selected districts. Although the agCDI correlated well with SRI in some of the stations (>0.6), its performance was somehow underestimated in some of the stations, perhaps due to the time lag of the streamflow response to drought. In general, agCDI showed its good performance in capturing the spatial and temporal patterns of the historic drought and, hence, the model can be used to develop agricultural drought monitoring and an early warning system to mitigate the adverse impacts of drought in Sri Lanka