Tutorial

Add Scenario

Initially no analyses will be present and you will need to add a new one. Do this by clicking on the menu button in the top-left corner and selecting Add Scenario. This will bring up a panel with various settings for the scenario that will be run. The settings are grouped under main headings that can be clicked on to reveal them. The main settings are

Scenario

These are options related to how the scenario is labelled and how many simulations will be performed. The label can be changed after the scenario has been run, but all other options will be fixed. The No. of runs option specifies how many simulations will be performed. The smaller the number of simulations, the less accurate the results will be, but the quicker the scenario will take to complete. It is advisable to have at least 100 runs (default setting) if this is feasible on the given machine.

Setting

These options are to do with the scenario at baseline. Vector species specifies which is the dominant vector species in the simulations (in general Anopheles in Africa and Culex in Asia although there are exceptions). There is also a slider to adjust for the Microfilaraemia prevalence. This gives a general baseline mf prevalence before the start of treatment, although due to the stochastic nature of the model, this is an approximation only.

Mass Drug Administration

This panel gives various options to do with all aspects of an MDA programme. Frequency of administration can be selected at either every year or every six months. It is assumed that treatment occurs simultaneously for all individuals. Coverage (%) can also base selected between 0 and 100%. Although note if selected 0% it is still assumed an MDA event occurs, however with no-one being treated. The Drug regimen can also be selected, where the efficacy of mf and adult worms killed are fixed. These values can also be varied by selecting custom in the drug regimen option. Finally Systematic adherence can be selected. At 0, coverage is completely random and there is no correlation in individuals who are treated ech round. At 1, the same individuals are treated each round according to the set coverage. The systematic adherence parameter can then scale between these two extremes.

Vector Control

There are two possible forms of vector control. Bed Net Coverage controls for coverage of a single round of bed-nets that are given out at the start of intervention, where coverage is assumed to be random. Note here bed-nets are only effective for Anopheles. Insecticide Coverage is assumed to affect the whole mosquito population and affects the vector to host ratio.

Once the desired options for the scenario have been selected, click Run Scenario to begin the calculations or close to close the panel and cancel the scenaro. Whilst running please wait for all simulations to complete. A progress bar at the bottom of the panel provides an estimate of the progress. Once completed the scenario should display automatically.

Scenario Overview

This is provided on the left-hand side and provides a detailed description of outcomes for the individual scenario selected. The blue line indicates the median value of the outputted statistic, whilst the grey lines show all the individual runs. The different scenarios that have been computed can be selected on using the tabs on top of this panel.

The label for the scenario can be changed by selecting the settings button. This also provides an overview of the scenario parameters that were used to run the simulation.

The individual runs for the scenario can be downloaded using the download button. This generates a csv file with columns time (years),run,microfilaraemia,antigenaemia and mosquito prevalence.

The scenario can be deleted using the delete button.

Scenario Comparisons

These can be selected on the right-hand side. Various comparison statistics can be selected and the results for each scenario computed are shown.

Further Reading