Deterministic labelling of data
The goal of labellr is to enable the use of tabular files (e.g. MS Excel) in defining each level of the summary/grouping variable according to set of rules (e.g. the presence/absence of a condition) - a definitions table. This definitions table of rules is then used by labellr::classify to categorise each row of the analysis dataset into one (or more) of the levels of the summary/grouping variable.
# install from the Github repo
# install.packages("devtools")
devtools::install_github("oizin/labellr")The core function in labellr is classify.
# read in a dataset
> clinic_data <- read.csv(file.path(ext_path, "clinic_data.csv"), stringsAsFactors = FALSE,na.strings = "")
> clinic_data
clinic_date xray fmri surgery_date complications
1 8/05/2014 y <NA> <NA> <NA>
2 9/05/2014 <NA> y <NA> <NA>
3 10/05/2014 y <NA> <NA> <NA>
4 11/05/2014 y <NA> <NA> <NA>
5 <NA> <NA> <NA> 10/05/2014 soreness around wound
6 <NA> <NA> <NA> 11/05/2014 none of note
7 <NA> <NA> <NA> 12/05/2014 <NA>
# read in definitions table
> tmt_def <- read.csv(file.path(ext_path, "treatment_definitions.csv"), stringsAsFactors = FALSE)
> print(tmt_def,quote=TRUE)
treatment clinic_date xray fmri surgery_date complications
1 "datatype" "date" "char" "char" "date" "char"
2 "xray" "1" "y" "!y" "0" ""
3 "fmri" "1" "!y" "y" "0" ""
4 "surgery" "0" "!y" "!y" "1" ""
# classify data the data into the summary variable based on the definitions table
> library(labellr)
> classify(clinic_data,tmt_def)
treatment clinic_date xray fmri surgery_date complications
1 xray 8/05/2014 y <NA> <NA> <NA>
2 fmri 9/05/2014 <NA> y <NA> <NA>
3 xray 10/05/2014 y <NA> <NA> <NA>
4 xray 11/05/2014 y <NA> <NA> <NA>
5 surgery <NA> <NA> <NA> 10/05/2014 soreness around wound
6 surgery <NA> <NA> <NA> 11/05/2014 none of note
7 surgery <NA> <NA> <NA> 12/05/2014 <NA>If you encounter a bug please open an issue on Github.