## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk[["set"]](collapse = TRUE, comment = "#>", eval = FALSE, fig.width = 7L, fig.height = 7L, message = FALSE, fig.align = "center", warning = FALSE, dpi = 300L) ## ----setup, eval=TRUE--------------------------------------------------------- # LOAD readepi library(readepi) ## ----------------------------------------------------------------------------- # # CONNECT TO A DHIS2 INSTANCE # dhis2_login <- login( # type = "dhis2", # from = "https://smc.moh.gm/dhis", # user_name = "test", # password = "Gambia@123" # ) # # # CONNECT TO THE TEST MYSQL SERVER # rdbms_login <- login( # type = "mysql", # from = "mysql-rfam-public.ebi.ac.uk", # user_name = "rfamro", # password = "", # driver_name = "", # db_name = "Rfam", # port = 4497 # ) # # # CONNECT TO A SORMAS SYSTEM # dhis2_login <- login( # type = "sormas", # from = "https://demo.sormas.org/sormas-rest", # user_name = "SurvSup", # password = "Lk5R7JXeZSEc" # ) ## ----eval=TRUE---------------------------------------------------------------- # CONNECT TO THE TEST MYSQL SERVER rdbms_login <- login( type = "mysql", from = "mysql-rfam-public.ebi.ac.uk", user_name = "rfamro", password = "", driver_name = "", db_name = "Rfam", port = 4497 ) ## ----eval=TRUE---------------------------------------------------------------- # DISPLAY THE LIST OF TABLES FROM A DATABASE OF INTEREST tables <- show_tables(login = rdbms_login) head(tables) ## ----eval=FALSE--------------------------------------------------------------- # # READING ALL FIELDS AND ALL RECORDS FROM ONE TABLE (`author`) USING AN SQL # # QUERY # dat <- read_rdbms( # login = rdbms_login, # query = "select * from author" # ) ## ----eval=FALSE--------------------------------------------------------------- # # READING ALL FIELDS AND ALL RECORDS FROM ONE TABLE (`author`) WHERE QUERY # # PARAMETERS ARE SPECIFIED AS A LIST # dat <- read_rdbms( # login = rdbms_login, # query = list(table = "author", fields = NULL, filter = NULL) # ) ## ----eval=FALSE--------------------------------------------------------------- # # SELECT FEW COLUMNS FROM ONE TABLE AND LEFT JOIN WITH ANOTHER TABLE # dat <- 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" # ) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- # LOAD THE DATA OBTAINED FROM THE COMMAND ABOVE dat <- readRDS( system.file("extdata", "server_data.RDS", package = "readepi") ) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- dat |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # CONNECT TO A DHIS2 INSTANCE dhis2_login <- login( type = "dhis2", from = "https://smc.moh.gm/dhis", user_name = "test", password = "Gambia@123" ) ## ----eval=TRUE---------------------------------------------------------------- # GET THE LIST OF ALL ORGANISATION UNITS IN AN HIERARCHICAL ORDER org_units <- get_organisation_units(login = dhis2_login) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- org_units |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # GET THE LIST OF ALL PROGRAMS programs <- get_programs(login = dhis2_login) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- programs |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # GET THE LIST OF ALL DATA ELEMENTS data_elements <- get_data_elements(login = dhis2_login) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- data_elements |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # GET THE LIST OF ALL PROGRAM STAGES FOR A GIVEN PROGRAM ID program_stages <- get_program_stages( login = dhis2_login, program = "E5IUQuHg3Mg", programs = programs ) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- program_stages |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # GET THE LIST OF ORGANISATION UNITS RUNNING THE SPECIFIED PROGRAM target_org_units <- get_program_org_units( login = dhis2_login, program = "E5IUQuHg3Mg", org_units = org_units ) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- target_org_units |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # IMPORT DATA FROM DHIS2 FOR THE SPECIFIED ORGANISATION UNIT AND PROGRAM IDs data <- read_dhis2( login = dhis2_login, org_unit = "GcLhRNAFppR", program = "E5IUQuHg3Mg" ) # IMPORT DATA FROM DHIS2 FOR THE SPECIFIED ORGANISATION UNIT AND PROGRAM NAMES data <- read_dhis2( login = dhis2_login, org_unit = "Keneba", program = "Child Registration & Treatment " ) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- data[1:50, 1:15] |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "300px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE) ## ----eval=TRUE---------------------------------------------------------------- # ESTABLISH THE CONNECTION TO THE SORMAS SYSTEM sormas_login <- login( type = "sormas", from = "https://demo.sormas.org/sormas-rest", user_name = "SurvSup", password = "Lk5R7JXeZSEc" ) # GET THE LIST OF ALL AVAILABLE DISEASES IN THE TEST SORMAS SYSTEM disease_names <- sormas_get_diseases( login = sormas_login ) ## ----eval=TRUE---------------------------------------------------------------- # DOWNLOAD AND SAVE THE DATA DICTIONARY IN YOUR CURRENT DIRECTORY path_to_dictionary <- sormas_get_data_dictionary(path = getwd()) path_to_dictionary ## ----eval=TRUE---------------------------------------------------------------- # FETCH ALL COVID (coronavirus) CASES FROM THE TEST SORMAS INSTANCE FROM THE # BEGINNING OF DATA COLLECTION covid_cases <- read_sormas( login = sormas_login, disease = "coronavirus", since = 0 ) # FETCH ALL COVID (coronavirus) CASES FROM THE TEST SORMAS INSTANCE SINCE # JUNE 01, 2025 covid_cases <- read_sormas( login = sormas_login, disease = "coronavirus", since = as.Date("2025-06-01") ) ## ----echo=FALSE, eval=TRUE---------------------------------------------------- covid_cases[, 1:15] |> kableExtra::kbl() |> kableExtra::kable_paper("striped", font_size = 14, full_width = TRUE) |> kableExtra::scroll_box(height = "200px", width = "100%", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL, fixed_thead = TRUE)