malaria-spat21-analysis

Cleaning and preliminary analysis of descriptive and qPCR data from human blood and mosquitoes.

Part of the Spatial R21 project, which investigates the molecular epidemiology of P. falciparum transmission in Western Kenya.

Preliminary mosquito data management

Processing data

• Standardize column names and sample IDs of all datasets.
• Reformat the descriptive Anopheles dataset such that each row corresponds to a single mosquito.
• Censor the qPCR dataset by Ct values of human β-tubulin (Hbtub) and Plasmodium (Pfr364) targets, as well as by parasitemia.

Cleaning data

• Correct formatting errors in household and sample IDs.
• Correct inconsistencies in village, household, and sample IDs within each sample.
• Correct inconsistencies in descriptions of each mosquito.
• Resolve duplicate entries of the same sample.
• Remove redundant columns.

Merging data

• Sort all datasets.
• Create a dataset pairing mosquito descriptions with corresponding qPCR results.
• Identify missing entries between datasets.
• Tabulate mosquito counts per village, abdominal status, and species.

Preliminary mosquito data analysis

Preliminary human data management

Collaborators

• Kelsey Sumner