parseRPDR (version 1.1.2)

convert_phy: Searches health history data for given codes

Description

Analyzes health history data loaded using load_phy. Searches health history columns for a specified set of codes. By default, the data.table is returned with new columns corresponding to boolean values, whether given group of health history data are present within the respective columns. 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_phy(
  d,
  code = "phy_code",
  code_type = "phy_code_type",
  codes_to_find = NULL,
  collapse = NULL,
  code_time = "time_phy",
  aggr_type = "earliest",
  nThread = parallel::detectCores() - 1
)

Value

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

Arguments

d

data.table, database containing health history information data loaded using the load_phy function.

code

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

code_type

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

codes_to_find

list, a list of string arrays corresponding to sets of code types and codes separated by :, i.e.: "LMR:3688". The function searches for the given health history 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 health history 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 multiple health history 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_phy. Used in case collapse is present to provide the earliest or latest instance of health history information.

aggr_type

string, if multiple health histories 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 Height and Weight codes
anthropometrics <- list(Weight = c("LMR:3688", "EPIC:WGT"), Height = c("LMR:3771", "EPIC:HGT"))
data_phy_parse <- convert_phy(d = data_phy, codes_to_find = anthropometrics, nThread = 2)

#Search for for Height and Weight codes and summarize per patient providing earliest time
anthropometrics <- list(Weight = c("LMR:3688", "EPIC:WGT"), Height = c("LMR:3771", "EPIC:HGT"))
data_phy_parse <- convert_phy(d = data_phy, codes_to_find = anthropometrics, nThread = 2,
collapse = "ID_MERGE", aggr_type = "earliest")
}