The graph shows the number of units in each infection state over time. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the number of units per infection state for a given time.



Export PNG

View or download as .csv file the number of units in each infection state over time.
The first column refers to the time (expressed in days). The other columns refer to the following infection states:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
R - Recovered and immune, ReD - Removed due to disease, V - Vaccinated

Download data


This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display

The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Chart zoom - click and drag on the chart to zoom in, double-click to zoom out.
Click on the infection states below to select or unselect them.

Roll over the lines to explore the impact of delays between the mortality threshold is reached to action.
You can also set different mortality thresholds and levels of baseline risks.

Explore median simulation outputs or individual simulations to further your understanding of disease spread. You can also discover how often the mortality threshold is actually reached across simulation and how many days this takes.
Please use the sliders below to add delays in the disease control process to investigate their impact on model outputs.


Click "submit" to update outputs after changing parameters in the left panel.

Delay between mortality threshold reached to action (days)  
Define mortality threshold  
Mortality level >
% for
Simulation median  
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Simulation number  
Export PNG
Mortality threshold  

To visualise a table presenting the number of units in each infection state over time, choose a simulation using the slider below. the first column refers to the time (expressed in days). The other columns refer to infection states (see below).

To download as .csv file the number of units in each infection state over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The second column refers to the number of the simulation. The other columns refer to the following infection states:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
ReD - Removed due to disease, Cumul_Inf - cumulative infectious, Cumul_Death - cumulative death

Download data



This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display

The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Chart zoom - click and drag on the chart to zoom in, double-click to zoom out.
Click on the infection states below to select or unselect them.

Roll over the lines to see the number of units for a selected infection state over time.
Please use the sliders below to add delays in the disease control process to investigate their impact on model outputs.


Click "submit" to update outputs after changing parameters in the left panel.


Infection to suspicion (days)  
Suspicion to detection (days)  
Detection to culling (days)  
Export PNG

To visualise a table presenting the number of units in each infection state over time, choose a simulation using the slider below. the first column refers to the time (expressed in days). The other columns refer to infection states (see below).

To download as .csv file the number of units in each infection state over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The second column refers to the number of the simulation. The other columns refer to the following infection states:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
ReD - Removed due to disease, Cumul_Inf - cumulative infectious, Cumul_Death - cumulative death

Download data



This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display


The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the median number of units per infection state for a given time.


Click "submit" to update outputs after changing parameters in the left panel.


Export PNG

The graph shows the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to see the number of units for a selected infection state over time.



The graph shows the number of units in each infection state over time, for a selected simulation. The time is expressed in days on the x-axis.
Select a simulation by moving the slider.
Click on the infection states below to select or unselect them.
Roll over the lines to get the number of units per infection state for a given time.



Export PNG

To visualise a table presenting the number of units in each infection state over time, choose a simulation using the slider below. the first column refers to the time (expressed in days). The other columns refer to infection states (see below).

To download as .csv file the number of units in each infection state over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The second column refers to the number of the simulation. The other columns refer to the following infection states:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
R - Recovered and immune, ReD - Removed due to disease, V - Vaccinated

Download data



This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display


The graphs show, for each group, the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the median number of units per infection state for a given time.


Click "submit" to update outputs after changing parameters in the left panel.


Group 1

Export PNG

Group 2

Export PNG

The graphs show, for each group, the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to get the median number of units per infection state for a given time.



The graphs show, for each group, the number of units in each infection state over time, for a selected simulation. The time is expressed in days on the x-axis.
Select a simulation by moving the slider.
Click on the infection states below to select or unselect them.
Roll over the lines to see the number of units for a selected infection state over time.



Group 1

Export PNG

Group 2

Export PNG

To visualise a table presenting the number of units in each infection state over time, choose a simulation using the slider below. the first column refers to the time (expressed in days). The other columns refer to infection states (see below).

To download as .csv file the number of units in each infection state over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The second column refers to the number of the simulation. The other columns refer to the following infection states:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
R - Recovered and immune, ReD - Removed due to disease, V - Vaccinated

Download data


Group 1

Group 2


This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display



Click "submit" to update outputs after changing parameters in the left panel.

Graph 1

The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the number of units per infection state for a given time.

Export PNG

Graph 2

The graph shows the number of infected populations and the number of populations with at least one unit at each timestep. The time is expressed in days on the x-axis.
Roll over the lines to get the number of infected and populated populations.

Export PNG

The graphs show, for each group, the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to see the number of units for a selected infection state over time.



The graphs show, for each group, the number of units in each infection state over time, for a selected simulation. The time is expressed in days on the x-axis.
Select a simulation by moving the slider.
Click on the infection states below to select or unselect them.
Roll over the lines to get the number of units per infection state for a given time.



