correct_subject_ids {cleanepi}

Correct the wrong subject IDs based on the user-provided values.

Description

After detecting incorrect subject IDs from the check_subject_ids() function, use this function to provide the correct IDs and perform the substitution.

Usage

correct_subject_ids(data, target_columns, correction_table)

Arguments

data

The input data frame or linelist

target_columns

A vector of column names with the subject ids.

correction_table

A data frame with the following two columns:

1. from: a column with the wrong subject IDs,

2. to: a column with the values to be used to substitute the incorrect ids.

Value

The input dataset where all subject ids comply with the expected format.

Examples

# detect the incorrect subject ids
dat <- check_subject_ids(
  data           = readRDS(system.file("extdata", "test_df.RDS",
                                       package = "cleanepi")),
  target_columns = "study_id",
  prefix         = "PS",
  suffix         = "P2",
  range          = c(1, 100),
  nchar          = 7
)

# generate the correction table
correction_table <- data.frame(
  from = c("P0005P2", "PB500P2", "PS004P2-1"),
  to   = c("PB005P2", "PB050P2", "PS004P2")
)

# perform the correction
dat <- correct_subject_ids(
  data             = dat,
  target_columns   = "study_id",
  correction_table = correction_table
)