From a6b98fe60ad5a73cd3cdba3580c9576b6186d3b1 Mon Sep 17 00:00:00 2001
From: unknown <kirar.kartikeya1@gmail.com>
Date: Mon, 29 Jan 2024 18:22:45 +0530
Subject: [PATCH] removing backtics from functions.

---
 R/dummy_functions.R              | 2 +-
 R/init.R                         | 7 +++----
 R/module_snapshot_manager.R      | 4 ++--
 R/modules.R                      | 6 +++---
 R/modules_debugging.R            | 2 +-
 R/reporter_previewer_module.R    | 8 ++++----
 R/teal.R                         | 2 +-
 R/teal_data_module.R             | 2 +-
 R/teal_reporter.R                | 6 +++---
 R/teal_slices.R                  | 4 ++--
 man/example_module.Rd            | 2 +-
 man/filter_calls_module.Rd       | 2 +-
 man/init.Rd                      | 3 +--
 man/module.Rd                    | 2 +-
 man/reporter_previewer_module.Rd | 2 +-
 man/snapshot_manager_module.Rd   | 4 ++--
 man/srv_teal_with_splash.Rd      | 3 +--
 man/teal-package.Rd              | 2 +-
 man/teal_data_module.Rd          | 2 +-
 man/teal_slices.Rd               | 4 ++--
 man/ui_teal_with_splash.Rd       | 3 +--
 21 files changed, 34 insertions(+), 38 deletions(-)

