esogettr

The goal of esogettr is to make it easy to import data from ESO EHR data sources and manipulate it for use in data analytics, modeling, and reporting purposes.

Installation

How to import:

install_github("samuelkordik/esogettr")

Data Sources

ESO Data

esogettr expects ESO data to be downloaded from Ad Hoc to a single directory with the following specifications:

• Flat file CSV
• Name: Either “YYYY-MM{table_name}” or “YYYY_{table_name}” with the table names following a pattern that isn’t necessarily logical.

Getting Started

Importing ESO data:

library(esogettr)
## set file_root
file_root <- get_file_root()

## set year and month
year <- set_year()
month <- set_month()

## import incidents (general function)
incidents <- import_eso_data(year, month, "incidents")

## import incidents (specific function)
incidents <- import_incidents(year, month)

Note that you have to set file_root first, as the path to the ESO data may vary based on machine, OS, or network. Years and months are passed as strings, and serve as the filter to get into the right flat file. I know, it’s clunky.

Custom import functions ensure consistent typing, and more:

• import_patients
• import_incidents: adds dtDate for incident and month, which is YYYY-MM format
• import_vitals: adds vsDate as date time field
• import_treatments: Combines General, Airway, Cardiac, Medications, and IV treatments (but strangely not labs). Also adds treatmentDate datetime field.
• import_stroke: Handles some unknown stuff.
• import_narrative
• import_cpr: handles some things. TODO here.
• import_all_data (imports all years/months/etc.) Garbage function
• filtered_incidents: Uses an existing data set to filter incidents for import. TODO here with example.

ESO Data Transformations

• join_crew: Adds Lead, Driver fields.
• cardiac_arrest: Adds OHCA field. Deprecate in favor of is_cardiac_arrest.
• rsi: Adds field for RSI meds or not
• rsi_onscene
• blood

Utilities

• merge_eso_data: Useful to merge multiple files downloaded from Ad Hoc together. Key for year-long or larger datasets that run into row length limitations.

Notes

FILE ROOTS:

#file_root <- "C:/Users/skordik/Data/"
#file_root <- "/Users/samuelkordik/Data/"
#file_root <- "W:/Monthly ESO Data/"