Malaria Tools User Documentation v2
Imperial College London
6.1 Installation
Full installation details are provided on the Malaria Tools website. Once installed, the
application will appear in the Windows menu bar. On running the program the main user
screen will appear as shown below.
Future updates cannot be installed without removing the original version. This can be done in
the standard way by using the Add/Remove Programs in the Windows Control Panel.
6.2 Colour scheme
By right-clicking anywhere on the screen two options are available for the colour palette. The
normal colour palette is grey. An alternative white background can be used by selecting white
colour palette.
6.3
Starting a new scenario
Click on the new scenario button in the bottom left-hand corner to begin a new scenario.
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The left-hand panel will now be active and allows the user to select the country and then the
first administrative unit. This will bring up a pre-defined transmission setting estimated for that
country. This setting is used for all subsequent runs until changed. Additional countries can be
viewed by dragging the scroll button to the right-hand side of the country/administrative unit
list. The bottom left-hand panel indicates which of the current scenarios is active (when
highlighted in grey).
6.4
Transmission Settings
The transmission setting is defined by a number of characteristics:

Seasonal pattern of transmission – shown in terms of rainfall (in blue) and the predicted
seasonality of disease incidence (in yellow)

Estimated average parasite prevalence across the year in 0 to 5 year olds in 2010

A baseline setting for the proportion of overall transmission attributable to the three
major vector species (An. funestus, An.arabiensis and An.gambiae s.s.).
Also shown is the estimated parasite prevalence in under 5s prior to scale-up of LLINs (assumed
to be representative of 2000). This is determined by the three quantities above (which indicate
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the current transmission levels) plus the later data on subsequent screens on past LLIN usage
and past treatment coverage and first-line drug policy.
Other than the seasonality pattern, each of these can be modified by the user (see later).
6.5
Past ITN Use
Clicking on the tab at the top of the screen labelled “Past ITN Use” takes the user to the
following screen. This displays country level estimates of ITN coverage by year from 2000 to
2011 taken from the WHO Global Malaria Report 2011.
These can be modified by the user by dragging the yellow sliders.
6.6 Past ACT Use
Clicking on the tab at the top of the screen labelled “Past ACT Use” takes the user to the
following screen.
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Default parameters are included which can be modified by the user:

Proportion of clinical cases treated – this is the proportion of all episodes of disease
(detected and not detected) that receive a course of antimalarials

Year ACTs introduced – prior to this year we assume the “pre-ACT” drug was
sulphadoxine-pyremethamine (SP)

Efficacy of 1st line therapy prior to ACTs– the assumed average efficacy of SP from 2000
until the switch to ACT as first-line therapy

ACT efficacy – the assumed average efficacy of the current first-line ACT therapy

Proportion of treatment courses with an ACT – from the introduction year, the
proportion those receiving a course of antimalarials that received an ACT
As for other parameters, these changes result in the re-calibration of the model the next time a
simulation is performed.
6.7 Updating transmission settings
Returning to the transmission settings page, two variables can be modified:

