Relevel serotype data into an factor based on PCV group status and serotype name.

Usage

relevel_serotypes(serotypes, ..., exprs)

Arguments

serotypes: a vector of serotypes as a factor or character.
...: an unwrapped version of the exprs parameter
exprs: a list of formulae with a predicate on the LHS and a PCV group name on the RHS. which are interpreted as the parameters for a dplyr::case_when call. This must be protected against interpretation by wrapping it in rlang::exprs(). The predicates are tested against avoncap::serotype_data$map and could use any of the following columns 'serotype', 'PCV7', 'PCV13', 'PCV15', 'PCV20', 'PPV23', 'PCV13on7', 'PCV15on13', 'PCV20on15', 'PPV23on20', 'PCV10SSI', 'PCV10GSK', 'PCV15Zhifei', 'PCV24Vaxcyte', 'PCV24Affinivax' a default option of the form TRUE ~ "Non PCV serotype" must exist to capture unmatched items.

Examples

x = rlang::exprs(
  PCV7 ~ "PCV7",
  PCV15 ~ "PCV15-7",
  TRUE ~ "Non-PCV15 serotype"
)
relevel_serotypes(avoncap::phe_serotypes, exprs=x)
#> [1] <NA>
#> 50 Levels: 4 6B 9V 14 18C 19F 23F 1 3 5 6A 7F 19A 22F 33F 2 6C 7C 8 9N ... 38
relevel_serotypes(avoncap::phe_serotypes)
#> [1] <NA>
#> 50 Levels: 4 6B 9V 14 18C 19F 23F 1 3 5 6A 7F 19A 22F 33F 8 10A 11A 12F ... 38

relevel_serotypes(avoncap::phe_serotypes,
  PCV24Affinivax ~ "Affinivax",
  TRUE ~ "Non-affinivax"
)
#> [1] <NA>
#> 50 Levels: 1 2 3 4 5 6A 6B 7F 8 9N 9V 10A 11A 12F 14 15B 17F 18C 19A 19F ... 38