joelewis101/blantyreSepsis

Reproducible analysis code and data for the manuscript: "A longitudinal observational study of aetiology and long-term outcomes of sepsis in Malawi revealing the key role of disseminated tuberculosisis" available here A Longitudinal, Observation… # blantyreSepsis The BlantyreSepsis R package contains data and code to replicate the analysis of the manuscript: *A longitudinal observational study of aetiology and long-term outcomes of sepsis in Malawi revealing the key role of disseminated tuberculosis* Joseph M Lewis 1,2,3 , , Madalitso Mphasa 1 , Lucy Keyala 1 , Rachel Banda 1 , Emma Smith 1 , 2 , Jackie Duggan 4 , Tim Brooks 4 , Matthew Catton 4 , Jane Mallewa 5 , Grace Katha 5 , Stephen B Gordon 1,2 , Brian Faragher 2 , Melita A Gordon 1,3 , Jamie Rylance 1,2 , Nicholas A Feasey 1,2 1. Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi 2. Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK 3. Department of Clinical Infection, Microbiology and Immunology, University of Liverpool, Liverpool, UK 4. Rare and Imported Pathogens Laboratory, Public Health England, UK 5. College of Medicine, University of Malawi, Malawi Now published in *Clinical Infectious Diseases* here ## Installing and accessing data Install the package from GitHub: ``` r install.packages("devtools") devtools::install_github("github.com") ``` Or check out the source code at GitHub Six datasets are included in the package; for details and variable definitions access the associated help file (e.g via `?BTparticipants`). They are lazy loaded so will be available on loading the package. - `BTparticipants` - Baseline characteristics and investigation results for included participants - `BTtreatments` - Antimicrobial therapy and intravenous fluid therapy received by included participants - `BTaetiology` - Results of malaria testing, aerobic blood culture, cerebrospinalfluid culture, tuberculosis diagnostic tests - `BTsera` - Results of serologic tests for arboviruses, Rickettsioses, Leptospirosis - `BTarraycard` - Results of multiplex PCR test for high consequence pathogens - `BTbc` - Results of aerobic blood culture This anal …