/RM_mosquito

Primary LanguageR

Present and future suitability of invasive and urban vectors through an environmentally-driven Mosquito Reproduction Number

This directory contains all the code and data in order to reproduce the figures in the main manuscript avaliable in: https://www.biorxiv.org/content/10.1101/2024.05.31.596775v1

In the folder code there is one script for each of the figures in the main manuscript. The names of the code files and the figures in the main text are related as follows:

  • Figure 1: plot1.R
  • Figure 2 , Figure 4 and Figure 5: panel_camb_clim.R
  • Figure 3: panel_validation.R

For the figures in the Supplementary material the respective code is in:

  • Figure S1: plot1.R
  • Figure S2: panel_thermal.R
  • Figure S3: panel_sensitivity.R
  • Figure S4-7: panel_camb_clim.R
  • Figure S8-9: panel_validation.R

The two data sources that are produced by the authors, used for the RM validation, are in the data folder (read Readme_data for more details):

  • BG_count_data_albopictus.csv
  • PA_Oct_2023_albopictus.csv

In this data folder there are other datasets, results of processing the enviromental data sets avaliable online, each data source is explained in the data section of the paper.

Computing $R_M$ at different scales

Below there is a brief explanation on how to compute Mosquito basic reproduction number, $R_M$, for $Aedes$ $albopictus$ and $Aedes$ $aegypti$ following the methodology in: https://www.biorxiv.org/content/10.1101/2024.05.31.596775v1

The Mosquito basic reproduction number is given by: $$R_{M} = \sqrt[3]{f\frac{a}{\delta_A}\frac{d_Eh}{(d_Eh + \delta_E)} \frac{d_I}{(d_I + \delta_I)}} = \sqrt[3]{f\frac{a}{\delta_A}p_{EL}p_{LA}}.$$

Each parameter in $R_M$ could be found in funcR0.R for both species: $Aedes$ $albopictus$ and $Aedes$ $aegypti$. All of them depend on temperature, rainfall or human density. In order to compute the Mosquito basic reproduction number, $R_M$, for a particular location you need average daily rainfall (mm), average temperature (Cº), and human density (number of habitants per km2). This will produce a number between 0 to 6.64 and 5.46 for $Aedes$ $albopictus$ and $Aedes$ $aegypti$ respectively. If this number is greater than 1 it means suitability for this species. This number represents the average number of female mosquitoes than one female mosquito will produce in her entire lifespan.

Example how to compute the Mosquito basic reproduction number in R:

source("~/RM_mosquito/funcR0.R") # Load the file with the functions
Te = 20 # Example of temperature in Cº
rain = 4 # Example of rainfall in mm
hum = 1000 # Example of human density in inhabitants per km2
R0_func_alb(Te,rain,hum) # R_M for Aedes albopictus
R0_func_aeg(Te,rain,hum) # R_M for Aedes aegypti

This number could be compute it at different scale but always taken the average rainfall. The units must be daily rainfall. So if we do it for a month there should be the average monthly rainfall NOT the accumulated rainfall.