## ----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) ## ----rdbms-login, eval=FALSE-------------------------------------------------- # # 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 # ) ## ----display-tables, eval=FALSE----------------------------------------------- # # DISPLAY THE LIST OF TABLES FROM A DATABASE OF INTEREST # tables <- show_tables(login = rdbms_login) # head(tables) ## ----rdbms-query, 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" # ) ## ----rdbms-data, 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) # ) ## ----rdbms-filter, 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" # ) ## ----pak-dat, echo=FALSE, eval=TRUE------------------------------------------- # LOAD THE DATA OBTAINED FROM THE COMMAND ABOVE dat <- readRDS( system.file("extdata", "server_data.RDS", package = "readepi") ) ## ----dispaly-data, 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) ## ----dhis2-login, eval=identical(Sys.getenv("NOT_CRAN"), "true")-------------- # # CONNECT TO A DHIS2 INSTANCE # dhis2_login <- login( # type = "dhis2", # from = "https://play.im.dhis2.org/stable-2-41-8", # user_name = "admin", # password = "district" # ) ## ----org-units, eval=identical(Sys.getenv("NOT_CRAN"), "true")---------------- # # GET THE LIST OF ALL ORGANISATION UNITS IN AN HIERARCHICAL ORDER # org_units <- get_organisation_units(login = dhis2_login) ## ----display-org-units, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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) ## ----dhis2-programs, eval=identical(Sys.getenv("NOT_CRAN"), "true")----------- # # GET THE LIST OF ALL PROGRAMS # programs <- get_programs(login = dhis2_login) ## ----display-programs, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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) ## ----dhis2-elements, eval=identical(Sys.getenv("NOT_CRAN"), "true")----------- # # GET THE LIST OF ALL DATA ELEMENTS # data_elements <- get_data_elements(login = dhis2_login) ## ----display-elements, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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) ## ----dhis2-stages, eval=identical(Sys.getenv("NOT_CRAN"), "true")------------- # # GET THE LIST OF ALL PROGRAM STAGES FOR A GIVEN PROGRAM ID # program_stages <- get_program_stages( # login = dhis2_login, # program = "IpHINAT79UW", # programs = programs # ) ## ----display-stages, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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) ## ----target-units, eval=identical(Sys.getenv("NOT_CRAN"), "true")------------- # # GET THE LIST OF ORGANISATION UNITS RUNNING THE SPECIFIED PROGRAM # target_org_units <- get_program_org_units( # login = dhis2_login, # program = "IpHINAT79UW", # org_units = org_units # ) ## ----display-target-units, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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) ## ----org-codes, eval=identical(Sys.getenv("NOT_CRAN"), "true")---------------- # # IMPORT DATA FROM DHIS2 FOR THE SPECIFIED ORGANISATION UNIT AND PROGRAM IDs # data <- read_dhis2( # login = dhis2_login, # org_unit = "XjpmsLNjyrz", # program = "IpHINAT79UW" # ) ## ----display-codes, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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) ## ----sormas-login, eval=identical(Sys.getenv("NOT_CRAN"), "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 # ) ## ----sormas-dict, eval=identical(Sys.getenv("NOT_CRAN"), "true")-------------- # # DOWNLOAD AND SAVE THE DATA DICTIONARY IN YOUR CURRENT DIRECTORY # path_to_dictionary <- sormas_get_data_dictionary(path = getwd()) # path_to_dictionary ## ----sormas-cases, eval=identical(Sys.getenv("NOT_CRAN"), "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") # ) ## ----display-cases, echo=FALSE, eval=identical(Sys.getenv("NOT_CRAN"), "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)