fbkengne/ssamixr

Social Contact Matrices for Sub-Saharan Africa # **Social Contact Matrices for Sub‑Saharan Africa** `ssamixr` provides harmonized, ready‑to‑use **social contact matrices** from empirical studies conducted across Sub‑Saharan Africa. The package includes **171 matrices** covering multiple countries, settings, and study designs, all standardized for infectious disease modeling and comparative epidemiology. ------------------------------------------------------------------------ # 🚀 Installation ``` r # Install pak if needed if (!requireNamespace("pak", quietly = TRUE)) { install.packages("pak") } # Install ssamixr package pak::pak("fbkengne/ssamixr") # Load the package library(ssamixr) ``` 🧭 Getting Started: A Simple Workflow Most users will want to: 1. List all available matrices 2. Filter matrices by country, study, or location 3. Select a matrix ID 4. Retrieve the matrix 5. Visualize it 1️⃣ List all matrices ``` r all_mats # A tibble: 6 × 7 #> matrix_id study_id author_year country location_type row_age_groups #> #> 1 201 Cameroon_Dobreva_2… Dobreva et… Camero… HH 0-17;18-55;56+ #> 2 202 Cameroon_Dobreva_2… Dobreva et… Camero… School;Work 0-17;18-55;56+ #> 3 203 Cameroon_Dobreva_2… Dobreva et… Camero… Other 0-17;18-55;56+ #> 4 204 Cameroon_Dobreva_2… Dobreva et… Camero… All 0-17;18-55;56+ #> 5 205 Cameroon_Dobreva_2… Dobreva et… Camero… All 0-17;18-55;56+ #> 6 206 DR_Congo_Dobreva_2… Dobreva et… Democr… HH 0-17;18-55;56+ #> # ℹ 1 more variable: col_age_groups ``` 2️⃣ Filter matrices Example: matrices from Kenya ``` r kenya Gradient palette ``` r plot_matrix_gradient(m) ``` 🔧 Visualization Parameters Both plot_matrix() and plot_matrix_gradient() support flexible, publication‑ready visualization of social contact matrices. Automatic label rotation By default: If the matrix has more than 10 age groups, column labels rotate vertically Otherwise, they remain horizontal You can override th …