convert matrix of comorbidities into data frame, preserving visit_name information
comorbid_df_to_mat(x, visit_name = get_visit_name(x),
stringsAsFactors = getOption("stringsAsFactors"))data frame, with a visit_name column (not necessarily first),
and other columns with flags for comorbidities, as such column names are
required.
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.
Single logical value, describing whether the resulting data frame should have strings, e.g.
visit_id converted to factor. Default is to follow the current session option. This is identical to the
argument used in, among other base functions as.data.frame.
Other ICD data conversion: comorbid_mat_to_df,
convert, decimal_to_short,
long_to_wide,
short_to_decimal,
wide_to_long
# NOT RUN {
longdf <- icd_long_data(
visit = c("a", "b", "b", "c"),
icd9 = c("441", "4240", "443", "441")
)
cmbdf <- icd9_comorbid_elix(longdf, return_df = TRUE)
class(cmbdf)
rownames(cmbdf)
mat.out <- comorbid_df_to_mat(cmbdf)
stopifnot(is.matrix(mat.out))
mat.out[, 1:4]
# }
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