delete in doc function "\link" to prevent CRAN NOTE + build site updated

R/map.R

@@ -8,11 +8,11 @@
 #' 
 #' @param x
 #'   Object of class \code{antaresDataList} created with 
-#'   \code{\link[antaresRead]{readAntares}} and containing areas and links data.
+#'   [antaresRead::readAntares()] and containing areas and links data.
 #'    It can be a list of \code{antaresData} objects. 
 #'    In this case, one chart is created for each object.
 #' @param mapLayout
-#'   Object created with function \code{\link{mapLayout}}
+#'   Object created with function [antaresViz::mapLayout()]
 #' @param colAreaVar
 #'   Name of a variable present in \code{x$areas}. The values of this variable
 #'   are represented by the color of the areas on the map. If \code{"none"}, then
@@ -28,7 +28,7 @@
 #'   \code{logical}. Select \code{sizeAreaVars} using alias ? Default to \code{FALSE}
 #' @param aliasSizeAreaVars
 #'   If \code{typeSizeAreaVars} is set to TRUE, name of alias. You can find the list 
-#'   of alias with the function \code{\link[antaresRead]{showAliases}}
+#'   of alias with the function [antaresRead::showAliases()]
 #' @param areaChartType
 #'   If parameter \code{sizeAreaVars} contains multiple variables, this parameter
 #'   determines the type of representation. Possible values are \code{"bar"} for
@@ -70,7 +70,7 @@
 #'   Title of the map.
 #' @param options
 #'   List of parameters that override some default visual settings. See the
-#'   help of \code{\link{plotMapOptions}}.
+#'   help of [antaresViz::plotMapOptions()].
 #' @param sizeMiniPlot \code{boolean} variable size for miniplot
 #' @param h5requestFiltering Contains arguments used by default for h5 request,
 #'   typically h5requestFiltering = list(mcYears = 3)

R/map_layout.R

@@ -8,19 +8,19 @@
 #' study. The result should then be saved in an external file and be reused.
 #' 
 #' @param layout
-#'   object returned by function \code{\link[antaresRead]{readLayout}}
+#'   object returned by function [antaresRead::readLayout()]
 #' @param what
 #'   Either "areas" or "districts". Indicates what type of object to place
 #'   on the map.
 #' @param map
-#'   An optional \code{\link[sp]{SpatialPolygons}} or 
-#'   \code{\link[sp:SpatialPolygons]{SpatialPolygonsDataFrame}} object. See \code{\link[spMaps:spMaps]{getSpMaps}}
+#'   An optional [sp::SpatialPolygons()] or 
+#'   [sp::SpatialPolygonsDataFrame()] object. See [spMaps::getSpMaps()]
 #'   
 #' @param map_builder \code{logical} Add inputs for build custom map ? Defaut to TRUE.
 #' 
 #' @details 
 #' With \code{map_builder} option, you can build a quiet custom map using \code{spMaps} package. 
-#' This package help you to build \code{\link[sp:SpatialPolygons]{SpatialPolygonsDataFrame}} on Europe. 
+#' This package help you to build [sp::SpatialPolygons()] on Europe. 
 #' Moreover, you can use two options in the module : 
 #' 
 #' \itemize{
@@ -51,7 +51,7 @@
 #' @export
 #' @import spMaps
 #'
-#' @seealso \code{\link{plotMapLayout}}
+#' @seealso [plotMapLayout()]
 mapLayout <- function(layout, what = c("areas", "districts"), map = getSpMaps(), map_builder = TRUE) {
 
   what <- match.arg(what)
@@ -73,7 +73,7 @@ mapLayout <- function(layout, what = c("areas", "districts"), map = getSpMaps(),
 #' Visualize mapLayout output.
 #' 
 #' @param mapLayout
-#'   object returned by function \code{\link{mapLayout}}
+#'   object returned by function [mapLayout()]
 #'   
 #' @examples 
 #' 
@@ -90,7 +90,7 @@ mapLayout <- function(layout, what = c("areas", "districts"), map = getSpMaps(),
 #' 
 #' @export
 #' 
-#' @seealso \code{\link{mapLayout}}
+#' @seealso [mapLayout()]
 plotMapLayout <- function(mapLayout){
 
