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rEHR

David A. Springate 2014, 2015

R tools for processing and extracting clinical information from Electronic Medical Records

This in development package provides tools for accelerating and automating the most common operations researchers perform to extract and analyse data from Electronic Medical Records Databases.

The package is currently only tested with CPRD data, but it should be possible to configure it with other EHR data. See the ehr_system code for details of how the interface with CPRD is implemented. See the vignette for more details.

The package can be installed from CRAN https://CRAN.R-project.org/package=rEHR or from github using devtools:

install.packages("devtools")
require(devtools)
install_github("rEHR", "rOpenHealth")
require(rEHR)

See the vignette for full usage details.

Clinical code list construction functions have been absorbed from the rpcdsearch package. See the [Codelist construction vignette]((https://github.com/rOpenHealth/rEHR/blob/master/vignettes/codelists.pdf>) for more details.

Issues can be reported here.

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Version

Install

install.packages('rEHR')

Monthly Downloads

9

Version

1.0

License

GPL (>= 2)

Issues

Pull Requests

Stars

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Repository

https://github.com/rOpenHealth/rEHR

Maintainer

Rosa Parisi

Last Published

January 23rd, 2017

Functions in rEHR (1.0)

add_to_database

Adds a series of files to a database

Compresses a dataframe to make more efficient use of resources

cprd_uniform_hba1c_values

Transforms hba1c values to mmol/mol

Clinical codes for 17 QOF conditions, smoking and HbA1c

append_to_temp_table

Appends rows to a temporary table

cut_tv - Cuts a survival dataset on a time varying variable

converts date fields from ISO character string format to R Date format

Function to build start/enddate helper fuctions

Wrapper for dbConnect

Converts a longitudinal data set from e.g. prev_terms to a cohort dataset. The dataset has a single row for each patient and includes only patients in the numerator or denominator for whichever cohort type is chosen. Columns are added for start and end dates and for start and end times as integer differences from the cohort start date. A binary column is added for membership of the case group. All patients with start date > end date are removed from the dataset.

An example EHR_definition object for defining parameters for simulating EHR data

A sample of 6 clinical tests and meaures used in UK primary care

export_definition_search

Exports definition searches to an excel file

definition_search

This function is used to build new definition lists based on medical definitions

extract_keywords

Function to extract rows from a lookup table based on keywords

Construct an EHR_definition object.

drop_temp_table

Checks if a temporary table exists and then deletes if it does

drop_all_temp_tables

drops all temporary tables from the database

Reads strings and expands sections wrapped in dotted parentheses

Exports to a variety of formats based on the file type argument

Selected controls matching a list of variables from a case

Find matched controls for a set of cases

Selects the earliest event grouped by patient

list_EHR_attributes

Lists all of the EHR attribute names in .ehr

get_EHR_attribute

Return the value of an attribute in the .ehr environment

import_definitions

Imports definitions to be searched from a csv file into a MedicalDefinition object

import_CPRD_data

Imports all selected CPRD data into an sqlite database

head.SQLiteConnection

head for SQLiteConnection object

Exports flat files from the database. One file per practice

Selects the earliest event grouped by patient

patients_per_medcode

Produce a dataset of CPRD medcodes with frequencies of patients in the clinical table

This function adds columns enabling one to calculate numerators and denominators for prevalence and incidence.

medcodes_to_read

Translate CPRD medcodes to Read/Oxmis

print.MedicalDefinition

Basic print method for medical definition classes

A sample of 500 medicines used in UK primary care

MedicalDefinition

Constructor function for MedicalDefinition class

Calculates the prevalence totals for the output of a data frame of events/patients etc.

patients_in_window

Select patients alive and registered between certain dates

print.EHR_definition

Tools for describing EMR_description objects.

Function for performing matching of controls to cases using the consultation files to generate a dummy index date for controls.

The rEHR package.

Reads a zipped data file to a dataframe

Helper function providing startdate and enddate for a given year

Helper function providing startdate and enddate for a given year

read_to_medcodes

Translate Read/Oxmis codes to CPRD medcodes

Sets EHR metadata to CPRD format When this is run, most functions in rEHR act as though the EHR database is CPRD

Extracts From the database

Generates random dates between a start and end day.

repsample_example

An example dataset to demonstrate the repsample function. 2474 theroetical UK GP Practices.

Runs a series of selects over a year range and collects in a list of dataframes

Function to simulate survival data.

Sets location of the db temporary store for temporary tables

simulate_ehr_patients

Generate a dataframe of simulated patients with exit dates based on presented comorbidities.

simulate_ehr_events

Generate simulated events tables

Creates a temporary table in the database

Send a dataframe to a temporary table in the database

Compresses a dataframe and saves in stata format. Options to save as Stata 12 or 13.

combines strings and vectors in a sensible way for select queries

set_EHR_attribute

Sets the value of an attribute in the .ehr environment

simulate_ehr_consultations

Generates simulated GP consultation tables.

simulate_ehr_practices

generates a simulated dataframe of primary care practices in the same format as is used in CPRD

Helper function providing startdate and enddate for a given year