nsqip_subset_pufs: Importing the raw National Surgical Quality Improvement...

In UKBiostatCIRCL/UK-Biostat-CIRCL: UKBiostatCIRCL: A package for the common functions of the Biostat CIRCL at the University of Kentucky

Importing the raw National Surgical Quality Improvement Program (NSQIP) Dataset

Description

This function is designed to specify a directory with multiple NSQIP datasets to be filtered and merged. Due to the size of many NSQIP datasets, importing each is likely to cause out-of-memory errors on most personal computers. This function is intended to be run prior to running the nsqip_clean_data() function. Exports a merged dataframe object.

Usage

nsqip_subset_pufs(
  puf_folder_path = "Raw Files",
  puf_years = 2012:2020,
  cpt_codes = NULL,
  cpt_codes_primary_only = TRUE,
  icd10_codes = NULL,
  icd9_codes = NULL,
  icd_codes_primary_only = TRUE,
  surgical_specialty = NULL
)

Arguments

puf_folder_path	a text string representing the path of the folder containing the PUF text files; the text string must not end with "/"!
puf_years	the years to include in the extract
cpt_codes	the CPT codes to include in the extract. If NULL, then return all codes. Based on the following fields: "CPT", "OTHERCPT1" - "OTHERCPT10", and "CONCPT1" - "CONCPT10"
cpt_codes_primary_only	if TRUE, then only consider cases where one of the "cpt_codes" is the primary CPT code (the "CPT" field). Ignore if cpt_codes = NULL.
icd10_codes	a character vector of ICD-10 codes to subset the extract to. Ignore when NULL. Based on the following fields: "PODIAG10", "PODIAG_OTHER10", "REOPOR1ICD101", "REOPOR2ICD101", "READMRELICD101", "READMUNRELICD101", "READMRELICD102", "READMUNRELICD102", "READMRELICD103", "READMUNRELICD103", "READMRELICD104", "READMUNRELICD104", "READMRELICD105", "READMUNRELICD105"
icd9_codes	a character vector of ICD-9 codes to subset the extract to (these become rare in more recent years). Ignore when NULL. Based on the following fields: "PODIAG", "PODIAG_OTHER", "REOPORICD91", "REOPOR2ICD91", "READMRELICD91", "READMUNRELICD91", "READMRELICD92", "READMUNRELICD92", "READMRELICD93", "READMUNRELICD93", "READMRELICD94", "READMUNRELICD94", "READMRELICD95", "READMUNRELICD95"
icd_codes_primary_only	if TRUE, then only use the "PODIAG10" and "PODIAG" fields for filtering.
surgical_specialty	a character vector of surgical specialty to subset to (based on the "SURGSPEC" field).

UKBiostatCIRCL/UK-Biostat-CIRCL documentation built on June 30, 2022, 4:42 a.m.