arbocartoR is a web interface, that allows generating simulations from a multi-level model including two different components: the deterministic population dynamics of Aedes mosquitoes ( albopictus and aegypti ) in various environments and the stochastic dynamics of transmission of dengue, zika and chikungunya viruses.

The underlying model is a spatialized compartmental model considering that mosquitoes and humans reside in independent parcels where their respective densities are assumed to be homogeneous. Humans can move between parcels, spatially spreading the diseases. Mosquito dynamics are mainly driven by rainfall, temperature, and land use (main covariates identified in the scientific literature). The user can modify the importation of viruses by humans, and characterize the implementation of various vector control strategies.

The tool proposes several synthetic outputs of the simulations. The results include the daily dynamics of mosquito populations, and vector/host infections; a map displaying the spatialized and temporal dynamics of the R0 over the simulation period and area; and the prediction intervals of the number of autochthonous infections and disease spread.

Using the tool

To use the tool, complete the following steps.

Click on the 'Tool' tab. Initialize the model by choosing:

  1. a vector ( Aedes albopictus (diapausing or not) or aegypti ),
  2. a pathogen (dengue, chikungunya or zika virus),
  3. a study area. Datasets are proposed for French departments and the region of Split (Croatia), nevertheless, those datasets are basic estimates and should be considered with caution. Those datasets are provided as examples, and we encourage you to use your own dataset (refer to the dedicated tab: 'Import data').

The input data can be explored through a dynamic map composed of 5 layers (administrative unit borders, temperature, rainfall, human population, and environmental carrying capacity for larvae). Local covariate values are accessible by clicking on the map.

Then, initialize the epidemiological scenario. You can either:

  1. parametrize simulations (dates) without specifying any introduction event or control measure. The results will focus on mosquito population dynamics and human densities.
  2. parametrize simulations with control measures, and/or exposed individual introductions in the population at a specific time and place. With control strategies implemented, the results can include the comparison with simulation without control. With virus introductions, the human mobility patterns can be modulated, and the results will include synthetic outputs for stochastic epidemiological simulations (the number of simulations can also be modulated).

Finally, click on the 'Run' button to launch the simulations.

Be patient, depending on your machine and scenario, the simulations and output display can take time. Moreover, the online version of the tool has a limited amount of memory available, the tool can crash if the simulations exceed its memory limits. If you need to run the tool locally on your computer, we can drive you through it. Please do not hesitate to contact us (elena.arsevska@cirad.fr).

Initialization


Latitude: Longitude:

Simulation

When simulation dates are changed, any preventive measures or introductory events occurring outside the simulation period will be removed.



Results

Epidemiological indicators (median [95% prediction interval])

With control

Without control




Latitude: Longitude:

Display output for a specific parcel by clicking on the map

Click and drag to zoom in (double click to zoom back out).

Download raw results

To use your own data, you must provide at least 6 files:

  1. a shapefile and associated files describing your polygons,
  2. a table describing the area (csv or txt file using ';' as separator and '.' for decimal),
  3. a table with the meteoroglogical data (csv or txt file using ';' as separator and '.' for decimal).

By submitting a shapefile, you can generate templates for both tables. If data are not included in the shapefile, the tool can generate estimates for some of the data. These estimates should be reviewed with caution.


Parcels

Meteorological data

About

Authors

Pachka Hammami1, Renaud Marti2, Annelise Tran2, Andrea Apolloni1 and Elena Arsevska1

Collaborators

Ewy Ortega1,3, Maxime Lenormand2, Marie Demarchi4

Affiliations

1 UMR ASTRE, CIRAD, INRAE, Université de Montpellier, 34000 Montpellier, France

2 UMR TETIS, INRAE, Cirad, AgroParisTech, CNRS, Maison de la télédetection, 34000 Montpellier, France

3 DGAL, Direction Générale de L'alimentation, 251 Rue de Vaugirard, 75015 Paris, France

4 Maison de la Télédétection, Montpellier, France

Contact:

Corresponding author: Arsevska Elena (elena.arsevska@cirad.fr)


Funding:

MOOD project: MOnitoring Outbreaks for Disease surveillance in a data science context


Origins:

ARBOCARTO: The mosquito population dynamics model was initially developed for the ARBOCARTO tool.

Licence:

Cirad is the owner of the arbocartR tool, which is distributed under the CECILL C free licence.