Remove \dontrun{} when not strictly required (#61)

* add the examples to the functions documentations * build documentation for show_tables() and visualise_table() * Update CITATION.cff * update function's examples * fix linters * add new lines * remove unnecessary nolint * use explicit URL * update show_example_file documentation * align argument in function documentation * Automatic readme update * add examples and remove dontrun{} when not needed in DHIS2 related functions * add examples and remove dontrun{} when not needed in Fingertips related functions * add examples and remove dontrun{} when not needed in REDCap related functions * add examples and remove dontrun{} when not needed in server related functions * add examples and remove dontrun{} when not needed in readepi related functions * run devtools::document() * remove README.html * rearrange arguments in read_from_readcap example * complete test example for dhis2_get_attributes_from_user * Update _pkgdown.yml to account for read_from_fingertips * update on dhis2_get_attributes_from_user() * Update CITATION.cff * remove examples in internal functions documentation - for functions without dontrun{} * Update R/read_from_fingertips.R remove @nord in the function documentation Co-authored-by: Hugo Gruson <[email protected]> --------- Co-authored-by: Karim-Mane <[email protected]> Co-authored-by: GitHub Action <[email protected]> Co-authored-by: Karim MANE <[email protected]> Co-authored-by: Hugo Gruson <[email protected]>
epiverse-trace · Jan 31, 2024 · 3d715e2 · 3d715e2
1 parent 0eae01f
commit 3d715e2
Show file tree

