Merge pull request #81 from inbo/deprecate

deprecate functions that are moved to inbodb

.travis.yml

@@ -4,9 +4,6 @@ cache: packages
 r_packages:
   - pkgdown
 
-r_binary_packages:
-  - rgdal
-
 apt_packages:
   - libudunits2-dev
   - libgdal1-dev

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: inborutils
 Title: Collection of Useful R Utilities
-Version: 0.1.0.9072
+Version: 0.1.0.9081
 Description: While working on research projects, typical small functionalities 
     are useful across these projects. Instead of copy-pasting these functions in 
     all indidivual project repositories/folders, this package collects these 

R/connect_inbo_dbase.R

@@ -12,19 +12,31 @@
 #'
 #' @return odbc connection
 #'
+#' @examples
+#' \dontrun{
+#' connection <- connect_inbo_dbase("D0021_00_userFlora")
+#' connection <- connect_inbo_dbase("W0003_00_Lims")
+#' }
+#'
+#' @name connect_inbo_dbase-deprecated
+#' @usage connect_inbo_dbase(database_name)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section connect_inbo_dbase:
+#' For \code{connect_inbo_dbase}, use [inbodb::connect_inbo_dbase()](https://inbo.github.io/inbodb/reference/connect_inbo_dbase.html)
 #' @export
 #'
 #' @importFrom DBI dbGetQuery dbConnect dbListTables
 #' @importFrom odbc odbc odbcListDrivers
 #' @importFrom utils tail
 #'
-#' @examples
-#' \dontrun{
-#' connection <- connect_inbo_dbase("D0021_00_userFlora")
-#' connection <- connect_inbo_dbase("W0003_00_Lims")
-#' }
 connect_inbo_dbase <- function(database_name) {
 
+  .Deprecated("inbodb::connect_inbo_dbase()", package = "inborutils")
+
     # datawarehouse databases (sql08) start with an M, S or W; most
     # transactional (sql07) with a D (by agreement with dba's)
     if (any(startsWith(database_name, c("M", "S", "W")))) {

R/florabank_queries.R

@@ -25,21 +25,6 @@ globalVariables("%LIKE%")
 #' Omschrijving en Rekenwaarde. The first four variables identify the taxon,
 #' the latter four variables relate to the taxon traits.
 #'
-#' @importFrom dplyr
-#' tbl
-#' collect
-#' distinct
-#' pull
-#' %>%
-#' inner_join
-#' left_join
-#' filter
-#' select
-#' rename
-#' @importFrom rlang .data
-#' @importFrom assertthat assert_that
-#'
-#' @export
 #' @family florabank
 #' @examples
 #' \dontrun{
@@ -65,9 +50,37 @@ globalVariables("%LIKE%")
 #' #disconnect from florabank
 #' dbDisconnect(db_connectie)
 #' }
+#'
+#' @name florabank_traits-deprecated
+#' @usage florabank_traits(connection, trait_name, collect = FALSE)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section florabank_traits:
+#' For \code{florabank_traits}, use [inbodb::florabank_traits()](https://inbo.github.io/inbodb/reference/get_florabank_traits.html)
+#'
+#' @importFrom dplyr
+#' tbl
+#' collect
+#' distinct
+#' pull
+#' %>%
+#' inner_join
+#' left_join
+#' filter
+#' select
+#' rename
+#' @importFrom rlang .data
+#' @importFrom assertthat assert_that
+#'
+#' @export
 
