readepi: Read data from health information systems

readepi is an R package for reading data from several health information systems (HIS) and relational database management systems (RDBMS).

readepi currently supports reading data from the followings:

• RDBMS (Relational Database Management Systems) including MS SQL, MySQL, PostgreSQL, and SQLite 
• DHIS2: an open source and web-based platform for managing health information
  
• SORMAS: an eHealth system for monitoring the spread of infectious diseases and responding to outbreak situations

readepi returns a data frame with the data from the specified system.

readepi is developed by Epiverse-TRACE team at the Medical Research Center, The Gambia unit at London School of Hygiene and Tropical Medicine.

Installation

readepi can be installed from CRAN using

install.packages("readepi")

The latest development version of readepi from GitHub with:

if (!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/readepi")
library(readepi)

Quick start

readepi currently has three main functions that read data from a specified source. While the arguments to these functions are generally similar, some are specific to their data source (see the vignette for more details). The examples below show how to use the package functionalities to import data from a variety of sources.

Reading data from RDBMS

The read_rdbms() function is used to import data from a variety of RDBMS, including MS SQL, MySQL, PostgreSQL, and SQLite. Reading data from a RDBMS requires:

• A MS SQL driver that is compatible with the version of DBMS of interest. The install drivers vignette vignette describes how to install the appropriate driver for each database management system.

Users can read data from a RDBMS by providing a list with the query parameters of interest or an SQL query (for more information, see the vignette).

# CONNECT TO THE TEST MYSQL SERVER
rdbms_login <- readepi::login(
  from = "mysql-rfam-public.ebi.ac.uk",
  type = "mysql",
  user_name = "rfamro",
  password = "",
  driver_name = "",
  db_name = "Rfam",
  port = 4497
)

# DISPLAY THE LIST OF TABLES FROM A DATABASE OF INTEREST
tables <- readepi::show_tables(login = rdbms_login)

# READING ALL FIELDS AND ALL RECORDS FROM ONE TABLE (`author`) USING AN SQL QUERY
dat <- readepi::read_rdbms(
  login = rdbms_login,
  query = "select * from author"
)

# SELECT FEW COLUMNS FROM ONE TABLE AND LEFT JOIN WITH ANOTHER TABLE
dat <- readepi::read_rdbms(
    login = rdbms_login,
    query = "select author.author_id, author.name,
  family_author.author_id from author left join family_author on
  author.author_id = family_author.author_id"
)

# READING ALL FIELDS AND ALL RECORDS FROM ONE TABLE (`author`) WHERE QUERY PARAMETERS ARE SPECIFIED AS A LIST
dat <- readepi::read_rdbms(
  login = rdbms_login,
  query = list(table = "author", fields = NULL, filter = NULL)
)

Reading data from DHIS2

# CONNECT TO A DHIS2 INSTANCE
dhis2_login <- readepi::login(
  type = "dhis2",
  from = "https://smc.moh.gm/dhis",
  user_name = "test",
  password = "Gambia@123"
)

# IMPORT DATA FROM DHIS2 FOR THE SPECIFIED ORGANISATION UNIT AND PROGRAM IDs
data <- readepi::read_dhis2(
  login = dhis2_login,
  org_unit = "GcLhRNAFppR",
  program = "E5IUQuHg3Mg"
)

Reading data from SORMAS

# CONNECT TO THE SORMAS SYSTEM
sormas_login <- readepi::login(
  type = "sormas",
  from = "https://demo.sormas.org/sormas-rest",
  user_name = "SurvSup",
  password = "Lk5R7JXeZSEc"
)

# FETCH ALL COVID (coronavirus) CASES FROM THE TEST SORMAS INSTANCE
covid_cases <- readepi::read_sormas(
  login = sormas_login,
  disease = "coronavirus",
)

Package Vignettes

The vignette of the readepi package contains detailed illustrations about the use of each function and the description of every argument. This can be accessed by typing the command below:

# OPEN THE VIGNETTE WITHIN RSTUDIO
vignette("readepi")

# OPEN THE VIGNETTE IN YOUR WEB BROWSER.
browseVignettes("readepi")

Development

Lifecycle

This package is currently maturing, as defined by the RECON software lifecycle. This means that it can be used in production with the understanding that the interface may still undergo minor changes.

Contributions

Contributions are welcome via pull requests.

Code of Conduct

Please note that the readepi project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.