In JayAchar/tbcleanr: tbcleanr: tools for cleaning TB datade

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tbcleanr

Simplify cleaning of MSF programmatic TB data

Introduction

The R package tbcleanr was developed to fix the challenge faced by managers to review routinely collected TB programme data. Despite bespoke data collection tools being available to all projects, reporting or analysis options from these tools is rudimentary and require inital exportation. Historically, this has resulted in analyses and reporting relying on Microsoft Excel due to the skills available in projects. Since the Excel-workflow limits transparency and reproducibility, it was felt that a solution in R was important to develop.

tbcleanr is designed to clean data generated by MSF OCA tools used to collect programmatic TB data. It has been designed with Epiinfo and Koch 6 options and will ultimately work with other packages including tbgeneratr, tbcheckr and tbreportr.

Functionality

tbcleanr currently simplifies cleaning of admission data sets from EpiInfo and Koch 6 only. In future, laboratory and drug change data options will be added. Further work to incorporate inclusion of Excel-based line-list data will be considered, although updating of standard Health Information Systems may result in this not being required.

Installation

You can install the released version of tbcleanr from Github with:

library(devtools)
install_github("JayAchar/tbcleanr")
library(tbcleanr)

Important functions

Function | Use it for -------------- | ------------------------------------------ adm_data_cleanr() | Streamlined admission data cleaning lab_data_cleanr() | Streamlined laboratory data cleaning