diff --git a/R/dummy_functions.R b/R/dummy_functions.R
index 6c03f07bb3..51c9c2e17a 100644
--- a/R/dummy_functions.R
+++ b/R/dummy_functions.R
@@ -3,7 +3,7 @@
 #' `r lifecycle::badge("experimental")`
 #'
 #' @inheritParams module
-#' @return A `teal` module which can be included in the `modules` argument to [`teal::init()`].
+#' @return A `teal` module which can be included in the `modules` argument to [init()].
 #' @examples
 #' app <- init(
 #'   data = teal_data(IRIS = iris, MTCARS = mtcars),
diff --git a/R/init.R b/R/init.R
index 4351a7e8e3..f8fa21dfc9 100644
--- a/R/init.R
+++ b/R/init.R
@@ -16,20 +16,19 @@
 #' defaults from the `teal_data` environment will be used.
 #'
 #' @param data (`teal_data` or `teal_data_module`)
-#' `teal_data` object as returned by [`teal.data::teal_data()`] or `teal_data_module`.
 #' @param modules (`list` or `teal_modules` or `teal_module`)
 #'   nested list of `teal_modules` or `teal_module` objects or a single
 #'   `teal_modules` or `teal_module` object. These are the specific output modules which
-#'   will be displayed in the `teal` application. See [`modules()`] and [`module()`] for
+#'   will be displayed in the `teal` application. See [modules()] and [module()] for
 #'   more details.
 #' @param title (`shiny.tag` or `character(1)`)
 #'   The browser window title. Defaults to a title "teal app" with the icon of NEST.
 #'   Can be created using the `build_app_title()` or
 #'   by passing a valid `shiny.tag` which is a head tag with title and link tag.
 #' @param filter (`teal_slices`)
-#'   Specification of initial filter. Filters can be specified using [`teal::teal_slices()`].
+#'   Specification of initial filter. Filters can be specified using [teal::teal_slices()].
 #'   Old way of specifying filters through a list is deprecated and will be removed in the
-#'   next release. Please fix your applications to use [`teal::teal_slices()`].
+#'   next release. Please fix your applications to use [teal::teal_slices()].
 #' @param header (`shiny.tag` or `character(1)`)
 #'   The header of the app.
 #' @param footer (`shiny.tag` or `character(1)`)
diff --git a/R/module_snapshot_manager.R b/R/module_snapshot_manager.R
index 4287dd30bd..0840158803 100644
--- a/R/module_snapshot_manager.R
+++ b/R/module_snapshot_manager.R
@@ -40,7 +40,7 @@
 #' The snapshot contains the `mapping` attribute of the initial application state
 #' (or one that has been restored), which may not reflect the current one,
 #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that,
-#' when passed to the `mapping` argument of [`teal::teal_slices`], would result in the current mapping.
+#' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping.
 #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list.
 #'
 #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object.
@@ -49,7 +49,7 @@
 #' The snapshot is then set as the current content of `slices_global`.
 #'
 #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring,
-#' and then saved to file with [`slices_store`].
+#' and then saved to file with [slices_store()].
 #'
 #' When a snapshot is uploaded, it will first be added to storage just like a newly created one,
 #' and then used to restore app state much like a snapshot taken from storage.
diff --git a/R/modules.R b/R/modules.R
index 6b653f5b78..f86c66968a 100644
--- a/R/modules.R
+++ b/R/modules.R
@@ -173,10 +173,10 @@ is_arg_used <- function(modules, arg) {
 #' This function embeds a `shiny` module inside a `teal` application. One `teal_module` maps to one `shiny` module.
 #'
 #' @param label (`character(1)`) Label shown in the navigation item for the module. Any label possible except
-#'  `"global_filters"` - read more in `mapping` argument of [`teal::teal_slices`].
+#'  `"global_filters"` - read more in `mapping` argument of [teal_slices()].
 #' @param server (`function`) `shiny` module with following arguments:
-#'  - `id` - `teal` will set proper `shiny` namespace for this module (see [`shiny::moduleServer()`]).
-#'  - `input`, `output`, `session` - (not recommended) then [`shiny::callModule()`] will be used to call a module.
+#'  - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]).
+#'  - `input`, `output`, `session` - (not recommended) then [shiny::callModule()] will be used to call a module.
 #'  - `data` (optional) module will receive a `teal_data` object, a list of reactive (filtered) data specified in
 #'     the `filters` argument.
 #'  - `datasets` (optional) module will receive `FilteredData`. (See [`teal.slice::FilteredData`]).
diff --git a/R/modules_debugging.R b/R/modules_debugging.R
index 2144eef13a..2b9aaa31c5 100644
--- a/R/modules_debugging.R
+++ b/R/modules_debugging.R
@@ -5,7 +5,7 @@
 #' Dummy module to show the filter calls generated by the right encoding panel
 #'
 #' Please do not remove, this is useful for debugging `teal` without
-#' dependencies and simplifies [`devtools::load_all`] which otherwise fails
+#' dependencies and simplifies [devtools::load_all()] which otherwise fails
 #' and avoids session restarts!
 #'
 #' @param label `character` label of module
diff --git a/R/reporter_previewer_module.R b/R/reporter_previewer_module.R
index 8b7e701c76..eb9f51f8fc 100644
--- a/R/reporter_previewer_module.R
+++ b/R/reporter_previewer_module.R
@@ -2,17 +2,17 @@
 #'
 #' @description `r lifecycle::badge("experimental")`
 #'
-#' This function wraps [`teal.reporter::reporter_previewer_ui()`] and
-#' [`teal.reporter::reporter_previewer_srv()`] into a `teal_module` to be
+#' This function wraps [teal.reporter::reporter_previewer_ui()] and
+#' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be
 #' used in `teal` applications.
 #'
-#' If you are creating a `teal` application using [`teal::init()`] then this
+#' If you are creating a `teal` application using [init()] then this
 #' module will be added to your application automatically if any of your `teal modules`
 #' support report generation.
 #'
 #' @inheritParams module
 #' @param server_args (named `list`)
-#'  Arguments passed to [`teal.reporter::reporter_previewer_srv()`].
+#'  Arguments passed to [teal.reporter::reporter_previewer_srv()].
 #' @return `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer
 #' functionality.
 #' @export
diff --git a/R/teal.R b/R/teal.R
index 0851568ebd..0d1b5d3d78 100644
--- a/R/teal.R
+++ b/R/teal.R
@@ -4,7 +4,7 @@
 #' interactive data analysis environment.
 #'
 #' To learn mode about the package either read the project website at
-#' [project website](https://insightsengineering.github.io/teal/latest-tag/) or read the [`init`] manual pages.
+#' [project website](https://insightsengineering.github.io/teal/latest-tag/) or read the [init()] manual pages.
 #'
 #' @keywords internal
 "_PACKAGE"
diff --git a/R/teal_data_module.R b/R/teal_data_module.R
index 46735f0e92..37fce73808 100644
--- a/R/teal_data_module.R
+++ b/R/teal_data_module.R
@@ -51,7 +51,7 @@
 #'
 #' @name teal_data_module
 #'
-#' @seealso [`teal_data-class`], [`teal.code::qenv()`]
+#' @seealso [teal.data::`teal_data-class`], [teal.code::qenv()]
 #'
 #' @export
 teal_data_module <- function(ui, server) {
diff --git a/R/teal_reporter.R b/R/teal_reporter.R
index 5e4b3b6913..6cb8df17a2 100644
--- a/R/teal_reporter.R
+++ b/R/teal_reporter.R
@@ -36,7 +36,7 @@ TealReportCard <- R6::R6Class( # nolint: object_name_linter.
     #'  the default `yaml::as.yaml` to format the list.
     #'  If the filter state list is empty, nothing is appended to the `content`.
     #'
-    #' @param fs (`teal_slices`) object returned from [`teal_slices()`] function.
+    #' @param fs (`teal_slices`) object returned from [teal_slices()] function.
     #' @return invisibly self
     append_fs = function(fs) {
       checkmate::assert_class(fs, "teal_slices")
@@ -81,7 +81,7 @@ TealSlicesBlock <- R6::R6Class( # nolint: object_name_linter.
     #'
     #' @details Returns a `TealSlicesBlock` object with no content and no parameters.
     #'
-    #' @param content (`teal_slices`) object returned from [`teal_slices()`] function.
+    #' @param content (`teal_slices`) object returned from [teal_slices()] function.
     #' @param style (`character(1)`) string specifying style to apply.
     #'
     #' @return `TealSlicesBlock`
@@ -99,7 +99,7 @@ TealSlicesBlock <- R6::R6Class( # nolint: object_name_linter.
     #' When `selected` field in `teal_slice` object is a range, then it is displayed as a "min"
     #'
     #'
-    #' @param content (`teal_slices`) object returned from [`teal_slices()`] function.
+    #' @param content (`teal_slices`) object returned from [teal_slices()] function.
     #' @return invisibly self
     set_content = function(content) {
       checkmate::assert_class(content, "teal_slices")
diff --git a/R/teal_slices.R b/R/teal_slices.R
index ae4ad906c3..accd5b4d26 100644
--- a/R/teal_slices.R
+++ b/R/teal_slices.R
@@ -19,7 +19,7 @@
 #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._
 #'
 #'  (named `list`) specifies which filters will be active in which modules on app start.
-#'  Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice()`]).
+#'  Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]).
 #'  Names of the list should correspond to `teal_module` `label` set in [module()] function.
 #'  - `id`s listed under `"global_filters` will be active in all modules.
 #'  - If missing, all filters will be applied to all modules.
@@ -35,7 +35,7 @@
 #' @return
 #' A `teal_slices` object.
 #'
-#' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [`slices_store`]
+#' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()]
 #'
 #' @examples
 #' filter <- teal_slices(
diff --git a/man/example_module.Rd b/man/example_module.Rd
index f9894da56d..0607501282 100644
--- a/man/example_module.Rd
+++ b/man/example_module.Rd
@@ -8,7 +8,7 @@ example_module(label = "example teal module", datanames = "all")
 }
 \arguments{
 \item{label}{(\code{character(1)}) Label shown in the navigation item for the module. Any label possible except
-\code{"global_filters"} - read more in \code{mapping} argument of \code{\link{teal_slices}}.}
+\code{"global_filters"} - read more in \code{mapping} argument of \code{\link[=teal_slices]{teal_slices()}}.}
 