The parasite prevalence, year of survey, and age-groups can each be changed, allowing
the user to update their most recent survey data;
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
The proportions of each vector species can be changed based on updated data or local
knowledge. These represent an average proportion over the transmission season and
hence at present do not take into account seasonal variations in species composition.
The revert button changes all parameters back to their default setting.
Similarly, updates to the past ITN use and past ACT use also result in a change to the baseline
prevalence estimate.
Once parameters have been changed, the scenario indicator shows that the model needs to be
run to be re-calibrated. This is shown by the icons on the right, for which a “wheel” is now
shown indicating that re-calibration is required. For example, below we have updated the
parasite prevalence data estimate by changing it from 0.189348 to 0.10:
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Re-calibration is performed once the “run” icon in the bottom left-hand corner is clicked. The
following screen will appear – the process takes up to a minute to perform.
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Once re-calibrated you will notice that the baseline prevalence in under 5s has now changed.
(in this example from 0.32 to 0.16). The left-hand wheel icon returns to a tick to indicate that
the model has been re-calibrated.
6.8
Running Intervention Scenarios
The final tab labelled “Intervention Options” allows a range of different interventions to be
explored. These are listed on the right-hand side of the screen. Ticking the box to the left of the
label indicates that this intervention is currently included. In the example below LLINs are to be
introduced from 2012 onwards with a target coverage of 80%.
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Note that the second tick on the scenario has now returned to a wheel icon. This indicates that,
whilst the re-calibration is still valid, the output screen is no longer showing the output for this
scenario and so the model needs to be run. This is achieved by clicking the “run” icon in the
bottom left-hand corner.
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Each scenario is labelled with COUNTRY.ADMINISTRATIVE_UNIT.NUMBER. When returning to
previous scenarios the parameters associated with that scenario are shown on the screen. The
scenario name can be edited to allow easier comparison by clicking on the grey scenario bar:
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To compare a new scenario with an existing run the new scenario button should be used
(bottom left-hand corner). This copies the current scenario across to a new record. Additional
interventions can now be included, or different coverage levels considered and compared on
the same graph. For example, in the scenario below we compare the original (ITNs at 80%
coverage) to addition of yearly IRS:
Similarly the location can be modified by returning to the left-hand menu of countries and
administrative units.
A summary of the parameters that can be varied for each intervention is given below.
6.8.1 Insecticide Treated Nets (LLIN)
All scenarios include a scale-up in LLINs between 2000 and 2011 according to the parameters in
the Past ITN Use tab.
Target Coverage – indicates the proportion of individuals in the population using nets and can
be varied between 0 (0%) and 1 (100%). All runs assume random distribution. The scenarios are
started in 2012 and coverage is increased over a 4 year period. Thus setting the coverage level
below the levels in the Past ITN Use in 2012 will result in an increase in transmission.
Interval (years) – indicates the interval between distribution and re-distribution of nets. The
default value is every 4 years.
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6.8.2 Indoor Residual Spraying
Target Coverage – indicates the proportion of individuals in the population sleeping in houses
in which IRS is implemented. All runs assume random distribution and implementation at the
target coverage level occurs the year that the intervention is introduced.
Interval (years) – indicates the interval between spraying and re-spraying. For example, a value
of 1 indicates spraying every year, a value of 0.5 every 6 months and a value of 2 every other
year. The default value is every year. The seasonal timing of yearly IRS is set at the time
determined to be optimal. More frequent spraying is distributed evenly throughout the year
starting at the optimal time. Less frequent spraying is started at the optimal time in the first
year and subsequently scheduled according to the user frequency entered.
Start year – indicates the year IRS spraying is introduced. Year zero corresponds to 2012.
6.8.3 IPT
IPTi – indicates 3 doses of SP given to infants via EPI at ages 3, 4 and 5 months.
SMC – indicates 3 doses of SP given to children between 6 months and five years of age in the
peak 3 months of the seasonal transmission setting.
IPTi and SMC cannot both be included (as per WHO recommendations).
For both IPTi and SMC:
Target Coverage – indicates the proportion of children of the relevant age who receive the
intervention. This target coverage is assumed to be achieved the year that the intervention is
introduced.
Start year – indicates the year that the intervention is introduced. Year zero corresponds to
2012.
6.8.4 Mass Treatment
Target Coverage – indicates the proportion of individuals in the population who receive the
intervention. For MDA this is the proportion receiving treatment, whilst for MSAT it is the
proportion screened, following which all who are parasite positive using microscopy are
treated. This target coverage is assumed to be achieved the year that the intervention is
introduced.
Interval (years) – indicates the interval between repeated rounds. For example, a value of 1
indicates mass treatment every year, a value of 0.5 every 6 months and a value of 2 every other
year. The default value is every year. The seasonal timing of yearly MDA/MSAT is set at the time
