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

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, check the package website here.

Purpose

This R package, tbcleanr, has been developed to support MSF field staff using either Koch 6 or EpiInfo to clean routinely collected programme TB data. Currently, the package will accept admission and laboratory data sets, Future work will allow automated cleaning of change and adherance data sets. Reported bugs or requested new features will be incorporated as time allows.

How to

To use this package, R experience is required. Future packages, such as tbgeneratr and tbreportr will allow automated variable construction and reporting.

After reading in the raw data export from either Koch 6 or EpiInfo, install and load the tbcleanr package.

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

A single function can be called to simplify admission data cleaning:

``` {r clean}
clean_adm <- adm_data_cleanr(raw_adm)

Where necessary, additional variables can be included for subsetting and manual cleaning:

``` {r addition} clean_adm <- adm_data_cleanr(raw_adm, add = "REGRP")

A similar process is required with laboratory data: 
```r
clean_lab <- lab_data_cleanr(raw_lab)

Additional variables can be included as for the adm_data_cleanr() function: ``` {r lab-addition} clean_lab <- lab_data_cleanr(raw_lab, add = "RES")

```

Further function-specific documentation are available within the package.

Future developments

Functionality will be added for laboratory and change drug data sets. In parallel, tbgeneratr and tbreportr are being developed to firstly generate new varialbe such as culture conversion time, and secondly to automate cohort reporting for programme evaluation purposes.

JayAchar/tbcleanr documentation built on Aug. 12, 2020, 8:40 a.m.