 florabank_traits <- function(connection, trait_name, collect = FALSE) {
 
+  .Deprecated("inbodb::get_florabank_traits()", package = "inborutils")
+
   assert_that(inherits(connection, what = "Microsoft SQL Server"),
               msg = "Not a connection object to database.")
   assert_that(connection@info$dbname == "D0021_00_userFlora")
@@ -149,14 +162,6 @@ florabank_traits <- function(connection, trait_name, collect = FALSE) {
 #' "Toponiem", "CommentaarTaxon", "CommentaarHabitat",
 #' "WaarnemingID", "X_waarneming", "Y_waarneming", "X_meting", "Y_meting"
 #'
-#' @importFrom glue glue_sql
-#' @importFrom assertthat assert_that
-#' @importFrom dplyr
-#' tbl
-#' collect
-#' sql
-#'
-#' @export
 #' @family florabank
 #' @examples
 #' \dontrun{
@@ -204,10 +209,31 @@ florabank_traits <- function(connection, trait_name, collect = FALSE) {
 #' # disconnect from florabank
 #' dbDisconnect(db_connectie)
 #' }
+#'
+#' @name florabank_observations-deprecated
+#' @usage florabank_observations(connection, names, fixed = FALSE, collect = FALSE)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section florabank_observations:
+#' For \code{florabank_observations}, use [inbodb::florabank_observations()](https://inbo.github.io/inbodb/reference/get_florabank_observations.html)
+#'
+#' @importFrom glue glue_sql
+#' @importFrom assertthat assert_that
+#' @importFrom dplyr
+#' tbl
+#' collect
+#' sql
+#'
+#' @export
 
 florabank_observations <- function(connection, names, fixed = FALSE,
                                    collect = FALSE) {
 
+  .Deprecated("inbodb::get_florabank_observations()", package = "inborutils")
+
   assert_that(inherits(connection, what = "Microsoft SQL Server"),
               msg = "Not a connection object to database.")
   assert_that(connection@info$dbname == "D0021_00_userFlora")
@@ -321,12 +347,6 @@ florabank_observations <- function(connection, names, fixed = FALSE,
 #' number of unique nested squares where the taxon was observed for that year
 #' and 4 x 4 square combination.
 #'
-#' @importFrom glue glue_sql
-#' @importFrom assertthat assert_that
-#' @importFrom dplyr %>% group_by summarize n ungroup sql collect
-#' @importFrom rlang .data
-#'
-#' @export
 #' @family florabank
 #' @examples
 #' \dontrun{
@@ -346,6 +366,27 @@ florabank_observations <- function(connection, names, fixed = FALSE,
 #' # disconnect from florabank
 #' dbDisconnect(db_connectie)
 #' }
+#'
+#' @name florabank_taxon_ifbl_year-deprecated
+#' @usage florabank_taxon_ifbl_year(connection,
+#'   starting_year = 2010, ifbl_resolution = c("1km-by-1km", "4km-by-4km"),
+#'   taxongroup =
+#'     c("Vaatplanten", "Mossen", "Lichenen (korstmossen)", "Kranswieren"),
+#'   collect = FALSE)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section florabank_taxon_ifbl_year:
+#' For \code{florabank_taxon_ifbl_year}, use [inbodb::florabank_taxon_ifbl_year()](https://inbo.github.io/inbodb/reference/get_florabank_taxon_ifbl_year.html)
+#'
+#' @importFrom glue glue_sql
+#' @importFrom assertthat assert_that
+#' @importFrom dplyr %>% group_by summarize n ungroup sql collect
+#' @importFrom rlang .data
+#'
+#' @export
 
 florabank_taxon_ifbl_year <- function(connection,
                                       starting_year = 2010,
@@ -357,6 +398,8 @@ florabank_taxon_ifbl_year <- function(connection,
                                                      "Kranswieren"),
                                       collect = FALSE) {
 
+  .Deprecated("inbodb::get_florabank_taxon_ifbl_year()", package = "inborutils")
+
   assert_that(inherits(connection, what = "Microsoft SQL Server"),
               msg = "Not a connection object to database.")
   assert_that(connection@info$dbname == "D0021_00_userFlora")

R/inborutils-deprecated.R

@@ -0,0 +1,8 @@
+#' @title Deprecated functions in package \pkg{inborutils}
+#' @description The functions listed below are moved to package \pkg{inbodb}
+#'   and deprecated in \pkg{inborutils}. They will be defunct here in the near
+#'   future. Help pages for deprecated functions are available at
+#'   \code{help("<function>-deprecated")}
+#' @name inborutils-deprecated
+#' @keywords internal
+NULL

