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