load_all {parseRPDR}

Loads allergy data information into R.

Description

Loads allergy information into the R environment.

Usage

load_all(
  file,
  merge_id = "EMPI",
  sep = ":",
  id_length = "standard",
  perc = 0.6,
  na = TRUE,
  identical = TRUE,
  nThread = parallel::detectCores() - 1,
  mrn_type = FALSE
)

Arguments

file

string, full file path to All.txt.

merge_id

string, column name to use to create ID_MERGE column used to merge different datasets. Defaults to EPIC_PMRN, as it is the preferred MRN in the RPDR system.

sep

string, divider between hospital ID and MRN. Defaults to :.

id_length

string, indicating whether to modify MRN length based-on required values id_length = standard, or to keep lengths as is id_length = asis. If id_length = standard then in case of MGH, BWH, MCL, EMPI and PMRN the length of the MRNs are corrected accordingly by adding zeros, or removing numeral from the beginning. In other cases the lengths are unchanged. Defaults to standard.

perc

numeric, a number between 0-1 indicating which parsed ID columns to keep. Data present in perc x 100% of patients are kept.

na

boolean, whether to remove columns with only NA values. Defaults to TRUE.

identical

boolean, whether to remove columns with identical values. Defaults to TRUE.

nThread

integer, number of threads to use to load data.

mrn_type

boolean, should data in MRN_Type and MRN be parsed. Defaults to FALSE, as it is not advised to parse these for all data sources as it takes considerable time.

Value

data table, with allergy information.

ID_MERGE

numeric, defined IDs by merge_id, used for merging later.

ID_all_EMPI

string, Unique Partners-wide identifier assigned to the patient used to consolidate patient information from all datasource, corresponds to EMPI in RPDR. Data is formatted using pretty_mrn().

ID_all_PMRN

string, Epic medical record number. This value is unique across Epic instances within the Partners network from all datasource, corresponds to EPIC_PMRN in RPDR. Data is formatted using pretty_mrn().

ID_all_loc

string, if mrn_type == TRUE, then the data in MRN_Type and MRN are parsed into IDs corresponding to locations (loc). Data is formatted using pretty_mrn().

time_all

POSIXct, Date when the allergy was first noted, corresponds to Noted_Date in RPDR. Converted to POSIXct format.

all_all

string, Name of the allergen, corresponds to Allergen in RPDR.

all_all_code

string, Epic internal identifier for the specific allergen, corresponds to Allergen_Code in RPDR.

all_all_type

string, Hierarchy for the type of allergy noted. Denotes known level of specificity of allergen, corresponds to Allergen_Type in RPDR.

all_reac

string, Noted reactions to the allergen, corresponds to Reactions in RPDR.

all_reac_type

string, Category of reaction to the allergen, corresponds to Reaction_Type in RPDR.

all_severity

string, Degree of severity of noted reactions, corresponds to Severity in RPDR.

all_status

string, Last known status of allergen, either active or deleted from the patient's allergy record, corresponds to Status in RPDR.

all_system

string, The source system where the data was collected, corresponds to System in RPDR.

all_comment

string, Free-text information about the allergen, corresponds to Comments in RPDR.

all_del_reason

string, Free-text information about why the allergen was removed from the patient's allergy list, corresponds to Deleted_Reason in RPDR.

Examples

## Not run: 
#Using defaults
d_all <- load_all(file = "test_All.txt")

#Use sequential processing
d_all <- load_all(file = "test_All.txt", nThread = 1)

#Use parallel processing and parse data in MRN_Type and MRN columns and keep all IDs
d_all <- load_all(file = "test_All.txt", nThread = 20, mrn_type = TRUE, perc = 1)

## End(Not run)