determined to be optimal. More frequent rounds are distributed evenly throughout the year
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starting at the optimal time. Less frequent rounds are started at the optimal time in the first
year and subsequently scheduled according to the user frequency entered.
Start year – indicates the year MDA/MSAT is introduced. Year zero corresponds to 2012.
MDA/MSAT – 0 indicates MDA and 1 indicates MSAT
MDA Drug – 0 indicates a non-ACT (sulfadoxine pyrimethamine) and 1 an ACT (artemetherlumefantrine)
6.8.5 EPI Vaccination
This allows the user to model the impact of a pre-erythrocytic vaccine similar to the RTS,S
vaccine given via the Expanded Program on Immunization (EPI). The 3 doses of the vaccine are
given via EPI at 3, 4 and 5 months of age.
Target Coverage – indicates the proportion of children of who receive the full course of the
vaccine. This target coverage is assumed to be achieved the year that the intervention is
introduced.
Start year – indicates the year that the intervention is introduced. Year zero corresponds to
2012.
Efficacy – the protective efficacy of the vaccine against infection.
Duration of protection – the half-life of the vaccine in years.
6.8.6 Mass Vaccination
This allows the user to model the impact of a pre-erythrocytic vaccine similar to the RTS,S
vaccine given via mass vaccination to the whole population. This vaccine can have different
characteristics to that given via EPI.
Target Coverage – indicates the proportion of the population who receive the full course of the
vaccine. Coverage is assumed to be random. This target coverage is assumed to be achieved the
year that the intervention is introduced.
Interval – the frequency of re-vaccination. For example a value of 3 means that the vaccination
program is repeated every 3 years.
Start year – indicates the year that the intervention is introduced. Year zero corresponds to
2012.
Lower and upper age – the lower and upper ages of the groups targeted for mass vaccination.
The default parameters ensure all ages are included.
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Efficacy – the protective efficacy of the vaccine against infection.
Duration of protection – the half-life of the vaccine in years.
6.9 Plotted Output
Four output statistics can be plotted on the screen:
Prevalence – Plasmodium falciparum parasite prevalence across all age-groups
Prevalence 0-5 – Plasmodium falciparum parasite prevalence in 0 to 5 year olds
Incidence –Clinical incidence in 0 to 5 year olds
EIR – the annual entomological inoculation rate
These different outputs can be displayed by clicking on the appropriate tabs above the graph.
The top two icons to the side of the graph allow the user to switch between the types of graph
displayed:
Line graph – displays the statistic over time from the start to end of the simulation
Bar chart – displays the statistic at the end of the run as a bar chart
By default the output is smoothed to remove seasonal fluctuations. The third and fourth icons
to the right-hand side of the graph allows the user to toggle between smoothed and seasonally
varying output.
The disc icon at the bottom right-hand corner of the graph screen allows the user to save the
currently displayed graph in either *.bmp, *.png or *.jpg formats.
6.10 Importing, saving and deleting runs
The scenarios box lists the runs that are currently loaded. By clicking on these the output from
the runs will be displayed in the Simulation Results. Runs can be deleted using the delete
button.
Model runs can be saved to text files by first selecting the model runs to be saved and then
using the save button. The location of the saved files is input by the user. Several output files
are saved for each selected scenario. To import previously saved model runs the user should
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use the load button and select the file [Selected Name].[Scenario Name].txt to import the run
parameters and output.
6.11 Saved Output
The output is saved as text files that can then be used in other applications.
[Selected Name].[Scenario Name].param.txt contains the scenario parameters that have been
selected.
[Selected Name].[Scenario Name].output.csv contains the following output in columns:
Column heading
Description
Year
Year of simulation relative to 2012. Output
starts from -2 (2010).
EIRY_mean
Annual EIR in adults
slide_pos_mean
Mean parasite prevalence by microscopy
across the whole population
slide_pos_2_10_mean
Mean parasite prevalence by microscopy in 2
to 10 year-olds
Mean parasite prevalence by microscopy in 6
age-groups:
slide_pos_a_mean, a=1 to 6
1 = [0-1); 2=[1,2); 3=[2-5), 4=[5-10), 5=[10-15),
6=15+
total_pos_mean
Mean parasite prevalence by PCR across the
whole population
total_pos_2_10_mean
Mean parasite prevalence by PCR in 2 to 10
year-olds
Mean parasite prevalence by PCR in 6 agegroups:
total_pos_a_mean, a=1..6
1 = [0-1); 2=[1,2); 3=[2-5), 4=[5-10), 5=[10-15),
6=15+
EIRY_mean_smooth
Smoothed annual EIR in adults
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slide_pos_mean_smooth
Smoothed mean parasite prevalence by
microscopy across the whole population
slide_pos_2_10_mean_smooth
Smoothed mean parasite prevalence by
microscopy in 2 to 10 year-olds
Smoothed mean parasite prevalence by
microscopy in 6 age-groups:
slide_pos_a_mean_smooth, a=1..6
1 = [0-1); 2=[1,2); 3=[2-5), 4=[5-10), 5=[10-15),
6=15+
total_pos_mean_smooth
Smoothed mean parasite prevalence by PCR
across the whole population
total_pos_2_10_mean_smooth
Smoothed mean parasite prevalence by PCR in
2 to 10 year-olds
Smoothed mean parasite prevalence by PCR in
6 age-groups:
total_pos_a_mean_smooth, a=1..6
1 = [0-1); 2=[1,2); 3=[2-5), 4=[5-10), 5=[10-15),
6=15+
Smoothed output is the mean over the previous year. Therefore in the first year this does not
appear and the missing data is represented by -999 in the text file.
6.12 Interrupting the program
The program can be interrupted while running a simulation by using the ESC key.
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