Hide file tree

Showing 39 changed files with 357 additions and 653 deletions.
diff --git a/CITATION.cff b/CITATION.cff
@@ -55,34 +55,34 @@ references:
   abstract: 'checkmate: Fast and Versatile Argument Checks'
   notes: Imports
   url: https://mllg.github.io/checkmate/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=checkmate
   authors:
   - family-names: Lang
     given-names: Michel
     email: [email protected]
     orcid: https://orcid.org/0000-0001-9754-0393
-  year: '2023'
+  year: '2024'
 - type: software
   title: DBI
   abstract: 'DBI: R Database Interface'
   notes: Imports
   url: https://dbi.r-dbi.org
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=DBI
   authors:
   - name: R Special Interest Group on Databases (R-SIG-DB)
   - family-names: Wickham
     given-names: Hadley
   - family-names: Müller
     given-names: Kirill
-    email: [email protected]
+    email: [email protected]
     orcid: https://orcid.org/0000-0002-1416-3412
-  year: '2023'
+  year: '2024'
 - type: software
   title: dplyr
   abstract: 'dplyr: A Grammar of Data Manipulation'
   notes: Imports
   url: https://dplyr.tidyverse.org
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=dplyr
   authors:
   - family-names: Wickham
     given-names: Hadley
@@ -100,7 +100,7 @@ references:
     given-names: Davis
     email: [email protected]
     orcid: https://orcid.org/0000-0003-4777-038X
-  year: '2023'
+  year: '2024'
 - type: software
   title: fingertipsR
   abstract: 'fingertipsR: Fingertips Data for Public Health'
@@ -115,69 +115,69 @@ references:
     email: [email protected]
   - family-names: Flowers
     given-names: Julian
-  year: '2023'
+  year: '2024'
   version: '>= 1.0.10.9001'
 - type: software
   title: glue
   abstract: 'glue: Interpreted String Literals'
   notes: Imports
   url: https://glue.tidyverse.org/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=glue
   authors:
   - family-names: Hester
     given-names: Jim
     orcid: https://orcid.org/0000-0002-2739-7082
   - family-names: Bryan
     given-names: Jennifer
-    email: jenny@rstudio.com
+    email: jenny@posit.co
     orcid: https://orcid.org/0000-0002-6983-2759
-  year: '2023'
+  year: '2024'
 - type: software
   title: httr
   abstract: 'httr: Tools for Working with URLs and HTTP'
   notes: Imports
   url: https://httr.r-lib.org/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=httr
   authors:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: magrittr
   abstract: 'magrittr: A Forward-Pipe Operator for R'
   notes: Imports
   url: https://magrittr.tidyverse.org
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=magrittr
   authors:
   - family-names: Bache
     given-names: Stefan Milton
     email: [email protected]
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: odbc
   abstract: 'odbc: Connect to ODBC Compatible Databases (using the DBI Interface)'
   notes: Imports
-  url: https://r-dbi.github.io/odbc/
-  repository: https://packagemanager.posit.co/cran/latest/
+  url: https://odbc.r-dbi.org
+  repository: https://CRAN.R-project.org/package=odbc
   authors:
   - family-names: Hester
     given-names: Jim
   - family-names: Wickham
     given-names: Hadley
-    email: hadley@rstudio.com
+    email: hadley@posit.co
   - family-names: Gjoneski
     given-names: Oliver
-  year: '2023'
+  year: '2024'
 - type: software
   title: pool
   abstract: 'pool: Object Pooling'
   notes: Imports
   url: http://rstudio.github.io/pool/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=pool
   authors:
   - family-names: Cheng
     given-names: Joe
@@ -187,25 +187,25 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
 - type: software
   title: REDCapR
   abstract: 'REDCapR: Interaction Between R and REDCap'
   notes: Imports
   url: https://ouhscbbmc.github.io/REDCapR/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=REDCapR
   authors:
   - family-names: Beasley
     given-names: Will
     email: [email protected]
     orcid: https://orcid.org/0000-0002-5613-5006
-  year: '2023'
+  year: '2024'
 - type: software
   title: RMySQL
   abstract: 'RMySQL: Database Interface and ''MySQL'' Driver for R'
   notes: Imports
   url: https://downloads.mariadb.org/connector-c/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=RMySQL
   authors:
   - family-names: Ooms
     given-names: Jeroen
@@ -220,19 +220,19 @@ references:
     email: [email protected]
   - family-names: Horner
     given-names: Jeffrey
-  year: '2023'
+  year: '2024'
 - type: software
   title: httptest
   abstract: 'httptest: A Test Environment for HTTP Requests'
   notes: Suggests
   url: https://enpiar.com/r/httptest/
-  repository: https://packagemanager.posit.co/cran/latest/
+  repository: https://CRAN.R-project.org/package=httptest
   authors:
   - family-names: Richardson
     given-names: Neal
     email: [email protected]
     orcid: https://orcid.org/0009-0002-7992-3520
-  year: '2023'
+  year: '2024'
 - type: software
   title: knitr
   abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
@@ -244,7 +244,7 @@ references:
     given-names: Yihui
     email: [email protected]
     orcid: https://orcid.org/0000-0003-0645-5666
-  year: '2023'
+  year: '2024'
 - type: software
   title: rmarkdown
   abstract: 'rmarkdown: Dynamic Documents for R'
@@ -287,7 +287,7 @@ references:
     given-names: Richard
     email: [email protected]
     orcid: https://orcid.org/0000-0003-3925-190X
-  year: '2023'
+  year: '2024'
 - type: software
   title: testthat
   abstract: 'testthat: Unit Testing for R'
@@ -298,7 +298,7 @@ references:
   - family-names: Wickham
     given-names: Hadley
     email: [email protected]
-  year: '2023'
+  year: '2024'
   version: '>= 3.0.0'
 identifiers:
 - type: url

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -46,6 +46,7 @@ Remotes:
     rOpenSci/fingertipsR
 Config/Needs/website: epiverse-trace/epiversetheme
 Config/testthat/edition: 3
+SystemRequirements: odbc, libmariadbclient-dev
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
diff --git a/R/check_dhis2_attributes-helpers.R b/R/check_dhis2_attributes-helpers.R
@@ -15,7 +15,16 @@
 #' @return an object of class `data.frame` that contains the information of
 #'    interest.
 #' @keywords internal
-
+#' @examples
+#' \dontrun{
+#'   response <- dhis2_make_api_request(
+#'     base_url  = file.path("https:/", "play.dhis2.org", "dev"),
+#'     user_name = "admin",
+#'     password  = "district",
+#'     which     = "dataElements"
+#'   )
+#' }
+#'
 dhis2_make_api_request <- function(base_url,
                                    user_name,
                                    password,
@@ -59,15 +68,14 @@ dhis2_make_api_request <- function(base_url,
 #' @examples
 #' \dontrun{
 #' result <- dhis2_get_relevant_attributes(
-#'   base_url = "https://play.dhis2.org/dev/",
-#'   user_name = "admin",
-#'   password = "district",
+#'   base_url     = "https://play.dhis2.org/dev/",
+#'   user_name    = "admin",
+#'   password     = "district",
 #'   attribute_id = "pBOMPrpg1QX,BfMAe6Itzgt",
-#'   which = "dataSets"
+#'   which        = "dataSets"
 #' )
 #' }
 #' @keywords internal
-
 dhis2_get_relevant_attributes <- function(base_url,
                                           user_name,
                                           password,