   if (!is.null(mapLayout$all_coords)){
@@ -513,10 +513,10 @@ changeCoordsServer <- function(input, output, session,
 #' 
 #' This method can be used to visualize the network of an antares study.
 #' It generates an interactive map with a visual representaiton of a
-#' map layout created with function \code{\link{mapLayout}}. 
+#' map layout created with function [mapLayout()]. 
 #' 
 #' @param x
-#'   Object created with function \code{\link{mapLayout}}
+#'   Object created with function [mapLayout()]
 #' @param colAreas
 #'   Vector of colors for areas. By default, the colors used in the Antares
 #'   software are used.
@@ -554,7 +554,7 @@ changeCoordsServer <- function(input, output, session,
 #' @return 
 #'   The function generates an \code{htmlwidget} of class \code{leaflet}. It can
 #'   be stored in a variable and modified with package 
-#'   \code{\link[leaflet]{leaflet}}
+#'   [leaflet::leaflet()]
 #'   
 #' @method plot mapLayout
 #'    

R/map_options.R

@@ -3,7 +3,7 @@
 #' Graphical options for plotMap
 #' 
 #' These functions get and set options that control some graphical aspects 
-#' of maps created with \code{\link{plotMap}}.
+#' of maps created with [plotMap()].
 #' 
 #' @param areaDefaultCol
 #'   default color of areas.

R/mod_rpart.R

@@ -2,7 +2,7 @@
 
 #' Make rpart from antares data
 #' 
-#' @param data an antaresData after use of \code{\link[antaresProcessing]{mergeAllAntaresData}}
+#' @param data an antaresData after use of [antaresProcessing::mergeAllAntaresData]
 #' 
 #' @examples 
 #' \dontrun{

R/plot.R

@@ -61,7 +61,7 @@
 #'   Label of the Y axis.
 #' @param colorScaleOpts
 #'   A list of parameters that control the creation of color scales. It is used
-#'   only for heatmaps. See \code{\link{colorScaleOptions}}() for available
+#'   only for heatmaps. See [colorScaleOptions()] for available
 #'   parameters.
 #' @param xyCompare
 #'   Use when you compare studies, can be "union" or "intersect". If union, all
@@ -106,7 +106,6 @@
 #' 
 #' @examples 
 #' \dontrun{
-#' setSimulationPath(path = path1)
 #' mydata <- readAntares(areas = "all", timeStep = "hourly")
 #' plot(x = mydata)
 #' 
@@ -170,8 +169,9 @@
 #' # Compare 2 studies with argument refStudy 
 #' plot(x = opts, refStudy = opts2)
 #' plot(x = opts, refStudy = opts2, type = "ts", interactive = FALSE, mcYearh5 = 2)
-#' plot(x = opts, refStudy = opts2, type = "ts", dateRange = DR, h5requestFiltering = list(
-#' mcYears = mcYears = mcYearToTest))
+#' plot(x = opts, refStudy = opts2, type = "ts", 
+#'     dateRange = DR, 
+#'     h5requestFiltering = list(mcYears = mcYears = mcYearToTest))
 #' 
 #' 
 #' }

R/savePlotAsPng.R

@@ -13,7 +13,7 @@
 #' @param height
 #'   height of the output file
 #' @param ...
-#'   Other parameters passed to function \code{\link[webshot]{webshot}}
+#'   Other parameters passed to function [webshot::webshot]
 #' 
 #' @return 
 #' The function only creates the required file. Nothing is returned

R/stack_exchanges.R

@@ -11,7 +11,7 @@
 #' 
 #' @param x
 #'   Object of class \code{antaresData} created with function
-#'   \code{\link[antaresRead]{readAntares}}. It is required to contain link data.
+#'   [antaresRead::readAntares]. It is required to contain link data.
 #'   If it also contains area data with column `ROW BAL.`, then exchanges with
 #'   the rest of the world are also displayed on the chart.
 #' @param stack

R/stack_map.R

@@ -6,7 +6,7 @@
 #' 
 #' @param x \code{antaresDataList} antaresDataList contian areas ans links.
 #' @param mapLayout
-#'   Object created with function \code{\link{mapLayout}}
+#'   Object created with function [mapLayout()]
 #'
 #' @examples 
 #' \dontrun{

