In JayAchar/tbgeneratr: tbgenratr: tools for generating new TB variables

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

Accessing instructions

This instruction vignette is available either online at Github or through emailing the author. Alternatively, you may ask your medical manager since they may also have a copy. For the most up to date version, it's recommended to visit the online repository linked.

Purpose

This R package, tbgeneratr, has been developed to support MSF field staff using either Koch 6 or EpiInfo to augment the output from tbcleanr, a package designed to automate cleaning of routine TB programme data. The package will eventually fit into a workflow incorporating tbcleanr and tbreportr, a package being developed to generate standardised TB programme reports.

How to

To use this package, R experience is required. The R langugage must be downloaded and installed on the computer. This, and the download of the tbgeneratr package will require a functioning internet connection.

This package accepts admission and laboratory data exported from Koch 6 or EpiInfo, then cleaned using tbcleanr.

``` {r install} require(devtools) install_github("JayAchar/tbgeneratr") library(tbgeneratr)

Aggregating functions have been developed to simplify multiple variable generation steps:

* `adm_generator` generates the age and BMI, in addition to splitting the start treatment date within the cleaned admission data frame. It is capable of working with data collected in Koch 6 and EpiInfo.
* `adm_lab_generator` generates baseline smear and culture status variables, with culture and smear conversion dates and baseline DST results. 

``` {r adm_generator}
adm <- adm_generator(adm, rm_orig = TRUE)

``` {r adm_lab_generator} adm <- adm_lab_generator(adm, lab, baseline_days = 90)

Help files for individual functions are available in the usual way:
``` {r help}
?tbgeneratr::converter

Future developments

Functionality will be added for adherance and change drug data sets. In parallel, tbreportr is being developed to automate cohort reporting for programme evaluation purposes and to monitor data quality within a programme.

JayAchar/tbgeneratr documentation built on Oct. 13, 2019, 1:47 a.m.