 \item{datanames}{(\code{character}) A vector with \code{datanames} that are relevant for the item. The
 filter panel will automatically update the shown filters to include only
diff --git a/man/filter_calls_module.Rd b/man/filter_calls_module.Rd
index 418bfeb0a3..056c538d42 100644
--- a/man/filter_calls_module.Rd
+++ b/man/filter_calls_module.Rd
@@ -11,7 +11,7 @@ filter_calls_module(label = "Filter Calls Module")
 }
 \description{
 Please do not remove, this is useful for debugging \code{teal} without
-dependencies and simplifies \code{\link[devtools:load_all]{devtools::load_all}} which otherwise fails
+dependencies and simplifies \code{\link[devtools:load_all]{devtools::load_all()}} which otherwise fails
 and avoids session restarts!
 }
 \examples{
diff --git a/man/init.Rd b/man/init.Rd
index 62d73a44b1..01ead3cbb1 100644
--- a/man/init.Rd
+++ b/man/init.Rd
@@ -15,8 +15,7 @@ init(
 )
 }
 \arguments{
-\item{data}{(\code{teal_data} or \code{teal_data_module})
-\code{teal_data} object as returned by \code{\link[teal.data:teal_data]{teal.data::teal_data()}} or \code{teal_data_module}.}
+\item{data}{(\code{teal_data} or \code{teal_data_module})}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
 nested list of \code{teal_modules} or \code{teal_module} objects or a single
diff --git a/man/module.Rd b/man/module.Rd
index a02606a24e..8ddd772189 100644
--- a/man/module.Rd
+++ b/man/module.Rd
@@ -29,7 +29,7 @@ module(
 }
 \arguments{
 \item{label}{(\code{character(1)}) Label shown in the navigation item for the module. Any label possible except
-\code{"global_filters"} - read more in \code{mapping} argument of \code{\link{teal_slices}}.}
+\code{"global_filters"} - read more in \code{mapping} argument of \code{\link[=teal_slices]{teal_slices()}}.}
 
