Arboviral disease risk in a Mediterranean wetland area

Here, we assess the potential risk of arboviral transmission in a high-risk Mediterranean region of northeast Spain, analyzing mosquito vector populations (Aedes albopictus, Culex pipiens, Culex modestus and Culex theileri), avian hosts for West Nile virus (WNV), and human hosts for dengue, Zika and chikungunya.

Installation

Make sure to have R 4.3.2 (or later) and, optionally, RStudio installed for an enhanced development environment.

1. Clone the repository: git clone https://github.com/username/project.git cd project

2. Install required packages: Open R or RStudio and run the following code to install the required packages:

packages <- c("readxl", "writexl", "tidyverse", "lubridate", "dplyr", "ggplot2", "purrr", "zoo", "parallelly", "parallel", "janitor", "pollen", "lme4", "DHARMa", "glmmTMB", "performance", "car", "MuMIn", "corrplot", "cmdstanr", "brms", "rstanarm", "loo", "tidybayes", "RColorBrewer", "sf", "raster", "viridis", "ggrepel", "vegan", "factoextra", "tibble", "MASS", "svglite", "pracma", "ggthemes", "betareg", "mgcv")

packages_to_install <- packages[!(packages %in% installed.packages()[,"Package"])] if(length(packages_to_install)) install.packages(packages_to_install) #Install packages that are not already installed

lapply(packages, library, character.only = TRUE) #Load packages

3. Run the project: Open the main script file (e.g., main.R) in R or RStudio and execute it: source("main.R")

Project Directory Structure

The project directory PNAE is organized as follows:

PNAE/
├── Code/                  		    
│   │
│   ├── 1_Aedes_albopictus.R    	    # Dataframe preparation, models, and predictions for Aedes albopictus data
│   ├── 1_Culex.R               	    # Dataframe preparation, models, and predictions for Culex spp. data
│   ├── 1_Culex_species.R                   # Exploring Culex spp. (pipiens, modestus and theileri)
│   ├── 2_Birds_experiments_review.R        # Host competence calculations using experimental infection data
│   ├── 3_Birds.R               	    # WNV host spatial analysis
│   ├── 4_Risk.R                	    # Overlapping mosquitoes and birds
│   ├── 5_Humans.R              	    # Human population dynamics
│   ├── 6_Reanalysis.R    	            # Birds + risk reanalysis using an alternative infection threshold (4 PFU/ml)
│   │	
├── Data/
│   │ 
│   ├── Birds_data/       		
│   │   ├── Data/
│   │   │   ├── Abundance_data_atlas.csv                     	# Abundance data from the "Atlas of Nesting Birds of Catalonia"
│   │   │   ├── PNAE_birds.xlsx                             	# List of bird species
│   │   │   └── Review_experimental_infections_birds_PNAE.xlsx  # WNV experimental infections global review
│   │   └── Outputs/                                         	# Output folder
│   │	
│   ├── Human_data/
│   │   ├── Barcelona_human_cases.xlsx                       	# Imported cases in Barcelona
│   │   ├── Catalunya_human_cases.xlsx                       	# Imported cases in Catalunya
│   │   ├── Girona_human_cases.xlsx                          	# Imported cases in Girona
│   │   └── Població_estacional_Alt_Empordà.csv              	# FTE seasonal population (Alt Empordà region)
│   │	
│   ├── Land_covers/      		
│   │   ├── UsosCobertes_2017/                               	# Land cover map            
│   │   ├── landcovers_buffer250.csv                         	# Land covers in a 250 m radius buffer around each mosquito trap
│   │   ├── landcovers_utm1x1.csv                            	# Land covers in each 1x1 km grid cell
│   │   └── study_area_shp.shp                               	# Study area shapefile (to generate predictions)
│   │	
│   ├── Meteo_data/       		
│   │   ├── Meteo_data_U2.csv                       	     	# Secondary meteo station data
│   │   └── Meteo_data_W1.csv             		     	# Main meteo station data
│   │	
│   ├── Mosquito_data/    		
│   │   ├── Aedes_albopictus/                                	# Aedes albopictus output folder
│   │   ├── Culex/                                           	# Culex spp. output folder
│   │   └── Mosquito_Surveillance_SCM/                       	# 20-year mosquito surveillance database
│   │	
│   └── Risk_data/        		                     	# Risk assessment output folder
│
├── Models/               		
│   │
│   ├── Aedes_albopictus/
│   │   ├── brms_models/  		# Bayesian models for Aedes albopictus
│   │   └── glm_models/   		# GLM models for Aedes albopictus
│   └── Culex/
│       ├── brms_models/  		# Bayesian models for Culex spp.
│       └── glm_models/   		# GLM models for Culex spp.
│
├── Plots/                		# Plots and visualizations generated from data
│   │
│   ├── Aedes_albopictus/
│   ├── Birds/
│   ├── Culex/
│   └── Humans/
│
└── Predictions/          		# Contains space-time prediction files
    │
    ├── Aedes_albopictus/
    └── Culex/

It is crucial that you recreate the directory structure as shown above. The project scripts expect specific folder locations for data input and output. Without the correct folders, the code might not run as expected. Ensure you create the following folders within the PNAE directory. Additionally, the data files should be placed in the appropriate subdirectories under Data/. Ensure that all CSV, Excel, and shapefiles are placed correctly for smooth execution of the scripts.