Recode Missing or Ambiguous UDS in a Subject Use Pattern

Replace all missing UDS "o" in a use pattern string

Usage

recode_missing_visits(
  use_pattern,
  missing_is = "o",
  missing_becomes = c("+", "", "-")
)

Arguments

use_pattern

A character string showing the daily, by visit, or weekly substance use pattern for a single subject

missing_is

Which single character is used to mark missing UDS in a use pattern string? Defaults to "o".

missing_becomes

How should missing UDS be treated? Defaults to marking the subject as positive for that missing period. Options are "+" for positive, "" for ignore, or "-" for negative (note that this last option should only be used in case where the "missing" UDS is a regular and expected artefact of the study design and the preceding and following UDS are both negative).

Value

A character string with all missing UDS values (marked as "o"

unless a different value is supplied to missing_is) replaces by the value supplied to missing_becomes.

Details

At current, we allow for many symbols in the use pattern "word", such as "_" for missing by study design, "o" missing for protocol non-compliance (the most common form of missing), "+" for positive, "-" for negative, and "*" for mixed positive and negative results (this usually comes up when the visit represents multiple days and there are both positive and negative results in those days; for example, a subject is tested weekly; they provided a positive test on Tuesday but came back to provide a negative test the following day).

Examples

  pattern_char <- "__++++*o-------+--+-o-o-o+o+"
  
  # Default: change all missing weeks to positive
  recode_missing_visits(pattern_char)
#> [1] "__++++*+-------+--+-+-+-++++"
  
  # Other example: remove all weeks with no UDS by design
  recode_missing_visits(pattern_char, missing_is = "_", missing_becomes = "")
#> [1] "++++*o-------+--+-o-o-o+o+"