Convert ICD data from long to wide format
Note the distinction between labelling existing data with any classes which
icd provides, and actually converting the structure of the data.
long_to_wide(x, visit_name = get_visit_name(x),
icd_name = get_icd_name(x), prefix = "icd_", min_width = 1L)data.frame of long-form data, one column for visit_name and one for ICD code
The name of the column in the data frame which contains the
patient or visit identifier. Typically this is the visit identifier, since
patients come leave and enter hospital with different ICD-9 codes. It is a
character vector of length one. If left empty, or NULL, then an
attempt is made to guess which field has the ID for the patient encounter
(not a patient ID, although this can of course be specified directly). The
guesses proceed until a single match is made. Data frames may be wide with
many matching fields, so to avoid false positives, anything but a single
match is rejected. If there are no successful guesses, and visit_id
was not specified, then the first column of the data frame is used.
The name of the column in the data.frame which
contains the ICD codes. This is a character vector of length one. If it is
NULL, icd9 will attempt to guess the column name, looking for
progressively less likely possibilities until it matches a single column.
Failing this, it will take the first column in the data frame. Specifying
the column using this argument avoids the guesswork.
character, default icd_ to prefix new columns
single integer, if specified, writes out this many columns even if no patients have that many codes. Must be greater than or equal to the maximum number of codes per patient.
As is common with many data sets, key variables can be concentrated in one column or spread over several. Tools format of clinical and administrative hospital data, we can perform the conversion efficiently and accurately, while keeping some metadata about the codes intact, e.g. whether they are ICD-9 or ICD-10.
Long or wide format ICD data are all expected to be
in a data frame. The data.frame itself does not carry any ICD
classes at the top level, even if it only contains one type of code;
whereas its constituent columns may have a class specified, e.g.
icd9 or icd10who.
This is more complicated than expected using base::reshape or
reshape2::dcast allows. This is a reasonably simple solution using
built-in functions.
Other ICD data conversion: comorbid_df_to_mat,
comorbid_mat_to_df, convert,
decimal_to_short,
short_to_decimal,
wide_to_long
# NOT RUN {
longdf <- data.frame(
visit_name = c("a", "b", "b", "c"),
icd9 = c("441", "4424", "443", "441")
)
long_to_wide(longdf)
long_to_wide(longdf, prefix = "ICD10_")
# }
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