R/inboveg_classification.R

@@ -24,12 +24,6 @@
 #' N2000-list, LocalClassification, Description of the Habitattype, Cover-code,
 #' Cover in percentage.
 #'
-#' @importFrom glue glue_sql
-#' @importFrom DBI dbGetQuery
-#' @importFrom assertthat assert_that
-#' @importFrom dplyr collect tbl sql
-#'
-#' @export
 #' @family inboveg
 #' @examples
 #' \dontrun{
@@ -46,12 +40,31 @@
 #' dbDisconnect(con)
 #' rm(con)
 #' }
+#'
+#' @name inboveg_classification-deprecated
+#' @usage inboveg_classification(connection, survey_name, classif, collect = FALSE)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section inboveg_classification:
+#' For \code{inboveg_classification}, use [inbodb::inboveg_classification()](https://inbo.github.io/inbodb/reference/get_inboveg_classification.html)
+#'
+#' @importFrom glue glue_sql
+#' @importFrom DBI dbGetQuery
+#' @importFrom assertthat assert_that
+#' @importFrom dplyr collect tbl sql
+#'
+#' @export
 
 inboveg_classification <- function(connection,
                                    survey_name,
                                    classif,
                                    collect = FALSE) {
 
+  .Deprecated("inbodb::get_inboveg_classification()", package = "inborutils")
+
   assert_that(inherits(connection, what = "Microsoft SQL Server"),
               msg = "Not a connection object to database.")
 

R/inboveg_header.R

@@ -27,12 +27,6 @@
 #' Latitude, Longitude, Area (in m2), Length (in cm), Width (in cm), VagueDateType,
 #' VagueDateBegin, VagueDateEnd, SurveyId, RecTypeID.
 #'
-#' @importFrom glue glue_sql
-#' @importFrom DBI dbGetQuery
-#' @importFrom assertthat assert_that
-#' @importFrom dplyr collect tbl sql
-#'
-#' @export
 #' @family inboveg
 #' @examples
 #' \dontrun{
@@ -54,6 +48,24 @@
 #' dbDisconnect(con)
 #' rm(con)
 #' }
+#'
+#' @name inboveg_header-deprecated
+#' @usage inboveg_header(connection, survey_name, rec_type, multiple = FALSE,
+#'   collect = FALSE)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section inboveg_header:
+#' For \code{inboveg_header}, use [inbodb::inboveg_header()](https://inbo.github.io/inbodb/reference/get_inboveg_header.html)
+#'
+#' @importFrom glue glue_sql
+#' @importFrom DBI dbGetQuery
+#' @importFrom assertthat assert_that
+#' @importFrom dplyr collect tbl sql
+#'
+#' @export
 
 
 inboveg_header <- function(connection,
@@ -62,6 +74,8 @@ inboveg_header <- function(connection,
                            multiple = FALSE,
                            collect = FALSE) {
 
+  .Deprecated("inbodb::get_inboveg_classification()", package = "inborutils")
+
   assert_that(inherits(connection, what = "Microsoft SQL Server"),
               msg = "Not a connection object to database.")
 

R/inboveg_qualifiers.R

@@ -22,11 +22,6 @@
 #' 2nd Description, 3rd QualifierCode, 3rd Description, Elucidation, in case
 #' qualifier is 'NotSure', ParentID, QualifierResource
 #'
-#' @importFrom glue glue_sql
-#' @importFrom DBI dbGetQuery
-#' @importFrom assertthat assert_that
-#'
-#' @export
 #' @family inboveg
 #' @examples
 #' \dontrun{
@@ -52,13 +47,31 @@
 #' rm(con)
 #' }
 #'
+#' @name inboveg_qualifiers-deprecated
+#' @usage inboveg_qualifiers(connection, survey_name, qualifier_type,
+#'   multiple = FALSE)
+#' @seealso \code{\link{inborutils-deprecated}}
+#' @keywords internal
+NULL
+
+#' @rdname inborutils-deprecated
+#' @section inboveg_qualifiers:
+#' For \code{inboveg_qualifiers}, use [inbodb::inboveg_qualifiers()](https://inbo.github.io/inbodb/reference/get_inboveg_qualifiers.html)
+#'
+#' @importFrom glue glue_sql
+#' @importFrom DBI dbGetQuery
+#' @importFrom assertthat assert_that
+#'
+#' @export
 
 
 inboveg_qualifiers <- function(connection,
                                survey_name,
                                qualifier_type,
                                multiple = FALSE) {
 
+  .Deprecated("inbodb::get_inboveg_classification()", package = "inborutils")
+
   assert_that(inherits(connection, what = "Microsoft SQL Server"),
               msg = "Not a connection object to database.")