Replication Data for: A scoping review of antimalarial drug resistance markers in Kenya (1987–2022): toward a National Surveillance Framework and Data Repository

This replication package contains all data, scripts, and outputs used in the study "A scoping review of antimalarial drug resistance markers in Kenya (1987–2022): toward a National Surveillance Framework and Data Repository."

The repository provides a reproducible workflow for the identification, extraction, standardization, analysis, and visualization of published molecular surveillance data on Plasmodium falciparum antimalarial drug resistance in Kenya.

The package includes:

01-scripts

R scripts used for data cleaning, harmonization, analysis, mapping, and figure generation.

02-search terms

Search strategies used across bibliographic databases.

03-studies

Bibliographic records and retrieved studies from PubMed, Embase, Scopus, Web of Science, and Google Scholar.

04-extracted-data

Curated datasets containing allele frequencies, microhaplotype frequencies, and mapping information extracted from eligible studies.

05-output

Reproducible analytical outputs, including tables, figures, maps, and summary datasets presented in the publication.

06-mapping

Geographic reference files and shapefiles used to generate spatial visualizations.

The repository aggregates data from 110 published studies and serves as a reproducible resource for malaria molecular surveillance, resistance monitoring, and future development of a national antimalarial drug resistance data repository for Kenya.

Directory structure:

• 01-scripts
• 02-search terms
• 03-studies
  • embase
  • google-scholar
  • pubmed
  • scopus
  • web-of-science
• 04-extracted-data
  • genotypes-alleles
  • genotypes-microhaplotypes
    • crt
    • dhfr
    • dhfr-dhps
    • dhps
    • mdr1
  • mapping
• 05-output
  • alleles
  • datapoints
  • graphs
  • maps
  • microhaplotypes
  • tables
    • alleles
    • datapoints
    • haplotypes
• 06-mapping
  • 01-shapefiles
    • ken_adm_iebc_20191031_shp
    • ken_lakes
    • kenya-sublocations

R, 4.6.0 RStudio, MacOS (2026.05.0+218)