Package index • readepi

Exported functions

readepi functions available to end-users

dhis2_login(): Establish connection to a DHIS2 instance

get_api_version(): Get DHIS2 API version

get_data_elements(): Get all data elements from a specific DHIS2 instance

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_tracked_entities(): Get tracked entity attributes, their corresponding IDs and event IDs

login(): Establish a connection to the HIS of interest.

lookup_table: Lookup table

read_dhis2(): Import data from DHIS2

read_rdbms(): Import data from relational database management systems (RDBMS).

read_sormas(): Import data from SORMAS

request_parameters: Request parameters

show_tables(): Display the list of tables in a database

sormas_get_api_specification(): Download the API specification file from SORMAS

sormas_get_data_dictionary(): Download SORMAS data dictionary

sormas_get_diseases(): Get the list of disease names from a SORMAS instance

Internal functions

readepi functions for internal use

Shared helpers

url_check(): Check if the value for the base_url argument has a correct structure

SORMAS

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

convert_to_date(): Convert numeric values into POSIXct,then into Date

DHIS2

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 IDs, and levels.

check_org_unit(): Validate user-specified organisation unit ID or name.

check_program(): Validate and retrieve program IDs

get_entity_attributes(): Get the attribute names and ids of the tracked entities

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

get_entity_data(): Get tracked entity attributes

get_event_ids(): Get event IDs for specific tracked entity

get_request_params(): Get the request query parameters for a specific API version

RDBMS

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

query_check(): Check whether the user-provided query is valid

fields_check(): Check whether the user-specified fields are valid