Graph 1

Export PNG

Graph 2

Export PNG

To visualise a table presenting the number of units in each infection state over time, choose a simulation using the slider below. The first column in Table 1 refers to the time (expressed in days). The other columns refer to infection states (see below). Table 2 shows the number of infected populations and number of populated populations over time.

To download as .csv file the number of units in each infection state over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The second column refers to the number of the simulation. The other columns refer to the following infection states:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
R - Recovered and immune, ReD - Removed due to disease, V - Vaccinated

The last two columns show the number of infected populations (Inf.) and number of populated populations (N).

Download data


Table 1

Table 2


This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display


The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the median number of units per infection state for a given time.


Export PNG

The graph shows the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to see the number of units for a selected infection state over time.



Each unit is represented by a dot, whereby each colour refers to an infection state. You can either visualise the infection state of each unit in the population at a selected time by moving the time slider, or you can visualise temporal changes in units' infection states over the course of a simulation by pressing the play button (triangle at the right bottom of the slider).
Select a given simulation by moving the simulation slider.


Infection states:
   Susceptible
   Infected (latent)
   Infectious asymptomatic
   Infectious symptomatic
   Recovered
   Removed
   Vaccinated
Export PNG

To visualise a table showing the infection state of each unit over time, choose a simulation using the slider below. The first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as shown below.

To download as .csv file the infection state of each unit over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as follows:

0 - Susceptible, 1 - Infected (latent), 2 - Infectious and asymptomatic, 3 - Infectious and symptomatic
4 - Recovered and immune, 5 - Removed due to disease, 6 - Vaccinated

Download data



This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display


The graphs show, for each group, the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the median number of units per infection state for a given time.


Click "submit" to update outputs after changing parameters in the left panel.



Group 1

Export PNG

Group 2

Export PNG

The graphs show, for each group, the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to see the number of units for a selected infection state over time.



Each unit within each group is represented by a dot, whereby each colour refers to an infection state. You can either visualise the infection state of each unit in the population at a selected time by moving the time slider, or you can visualise temporal changes in units' infection states over the course of a simulation by pressing the play button (triangle at the right bottom of the slider).
Select a given simulation by moving the simulation slider.


Infection states:
   Susceptible
   Infected (latent)
   Infectious asymptomatic
   Infectious symptomatic
   Recovered
   Removed
   Vaccinated

Group 1
Export PNG
Group 2
Export PNG

To visualise a table showing the infection state of each unit over time, choose a simulation using the slider below. The first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as shown below.

To download as .csv file the infection state of each unit over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as follows:

0 - Susceptible, 1 - Infected (latent), 2 - Infectious and asymptomatic, 3 - Infectious and symptomatic
4 - Recovered and immune, 5 - Removed due to disease, 6 - Vaccinated

Download data



This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display


The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the median number of units per infection state for a given time.


Click "submit" to update outputs after changing parameters in the left panel.




Export PNG

The graph shows the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to see the number of units for a selected infection state over time.



Each unit is represented by a dot, of which its colour refers to its infection state. A contact (or link) between two units is represented by a grey line.
You can either visualise the infection state of each unit in the population at a selected time by moving the time slider, or you can visualise temporal changes in units' infection states over the course of a simulation by pressing the play button (triangle at the right bottom of the slider).
Select a given simulation by moving the simulations slider.


Infection states:
   Susceptible
   Infected (latent)
   Infectious asymptomatic
   Infectious symptomatic
   Recovered
   Removed
   Vaccinated
Export PNG

Each unit is represented by a dot, of which its colour refers to its infection state. A contact (or link) between two units is represented by a black line. When passing your mouse on a dot, the ID of the corresponding unit will appear. You can zoom in and out by scrolling your mouse wheel while hovering over the graph.
You can visualise the infection state of each unit in the population at a selected time by moving the time slider.
Select a given simulation by moving the simulations slider.


Infection states:
   Susceptible
   Infected (latent)
   Infectious asymptomatic
   Infectious symptomatic
   Recovered
   Removed
   Vaccinated
Export PNG


To visualise a table showing the infection state of each unit over time, choose a simulation using the slider below. The first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as shown below.

To download as .csv file the infection state of each unit over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as follows:

0 - Susceptible, 1 - Infected (latent), 2 - Infectious and asymptomatic, 3 - Infectious and symptomatic
4 - Recovered and immune, 5 - Removed due to disease, 6 - Vaccinated

Download data



This is the list of links (or contacts). Each row refers to a link between two units, and the columns Unit 1 and Unit 2 provide the IDs of the units which are linked. The order of the unit IDs (cited in the first or second column) is not relevant, as links are undirected.
Download data


This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display

On this page you can upload a custom edge list and then display transmission within the resulting network based on the parameters setting selected on the left hand panel. We also provide a CSV template for you to download and use. With N units in the population, each unit should be labelled with a unique figure, from 1 to N. For instance, if there are 10 units, they should be labelled as 1, 2, 3, ..., 10. N should not be larger than 100. The directions of edges are ignored and each edge should only appear once in the list. Like in the generic simulation each unit is represented by a dot, of which its colour refers to its infection state. A contact (or link) between two units is represented by a grey line.

