readepi1.0.3 package

Read Data from Relational Database Management Systems and Health Information Systems

check_org_unit

Validate user-specified organisation unit ID or name.

check_program

Validate and retrieve program IDs

convert_to_date

Convert numeric values into POSIXct,then into Date

dhis2_login

Establish connection to a DHIS2 instance

fields_check

Check whether the user-specified fields are valid

get_api_version

Get DHIS2 API version

get_data_elements

Get all data elements from a specific DHIS2 instance

get_entity_attributes

Get the attribute names and ids of the tracked entities

get_entity_data

Get tracked entity attributes

get_event_data

Get event data from the newer DHIS2 versions (version >= 2.41)

get_event_ids

Get event IDs for specific tracked entity

get_org_unit_as_long

Transform the organisation units data frame from large to long format

get_org_unit_levels

Extract the DHSI2 organization unit's hierarchical levels.

get_org_units

Retrieve DHIS2 organization units, along with their IDs, names, parent...

get_organisation_units

Get the organization units from a specific DHIS2 instance

get_program_org_units

Get organisation units that are associated with a given program

get_program_stages

Get program stages for one or more DHSI2 programs

get_programs

get all programs from a given specific DHIS2 instance

get_request_params

Get the request query parameters for a specific API version

get_tracked_entities

Get tracked entity attributes, their corresponding IDs and event IDs

login

Establish a connection to the HIS of interest.

query_check

Check whether the user-provided query is valid

read_dhis2

Import data from DHIS2

read_rdbms

Import data from relational database management systems (RDBMS).

read_sormas

Import data from SORMAS

server_fetch_data

Fetch all or specific rows and columns from a table

server_make_query

Make an SQL query from a list of query parameters

server_make_sql_expression

Convert R expression into SQL expression

server_make_subsetting_query

Create a subsetting query

show_tables

Display the list of tables in a database

sormas_get_api_specification

Download the API specification file from SORMAS

sormas_get_cases_data

Get case data from a SORMAS instance

sormas_get_contact_data

Get contact data from SORMAS

sormas_get_data_dictionary

Download SORMAS data dictionary

sormas_get_diseases

Get the list of disease names from a SORMAS instance

sormas_get_pathogen_data

Get pathogen tests data from SORMAS

sormas_get_persons_data

Get personal data of cases from a SORMAS instance

url_check

Check if the value for the base_url argument has a correct structure

Import Data from Relational Database Management Systems (RDBMS) and Health Information Systems ('HIS'). The current version of the package supports importing data from RDBMS including 'MS SQL', 'MySQL', 'PostGRESQL', and 'SQLite', as well as from two HIS platforms: 'DHIS2' and 'SORMAS'.

  • Maintainer: Bubacarr Bah
  • License: MIT + file LICENSE
  • Last published: 2025-10-29