parseRPDR (version 1.1.2)

convert_dia: Searches diagnosis columns for given diseases.

Description

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

Usage

convert_dia(
  d,
  code = "dia_code",
  code_type = "dia_code_type",
  codes_to_find = NULL,
  collapse = NULL,
  code_time = "time_dia",
  aggr_type = "earliest",
  nThread = parallel::detectCores() - 1
)

Value

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

Arguments

d

data.table, database containing diagnosis information data loaded using the load_dia function.

code

string, column name of the diagnosis code column. Defaults to dia_code.

code_type

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

codes_to_find

list, a list of string arrays corresponding to sets of code types and codes separated by :, i.e.: "ICD9:250.00". The function searches for the given disease 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 disease 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 whether given disease 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_dia. Used in case collapse is present to provide the earliest or latest instance of diagnosing the given disease.

aggr_type

string, if multiple diagnoses 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 Hypertension and Stroke ICD codes
diseases <- list(HT = c("ICD10:I10"), Stroke = c("ICD9:434.91", "ICD9:I63.50"))
data_dia_parse <- convert_dia(d = data_dia, codes_to_find = diseases, nThread = 2)

#Search for Hypertension and Stroke ICD codes and summarize per patient providing earliest time
diseases <- list(HT = c("ICD10:I10"), Stroke = c("ICD9:434.91", "ICD9:I63.50"))
data_dia_disease <-  convert_dia(d = data_dia, codes_to_find = diseases, nThread = 2,
collapse = "ID_MERGE", aggr_type = "earliest")
}