diff --git a/R/read_from_dhis2-helpers.R b/R/read_from_dhis2-helpers.R
@@ -11,10 +11,17 @@
 #' @return a message if the dhis2_login was successful,
 #'    throws an error otherwise.
 #'
-#' @return a message if the login was successfull, thows an error otherwise.
+#' @return a message if the login was successful, throws an error otherwise.
 #'
 #' @keywords internal
-#'
+#' @examples
+#' \dontrun{
+#'   dhis2_login(
+#'     base_url  = file.path("https:/", "play.dhis2.org", "dev"),
+#'     user_name = "admin",
+#'     password  = "district"
+#'   )
+#' }
 dhis2_login <- function(base_url,
                         user_name,
                         password) {
@@ -43,7 +50,7 @@ dhis2_login <- function(base_url,
 #' results <- dhis2_subset_fields(
 #'   data = readepi(
 #'     credentials_file   = system.file("extdata", "test.ini",
-#'     package = "readepi"),
+#'                                      package = "readepi"),
 #'     data_source        = "https://play.dhis2.org/dev",
 #'     dataset            = "pBOMPrpg1QX,BfMAe6Itzgt",
 #'     organisation_unit  = "DiszpKrYNg8",
@@ -99,8 +106,7 @@ dhis2_subset_fields <- function(data,
 #' result <- dhis2_subset_records(
 #'   data = readepi(
 #'     credentials_file   = system.file("extdata", "test.ini",
-#'       package = "readepi"
-#'     ),
+#'                                      package = "readepi"),
 #'     data_source        = "https://play.dhis2.org/dev",
 #'     dataset            = "pBOMPrpg1QX",
 #'     organisation_unit  = "DiszpKrYNg8",

diff --git a/R/read_from_dhis2.R b/R/read_from_dhis2.R
@@ -20,7 +20,6 @@
 #' @returns a `list` of 1 element of type `data frame`.
 #' @keywords internal
 #'
-#'
 #' @examples
 #' \dontrun{
 #' data <- read_from_dhis2(

diff --git a/R/read_from_fingertips-helpers.R b/R/read_from_fingertips-helpers.R
@@ -250,6 +250,18 @@ fingertips_get_id_from_dm_name <- function(metadata =
 #' @return a `list` of 2 elements of type `character` and `numeric`. These are
 #'    the `profile name` and their correspondent indexes.
 #' @keywords internal
+#' @examples
+#' \dontrun{
+#'   res <- fingertips_get_profile_name(
+#'     profile_id   = 19L,
+#'     profile_name = "Public Health Outcomes Framework",
+#'     metadata = list(
+#'       indicator_profile_domain = fingertipsR::indicators(),
+#'       indicator_ids_names      = fingertipsR::indicators_unique(),
+#'       area_type                = fingertipsR::area_types()
+#'     )
+#'   )
+#' }
 #'
 fingertips_get_profile_name <- function(metadata =
                                           list(indicator_profile_domain =
@@ -282,8 +294,7 @@ fingertips_get_profile_name <- function(metadata =
                    profile_id)
   } else if (!is.null(profile_name) && is.null(profile_id)) {
     profile_name <- unlist(strsplit(profile_name, ",", fixed = TRUE))
-    idx <- which(
-                 metadata[["indicator_profile_domain"]][["ProfileName"]] ==
+    idx <- which(metadata[["indicator_profile_domain"]][["ProfileName"]] ==
                    profile_name)
   }
 

diff --git a/R/read_from_fingertips.R b/R/read_from_fingertips.R
@@ -20,6 +20,8 @@
 #' @return a `list` of 1 element of type `data.frame`. This contains the
 #'    imported dataset of interest.
 #'
+#' @keywords internal
+#'
 #' @examples
 #' \dontrun{
 #'   data <- read_from_fingertips(indicator_id = 90362, area_type_id = 202)