You can either visualise the infection state of each unit in the population at a selected time by moving the time slider, or you can visualise temporal changes in units' infection states over the course of a simulation by pressing the play button (triangle at the right bottom of the slider). Select a given simulation by moving the simulations slider.

NOTE: visualisations of model outputs on other tabs are not based on the custom network, but on the simulated network of which the characteristics are defined under "Define network specific population and transmission parameters" on the left hand panel.

Upload edgelist (csv file)  


The graph shows the median number of units in each infection state over time and over all simulations. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the median number of units per infection state for a given time.


Click "submit" to update outputs after changing parameters in the left panel.


Export PNG

The graph shows the median number of units over time for a selected infection state, as well as the 10th and 90th percentiles. The time is expressed in days on the x-axis.
Click on the legend to show or hide the 10th percentile, the median and the 90th percentile.
Roll over the lines to see the number of units for a selected infection state over time.




Each unit is represented by a dot and each colour refers to an infection state. Units are plotted according to their geographical position.
You can either visualise the infection state of each unit in the population at a selected time by moving the time slider, or you can visualise temporal changes in units' infection states over the course of a simulation by pressing the play button (triangle at the right bottom of the slider).
Select a given simulation by moving the simulation slider.




The line chart displays the kernel as a function of the distance.


Export PNG


To visualise a table showing the infection state of each unit over time, choose a simulation using the slider below. The first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as shown below.

To download as .csv file the infection state of each unit over time for all simulations, click on "Download data". In the .csv file, the first column refers to the time (expressed in days). The other columns refer to the unit IDs (e.g. U1: unit 1, U2: unit 2, etc). The infection state of a given unit at a given time is coded as follows:

0 - Susceptible, 1 - Infected (latent), 2 - Infectious and asymptomatic, 3 - Infectious and symptomatic
4 - Recovered and immune, 5 - Removed due to disease, 6 - Vaccinated

Download data



View or download coordinates of the units.
The first column lists all unit IDs, and the second and third the unit's coordinates on the x- and y-axes.
Download data


This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display

On this page you can upload custom spatial coordinates then display transmission within the locations based on the parameters setting selected on the left hand panel. We also provide a CSV template (both for longitude and latitude as well as x and y coordinates) for you to download and use. The number of units should not exceed 100.

Like in the generic simulation each unit is represented by a dot and each colour refers to an infection state. Units are plotted according to their geographical position. You can either visualise the infection state of each unit in the population at a selected time by moving the time slider, or you can visualise temporal changes in units' infection states over the course of a simulation by pressing the play button (triangle at the right bottom of the slider). Select a given simulation by moving the simulation slider.

NOTE: visualisations of model outputs on other tabs are not based on the custom spatial coordinates, but on the simulated coordinates of which the characteristics are defined under "Define spatial specific population and transmission parameters" on the left hand panel.

Upload spatial coordinates (csv file)  
Longitude/Latitude
X/Y in Grid

The graphs show the number of units in each infection state and in each group over time. The time is expressed in days on the x-axis.
Click on the infection states below to select or unselect them.
Roll over the lines to get the number of units per infection state for a given time.


Group 1

Export PNG

Group 2

Export PNG

View or download as .csv file the number of units in each infection state and in each group over time.
The first column refers to the time (expressed in days). The other columns refer to the following infection states, for group 1 and group 2:

S - Susceptible, E - Infected (latent), Ia - Infectious and asymptomatic, Is - Infectious and symptomatic
R - Recovered and immune, ReD - Removed due to disease, V - Vaccinated

Download data

Group 1

Group 2


This page allows you to compare how different parameter settings affect selected outcomes. Simply select a parameter you would like to explore from the available parameters; choose up to three different values for it and then compare the outputs. For example, you can compare how different levels of vaccination result in different number of infected units at different time points.
Parameter
Preset
Comparison 1
Comparison 2
Pick outputs to display


Click "submit" to update outputs after changing parameters in the left panel.

Chart zoom - click and drag on the chart to zoom in, double-click to zoom out.

Click on the infection states below to select or unselect them.
Roll over the lines to get the number of units per infection state for a given time.

Export PNG
Export PNG

This graph shows the number of people becoming newly infectious on a given day, and the fraction accounted by sub-clinical infections.


Click "submit" to update outputs after changing parameters in the left panel.

Export PNG

Click "submit" to update outputs after changing parameters in the left panel.

Age population structure

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Contact matrix

Each cell of the matrix represents the median number of contacts that an individual in a given age group has with other individuals, stratified by age groups. The colour intensity represents the number of contacts.

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