tve_malaria

R code and outputs to support Carrasco-Escobar G, Qquellon J, Villa D, Cava R, Llanos-Cuentas A, Benmarhnia T. Time-Varying Effects of Meteorological Variables on Malaria Epidemiology in the Context of Interrupted Control Efforts in the Amazon Rainforest, 2000-2017. Front Med (Lausanne). 2021 Sep 29;8:721515. doi: 10.3389/fmed.2021.721515. PMID: 34660633; PMCID: PMC8511324.

Figure 2. Fitted time-varying meteorological effects on MIR by parasite species. Fitted time-varying meteorological effects due to P. vivax (red) and P. falciparum (light blue) and their 95% CI (shading of each colored curve). The period shaded in gray represents the PAMAFRO intervention.

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Study description

In this study, we hypothesized that the interruption of malaria control interventions may modify the meteorological-malaria relationships over time (i.e., temporal changes in the dose-response between meteorological variables and malaria incidence). For instance, we assessed the extent that relationships between meteorological variables and malaria changed temporally using data of monthly malaria incidence due to Plasmodium vivax or P. falciparum in Loreto, Peru (2000–2017). Generalized additive models were used to explore how the effects of meteorological variables changed in magnitude before, during, and after the PAMAFRO intervention (2006–2010) - a Global Fund-sponsored project for the strengthening of malaria control and surveillance in multiple countries in Latin America.

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Repository structure

• analysis R markdowns and outputs.
  • figs Main and supplementary figures.
    • supplementary-figs
      • districts Meteorological variables time-series plot for every district in Loreto, Peru.
      • provinces Meteorological variables time-series plot aggregated for every province in Loreto, Peru.
    • figure-1-with-map.jpg Annual malaria incidence rates variation by parasite species (Peru map added).
    • figure-1.pdf Annual malaria incidence rates variation by parasite species.
    • figure-2.png Fitted time-varying meteorological effects on MIR by parasite species.
    • figure-3.png Fitted time-varying meteorological effects on MIR by parasite species at different time lags.
  • 00-data-preparation.Rmd R markdown for data preparation and preprocessing.
  • 01-exploratory-data-analysis.Rmd R markdown for exploratory data analysis.
  • 02-time-vaying-coef-models.Rmd R markdown for model building and interpretation.
• renv
• .Rprofile
• .gitignore
• README.md
• renv.lock
• tve_malaria.Rproj R project file.

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R environment and version

Detailed information about the R environment and version used for running this project.

               _                           
platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          4                           
minor          1.0                         
year           2021                        
month          05                          
day            18                          
svn rev        80317                       
language       R                           
version.string R version 4.1.0 (2021-05-18)
nickname       Camp Pontanezen