R/stack_prod.R

@@ -8,13 +8,13 @@
 #' 
 #' @param x
 #'   An object of class \code{antaresData} created with function 
-#'   \code{\link[antaresRead]{readAntares}} containing data for areas and or
+#'   [antaresRead::readAntares()] containing data for areas and or
 #'   districts. it can be a list of \code{antaresData} objects. 
 #'   In this case, one chart is created for each object. 
 #'   Can also contains opts who refer to a h5 file or list of opts.
 #' @param refStudy
 #'   An object of class \code{antaresData} created with function 
-#'   \code{\link[antaresRead]{readAntares}} containing data for areas and or
+#'   [antaresRead::readAntares()] containing data for areas and or
 #'   districts. Can also contains an opts who refer to a h5 file.
 #' @param stack
 #'   Name of the stack to use. One can visualize available stacks with 
@@ -49,7 +49,7 @@
 #' @param compareOpts
 #'   List of options that indicates the number of charts to create and their 
 #'   position. Check out the documentation of 
-#'   \code{\link[manipulateWidget]{compareOptions}} to see available options.
+#'   [manipulateWidget::compareOptions] to see available options.
 #' @param width
 #'   Width of the graph expressed in pixels or in percentage of 
 #'   the parent element. For instance "500px" and "100\%" are valid values.
@@ -62,10 +62,10 @@
 #' @param legend
 #'   Logical value indicating if a legend should be drawn. This argument is 
 #'   usefull when one wants to create a shared legend with
-#'   \code{\link{prodStackLegend}}
+#'   [prodStackLegend()]
 #' @param legendId Id of the legend linked to the graph. This argument is 
 #'   usefull when one wants to create a shared legend with 
-#'   \code{\link{prodStackLegend}}
+#'   [prodStackLegend()]
 #' @param groupId Parameter that can be used to synchronize the horizontal 
 #'   zoom of multiple charts. All charts that need to be synchronized must
 #'   have the same group. 
@@ -76,7 +76,7 @@
 #' @param name
 #'   name of the stack to create or update
 #' @param variables
-#'   A named list of expressions created with \code{\link[base:list]{alist}}. The
+#'   A named list of expressions created with [base::alist]. The
 #'   name of each element is the name of the variable to draw in the stacked
 #'   graph. The element itself is an expression explaining how to compute the
 #'   variable (see examples).
@@ -85,7 +85,7 @@
 #'   \code{variables} is an alias, then this argument should be \code{NULL} in 
 #'   order to use default colors.
 #' @param lines
-#'   A named list of expressions created with \code{\link[base:list]{alist}}
+#'   A named list of expressions created with [base::alist]
 #'   indicating how to compute the curves to display on top of the stacked graph.
 #'   It should be \code{NULL} if there is no curve to trace or if parameter
 #'   \code{variables} is an alias.
@@ -111,7 +111,7 @@
 #' @param tablesh5 \code{character} tables for h5 ("areas" "links", "clusters" or "disticts"). Only for Non interactive mode.
 #' @param language \code{character} language use for label. Defaut to 'en'. Can be 'fr'.
 #' @param hidden \code{logical} Names of input to hide. Defaut to NULL
-#' @param ... Other arguments for \code{\link{manipulateWidget}}
+#' @param ... Other arguments for [manipulateWidget::manipulateWidget]
 #'  
 #' @return 
 #' \code{prodStack} returns an interactive html graphic. If argument
@@ -123,7 +123,7 @@
 #' 
 #' \code{setProdStackAlias} creates or updates a stack alias.
 #' 
-#' @seealso \code{\link{prodStackLegend}}
+#' @seealso [prodStackLegend()]
 #' 
 #' @details 
 #' compare argument can take following values :

cran-comments.md

@@ -26,4 +26,5 @@ Check: tests, Result: NOTE
 new version to fix pb with dependencies `AntaresRead` :  
  - "M1mac" issue  
 
-We have to fix dependencies with package `rhdf5` on this package before to push `antaresRead` 2.7.1
+We have to fix dependencies with package `rhdf5` on this package before to push `antaresRead` 2.7.1
+