Uses the code mapping file provided by UK Biobank (resource 592).
map_codes(
codes,
from,
to,
all_lkps_maps = NULL,
codes_only = FALSE,
standardise_output = TRUE,
unrecognised_codes = "error",
preferred_description_only = NULL,
reverse_mapping = "error",
col_filters = default_col_filters()
)A character vector of codes to be mapped.
Coding system that codes belong to.
Coding system to map codes to.
Either a named list of lookup and mapping tables (either
data frames or tbl_dbi objects), or the path to a SQLite database
containing these tables (see also build_all_lkps_maps() and
all_lkps_maps_to_db()). If NULL, will attempt to connect to an SQLite
database named 'all_lkps_maps.db' in the current working directory, or to a
a SQLite database specified by an environmental variable named
'ALL_LKPS_MAPS_DB' (see
here
for how to set environment variables using a .Renviron file). The latter
method will be used in preference.
bool. If TRUE, return a character vector of
unique codes. If FALSE (default), return a data frame of all
results including code descriptions (useful for manual validation).
bool. If TRUE (default), outputs a data
frame with columns named 'code', 'description' and 'code_type'. Otherwise
returns a data frame with all columns for the relevant lookup sheet from
(UK Biobank
resource 592).
Either 'error' (default) or 'warning'. If any input
codes are unrecognised for the coding system being mapped from, then
either an error or warning will be raised.
If TRUE, return only preferred
descriptions for clinical codes with synonyms. Can only be TRUE if
standardise_output is also TRUE. Default value is
NULL.
If 'error' (default), an error raised if attempting to map between coding systems for which a mapping table does not exist. If 'warning', will raise a warning and attempt to use an existing mapping table in the opposite direction (for example, a mapping from ICD10 to Read 3 would be attempted using the Read 3-to-ICD10 mapping table).
A named list where each name in the list refers to the
name of a lookup or mapping table. Each item is also a named list, where
the names refer to column names in the corresponding table, and the items
are vectors of values to filter for. For example, list(my_lookup_table = list(colA = c("A", "B")) will result in my_lookup_table being filtered
for rows where colA is either 'A' or 'B'. Uses default_col_filters() by
default. Set to NULL to remove all filters.
The values for arguments from and to must be one of
read2, read3, icd9, icd10, bnf,
dmd, read2_drugs or opcs4.
Other Clinical code lookups and mappings:
codes_starting_with(),
default_col_filters(),
get_mapping_df(),
lookup_codes(),
reformat_icd10_codes()
# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()
# map codes from Read 2 to ICD10
map_codes(
codes = "G20..",
from = "read2",
to = "icd10",
all_lkps_maps = all_lkps_maps_dummy
)
#> # A tibble: 1 × 3
#> code description code_type
#> <chr> <chr> <chr>
#> 1 I10X Essential (primary) hypertension icd10