Climate Change and Malaria Transmission: Knowledge and Perceptions Among Communities in Dar es Salaam, Tanzania

Reproducibility materials for the analysis and figures supporting this study. Survey data and R Markdown workflows are provided so reviewers and readers can regenerate tables and figures from the raw CSV.

Authors

Iddi Mapande^1,*, Hussein Mohamed^1,*, Jovine Bachwenkizi¹, January G. Msemakweli², Oscar Punguti³, Rajendra P. Shrestha⁴

Affiliations

1. Department of Environmental and Occupational Health, School of Public Health and Social Sciences, Muhimbili University of Health and Allied Sciences, Tanzania
2. Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
3. Department of Medical Sciences and Technology, Mbeya University of Science and Technology, Mbeya, Tanzania
4. Faculty of Food, Agriculture and Natural Resources, Asian Institute of Technology, Thailand, and Faculty of Social Science, Universitas Negeri Malang, Indonesia

^* Iddi Mapande and Hussein Mohamed contributed equally and should both be indexed as first co-authors.

Corresponding author: January G. Msemakweli — jmsemak1@jh.edu

Repository Contents

• Malaria & Climate Dar es Salaam Survey Data.csv De-identified survey data encoded in Windows-1252 (extended Latin). Note that some items are multi-response and space-separated within a single cell.
• Main Analysis.Rmd Contains the workflow for data preparation, descriptive tables (Tables 1–4), chi-squared tests, and modified Poisson models with robust SEs. This file knits to PDF using xelatex.
• Figures.Rmd Generates all manuscript figures, including the study map, information sources, observed climate changes, and Likert/mean scores. It exports high-resolution TIFFs directly to the figures_out/ folder.
• SHAPEFILES/ Tanzania 2022 PHC ward boundaries. The code specifically uses a subset of the Dar es Salaam region to generate the participant map.

Generated outputs (after knitting) typically include figures/, figures_out/, Main Analysis.pdf, and Figures.pdf. You may omit large binary outputs from Git if you prefer; they can always be reproduced from the .Rmd files.

Requirements

• R (recent 4.x recommended)
• RStudio or any environment that can render R Markdown (optional but convenient)
• A LaTeX distribution with XeLaTeX for PDF output (e.g. TinyTeX or TeX Live)

R packages

Main Analysis (Main Analysis.Rmd):

dplyr, tidyr, readr, stringr, forcats, knitr, kableExtra, sandwich, lmtest

Figures (Figures.Rmd):

dplyr, tidyr, readr, stringr, forcats, ggplot2, scales, patchwork, ggrepel, sf, ggspatial

Install in R, for example:

pkgs <- c(
  "dplyr", "tidyr", "readr", "stringr", "forcats", "knitr", "kableExtra",
  "sandwich", "lmtest", "ggplot2", "scales", "patchwork", "ggrepel", "sf",
  "ggspatial", "rmarkdown"
)
install.packages(setdiff(pkgs, rownames(installed.packages())))

How to reproduce

1. Clone this repository and open the project folder in R (working directory = folder containing the CSV and .Rmd files).
2. Run Main Analysis.Rmd → Knit (or rmarkdown::render("Main Analysis.Rmd")) to produce the analysis PDF and tables.
3. Run Figures.Rmd → Knit (or rmarkdown::render("Figures.Rmd")) to produce the figures PDF and TIFF exports under figures_out/.

The map in Figures.Rmd expects the shapefile SHAPEFILES/TANZANIA_2022PHC_WARDS_SHAPEFILES.shp and the survey CSV in the same relative paths as in the repository.

Encoding: the survey CSV should be read as Windows-1252 (as encoded in the .Rmd files) so characters such as curly apostrophes render correctly in PDFs.

Data use

Use of the survey data should respect the terms under which it was collected and any requirements of the originating institutions. If you reuse these materials, cite the associated publication when it is available.

License

Creative Commons Attributio…: you may share and adapt the materials with attribution; see the license text for full terms. CC BY 4.0 is standard for open reproducibility bundles that include data and analysis code together. A LICENSE file in this repository states the same terms for GitHub.

README generated for GitHub.