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

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Introduction

The tbgeneratr package takes programmatic TB data cleaned using the tbcleanr package and generates additional variables. This vignette describes which variables can be calculated using only the cleaned admission data object. tbgeneratr has been developed for EpiInfo and Koch 6 data exports. It relies on standard variable naming by these software packages.

Workflow

``` {r adm-workflow} library(tbcleanr) library(tbgeneratr)

adm %>% # clean imported admission data using tbcleanr tbcleanr::adm_data_cleanr() %>% # generate adm variables using tbgeneratr tbgeneratr::adm_generator()

The `adm_generator()` function incorporates three functions - `age_generator()`, `bmi_generator()` and `start_splittr()`. These functions calculate the age in years at treatment start, the body mass index (BMI), and breaks apart the start treatment variable to alow easier grouping. 

# Additional arguments

``` {r adm-args}

adm %>%
  adm_generator(categorise = TRUE,
                paediatric = TRUE, 
                rm_orig = TRUE)

Three optional arguments can also be used with adm_generator():

• categorise - adds a factor variable age_cat splitting age in years into three categories;
• paediatric - adds a factor varialbe age_paeds splitting age < 18 years into three additional categories;
• rm_orig - removes variables used to generate the age and BMI variables.

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