This is different enough to dcast in reshape2 that
it needs writing again specifically for ICD codes. This function packages
the core reshape function. Empty strings and NA values will be
dropped, and everything else kept. No validation of the ICD codes is done.
icd9WideToLong(x, visitId = NULL, icdLabels = NULL, icdName = "icdCode",
icdRegex = c("icd", "diag", "dx_", "dx"), verbose = FALSE)data.frame in wide format, i.e. one row per patient, and
multiple columns containing ICD codes, empty strings or NA.
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 visitId
was not specified, then the first column of the data frame is used.
vector of column names in which codes are found. If NULL, all columns matching icd or ICD will be included.
character vector length one containing the new column name for the ICD codes, defaults to "icdCode"
vector of character strings containg a regex to identify ICD-9 diagnosis
columns to try (case-insensitive) in order. Default is c("icd", "diag", "dx_", "dx")
single logical value, defaults to FALSE in most functions.
data frame with visitId column named the same as input, and a column
named by icd.name containing all the non-NA and non-empty codes
found in the wide input data.
Other ICD-9 convert: convert,
icd9DecimalToParts,
icd9MajMinToCode,
icd9MajMinToDecimal,
icd9MajMinToParts,
icd9MajMinToParts_list,
icd9MajMinToShort,
icd9PartsToDecimal,
icd9PartsToShort,
icd9ShortToParts;
icd9ChaptersToMap;
icd9DropLeadingZeroes,
icd9DropLeadingZeroesDecimal,
icd9DropLeadingZeroesMajor,
icd9DropLeadingZeroesShort;
icd9LongToWide
# NOT RUN {
widedf <- data.frame(visitId = c("a", "b", "c"),
icd9_01 = c("441", "4424", "441"),
icd9_02 = c(NA, "443", NA))
icd9WideToLong(widedf)
# }
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