parseRPDR (version 1.1.2)

convert_prc: Searches procedures columns for given procedures.

Description

Analyzes procedure data loaded using load_prc. Searches procedures columns for a specified set of procedures. By default, the data.table is returned with new columns corresponding to boolean values, whether given group of procedures are present in the given procedure. If collapse is given, then the information is aggregated based-on the collapse column and the earliest of latest time of the given procedure is provided.

Usage

convert_prc(
  d,
  code = "prc_code",
  code_type = "prc_code_type",
  codes_to_find = NULL,
  collapse = NULL,
  code_time = "time_prc",
  aggr_type = "earliest",
  nThread = parallel::detectCores() - 1
)

Value

data.table, with indicator columns whether the any of the given procedures are reported. If collapse is present, then only unique ID and the summary columns are returned.

Arguments

d

data.table, database containing procedure information data loaded using the load_prc function.

code

string, column name of the procedure code column. Defaults to prc_code.

code_type

string, column name of the code_type column. Defaults to prc_code_type.

codes_to_find

list, a list of string arrays corresponding to sets of code types and codes separated by :, i.e.: "CPT:00104". The function searches for the given procedure code type and code pair and adds new boolean columns with the name of each list element. These columns are indicators whether any of the procedure code type and code pair occurs in the set of codes.

collapse

string, a column name on which to collapse the data.table. Used in case we wish to assess multiple procedure codes are present within all the same instances of collapse. See vignette for details.

code_time

string, column name of the time column. Defaults to time_prc. Used in case collapse is present to provide the earliest or latest instance of the given procedure.

aggr_type

string, if multiple procedures are present within the same case of collapse, which timepoint to return. Supported are: "earliest" or "latest". Defaults to earliest.

nThread

integer, number of threads to use for parallelization. If it is set to 1, then no parallel backends are created and the function is executed sequentially.

Examples

if (FALSE) {
#Search for Anesthesia CPT codes
procedures <- list(Anesthesia = c("CTP:00410", "CPT:00104"))
data_prc_parse <- convert_prc(d = data_prc, codes_to_find = procedures, nThread = 2)

#Search for Anesthesia CPT codes
procedures <- list(Anesthesia = c("CTP:00410", "CPT:00104"))
data_prc_procedures <- convert_prc(d = data_prc, codes_to_find = procedures,
nThread = 2, collapse = "ID_MERGE", aggr_type = "earliest")
}