RCodingSupport

RCodingSupport is a teaching package for the R Coding Support Sessions. It provides synthetic datasets students use to practise R, from basic manipulation to more advanced workflows.

Every dataset describes one fictional scenario: endemic, seasonal malaria in the fictional Republic of Amani, under surveillance across 12 districts over five years. All data are fictional and simulated purely for teaching; all place names are invented.

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Installation

# install.packages("remotes")
remotes::install_github("mrc-ide/RCodingSupport")
library(RCodingSupport)

Teaching materials pin a tagged version per year, e.g. remotes::install_github("mrc-ide/RCodingSupport@teaching-2026").

The single scenario

Almost every object is derived from two master datasets:

• case_linelist — individual-level line-list of reported malaria cases (the master).
• environment_weekly — weekly rainfall and temperature per district (drives transmission).

Supporting masters: testing_weekly, districts, facilities.

Available data objects

• case_linelist — malaria case line-list (~114k cases, 20 variables).
• environment_weekly — weekly rainfall + temperature per district (rainfall drives transmission with a six-week lag).
• testing_weekly — weekly tests and confirmed cases per district.
• districts / facilities — geography, population, bednet coverage, health facilities.
• incidence_weekly_age — weekly case counts by 5-year age band (matrix).
• incidence_weekly — total weekly case counts (vector).
• patient_records — 150-patient demographic sample with messy names (data frame).
• district_weekly_list — weekly surveillance for the two focus cities (list).
• allele_freq_matrix — parasite SNP allele frequencies, with artefacts and missingness (matrix).
• resistance_trajectories — drug-resistance marker prevalence + modelled bands (list).
• analysis_bundle — bednet coverage vs malaria incidence: data, summary stats, fitted lm (list).
• posterior_density — 2D posterior over transmission-model parameters (list).
• chw_trial — community health worker intervention trial summary (data frame).

Data-import practice

export_examples() writes file copies of these datasets (in various formats, with deliberate "messiness") so students can practise reading data from disk — the file they import is the same data they can also load directly from the package:

dir.create("data_raw")
RCodingSupport::export_examples("data_raw")