 \item{server}{(\code{function}) \code{shiny} module with following arguments:
 \itemize{
diff --git a/man/reporter_previewer_module.Rd b/man/reporter_previewer_module.Rd
index 38f1bee946..809b793602 100644
--- a/man/reporter_previewer_module.Rd
+++ b/man/reporter_previewer_module.Rd
@@ -8,7 +8,7 @@ reporter_previewer_module(label = "Report previewer", server_args = list())
 }
 \arguments{
 \item{label}{(\code{character(1)}) Label shown in the navigation item for the module. Any label possible except
-\code{"global_filters"} - read more in \code{mapping} argument of \code{\link{teal_slices}}.}
+\code{"global_filters"} - read more in \code{mapping} argument of \code{\link[=teal_slices]{teal_slices()}}.}
 
 \item{server_args}{(named \code{list})
 Arguments passed to \code{\link[teal.reporter:reporter_previewer_srv]{teal.reporter::reporter_previewer_srv()}}.}
diff --git a/man/snapshot_manager_module.Rd b/man/snapshot_manager_module.Rd
index aa976100eb..5bf1a6382f 100644
--- a/man/snapshot_manager_module.Rd
+++ b/man/snapshot_manager_module.Rd
@@ -72,7 +72,7 @@ Once a name has been accepted, \code{slices_global} is converted to a list of li
 The snapshot contains the \code{mapping} attribute of the initial application state
 (or one that has been restored), which may not reflect the current one,
 so \code{mapping_matrix} is transformed to obtain the current mapping, i.e. a list that,
-when passed to the \code{mapping} argument of \code{\link{teal_slices}}, would result in the current mapping.
+when passed to the \code{mapping} argument of \code{\link[=teal_slices]{teal_slices()}}, would result in the current mapping.
 This is substituted as the snapshot's \code{mapping} attribute and the snapshot is added to the snapshot list.
 
 To restore app state, a snapshot is retrieved from storage and rebuilt into a \code{teal_slices} object.
@@ -81,7 +81,7 @@ and set anew according to the \code{mapping} attribute of the snapshot.
 The snapshot is then set as the current content of \code{slices_global}.
 
 To save a snapshot, the snapshot is retrieved and reassembled just like for restoring,
-and then saved to file with \code{\link{slices_store}}.
+and then saved to file with \code{\link[=slices_store]{slices_store()}}.
 
 When a snapshot is uploaded, it will first be added to storage just like a newly created one,
 and then used to restore app state much like a snapshot taken from storage.
diff --git a/man/srv_teal_with_splash.Rd b/man/srv_teal_with_splash.Rd
index 9ffdfbc3c7..991e763bfb 100644
--- a/man/srv_teal_with_splash.Rd
+++ b/man/srv_teal_with_splash.Rd
@@ -14,8 +14,7 @@ the server function must be called with \code{\link[shiny:moduleServer]{shiny::m
 See the vignette for an example. However, \code{\link[=ui_teal_with_splash]{ui_teal_with_splash()}}
 is then preferred to this function.}
 
-\item{data}{(\code{teal_data} or \code{teal_data_module})
-\code{teal_data} object as returned by \code{\link[teal.data:teal_data]{teal.data::teal_data()}} or \code{teal_data_module}.}
+\item{data}{(\code{teal_data} or \code{teal_data_module})}
 
 \item{modules}{(\code{teal_modules}) object containing the output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
diff --git a/man/teal-package.Rd b/man/teal-package.Rd
index c8abaa6914..2612142fcd 100644
--- a/man/teal-package.Rd
+++ b/man/teal-package.Rd
@@ -11,7 +11,7 @@ interactive data analysis environment.
 }
 \details{
 To learn mode about the package either read the project website at
-\href{https://insightsengineering.github.io/teal/latest-tag/}{project website} or read the \code{\link{init}} manual pages.
+\href{https://insightsengineering.github.io/teal/latest-tag/}{project website} or read the \code{\link[=init]{init()}} manual pages.
 }
 \seealso{
 Useful links:
diff --git a/man/teal_data_module.Rd b/man/teal_data_module.Rd
index fbae41c2e5..fba01907c4 100644
--- a/man/teal_data_module.Rd
+++ b/man/teal_data_module.Rd
@@ -98,5 +98,5 @@ valid_species <- "versicolor"
 within(tdm, dataset1 <- subset(dataset1, Species \%in\% species), species = valid_species)
 }
 \seealso{
-\code{\linkS4class{teal_data}}, \code{\link[teal.code:qenv]{teal.code::qenv()}}
+, \code{\link[teal.code:qenv]{teal.code::qenv()}}
 }
diff --git a/man/teal_slices.Rd b/man/teal_slices.Rd
index b466ebb644..9318d64935 100644
--- a/man/teal_slices.Rd
+++ b/man/teal_slices.Rd
@@ -57,7 +57,7 @@ Modules can have different set of filters specified - see \code{mapping} argumen
 \href{https://github.com/insightsengineering/teal/}{\code{teal}'s GitHub repository}.}
 
 (named \code{list}) specifies which filters will be active in which modules on app start.
-Elements should contain character vector of \code{teal_slice} \code{id}s (see \code{\link[teal.slice:teal_slice]{teal.slice::teal_slice()}}).
+Elements should contain character vector of \code{teal_slice} \code{id}s (see \code{\link[teal.slice:teal_slice]{teal.slice::teal_slice}}).
 Names of the list should correspond to \code{teal_module} \code{label} set in \code{\link[=module]{module()}} function.
 \itemize{
 \item \code{id}s listed under \verb{"global_filters} will be active in all modules.
@@ -115,6 +115,6 @@ if (interactive()) {
 
 }
 \seealso{
-\code{\link[teal.slice:teal_slices]{teal.slice::teal_slices}}, \code{\link[teal.slice:teal_slice]{teal.slice::teal_slice}}, \code{\link{slices_store}}
+\code{\link[teal.slice:teal_slices]{teal.slice::teal_slices}}, \code{\link[teal.slice:teal_slice]{teal.slice::teal_slice}}, \code{\link[=slices_store]{slices_store()}}
 }
 \keyword{internal}
diff --git a/man/ui_teal_with_splash.Rd b/man/ui_teal_with_splash.Rd
index ab2a7994b0..2139223661 100644
--- a/man/ui_teal_with_splash.Rd
+++ b/man/ui_teal_with_splash.Rd
@@ -16,8 +16,7 @@ ui_teal_with_splash(
 \item{id}{(\code{character(1)})
 module id}
 
-\item{data}{(\code{teal_data} or \code{teal_data_module})
-\code{teal_data} object as returned by \code{\link[teal.data:teal_data]{teal.data::teal_data()}} or \code{teal_data_module}.}
+\item{data}{(\code{teal_data} or \code{teal_data_module})}
 
 \item{title}{(\code{shiny.tag} or \code{character(1)})
 The browser window title. Defaults to a title "teal app" with the icon of NEST.