played around with roxygen_md documentation

DESCRIPTION

@@ -64,3 +64,4 @@ BugReports: https://github.com/marton-balazs-kovacs/tenzing/issues
 VignetteBuilder: knitr
 Depends: 
     R (>= 2.10)
+Roxygen: list(markdown = TRUE)

R/contributors_table_template.R

@@ -38,5 +38,5 @@
 #'   \item{ORCID iD}{character, ORCID iD of the contributor}
 #'   \item{'Corresponding author?'}{logical, TRUE for contributor who is the corresponding author}
 #'}
-#'@source \url{https://docs.google.com/spreadsheets/d/1Gl0cwqN_nTsdFH9yhSvi9NypBfDCEhViGq4A3MnBrG8/edit?usp=sharing}
-"contributors_table_template"
+#'@source <https://docs.google.com/spreadsheets/d/1Gl0cwqN_nTsdFH9yhSvi9NypBfDCEhViGq4A3MnBrG8/edit?usp=sharing>
+"contributors_table_template"

R/initials.R

@@ -61,7 +61,7 @@ abbreviate <- function(string, collapse) {
 
 #' Abbreviate middle names in a dataframe
 #' 
-#' The function calls the \code{\link{abbreviate}} function to
+#' The function calls the [abbreviate()] function to
 #' abbreviate middle names in the `Middle name` variable in a
 #' dataframe if they are present. The function requires a valid
 #' `contributors_table` as an input to work.

R/moduleServer.R

@@ -1,14 +1,14 @@
-#' Wrapper function around \code{shiny::callModule}
+#' Wrapper function around `shiny::callModule`
 #' 
-#' The function dodge the explicit usage of \code{callModule} on
-#' the server side. This style will be the default for \code{shiny}
+#' The function dodge the explicit usage of `callModule` on
+#' the server side. This style will be the default for `shiny`
 #' from version 1.5.0. To be deleted after update.
 #' 
 #' @param id Unique character id of the module
 #' @param module Name of the module server function
 #' 
 #' @section Source:
-#' \url{https://mastering-shiny.org/scaling-modules.html}
+#' <https://mastering-shiny.org/scaling-modules.html>
 moduleServer <- function(id, module) {
   callModule(module, id)
-}
+}

R/print_credit_roles.R

@@ -2,8 +2,8 @@
 #' 
 #' The function generates rmarkdown formatted text of the contributions according
 #' to the CRediT taxonomy. The output is generated from an `contributors_table` validated with
-#' the \code{\link{validate_contributors_table}} function. The `contributors_table` must be based on the
-#' \code{\link{contributors_table_template}}. The function can return the output string as
+#' the [validate_contributors_table()] function. The `contributors_table` must be based on the
+#' [contributors_table_template()]. The function can return the output string as
 #' rmarkdown or html formatted text or without any formatting.
 #' 
 #' @section Warning:

R/print_funding.R

@@ -2,8 +2,8 @@
 #' 
 #' The functions generates the funding information section of the manuscript.
 #' The output is generated from an contributors_table validated with
-#' the \code{\link{validate_contributors_table}} function.
-#' The contributors_table must be based on the \code{\link{contributors_table_template}}.
+#' the [validate_contributors_table()] function.
+#' The contributors_table must be based on the [contributors_table_template()].
 #' 
 #' @family output functions
 #' 

R/print_title_page.R

@@ -1,8 +1,8 @@
 #' Generate title page
 #' 
 #' The function generates rmarkdown formatted contributors' affiliation text from
-#' an contributors_table validated with the \code{\link{validate_contributors_table}} function. The 
-#' contributors_table must be based on the \code{\link{contributors_table_template}}. The function can
+#' an contributors_table validated with the [validate_contributors_table()] function. The 
+#' contributors_table must be based on the [contributors_table_template()]. The function can
 #' return the output string as rmarkdown or html formatted text or without any formatting.
 #' 
 #' @section Warning:
@@ -19,7 +19,7 @@
 #' 
 #' @return The output is string containing the contributors' name and
 #'   the corresponding affiliations in the the order defined by the
-#'   \code{Order in publication} column of the contributors_table.
+#'   `Order in publication` column of the contributors_table.
 #' @export
 #' @examples 
 #' example_contributors_table <- read_contributors_table(

R/print_xml.R

@@ -3,8 +3,8 @@
 #' The function generates an XML nodeset that contains the contributors' name,
 #' affiliation, and their CRediT roles with a structure outlined in the
 #' JATS 1.2 DTD specifications (eLife). The output is generated from an 
-#' `contributors_table` validated with the \code{\link{validate_contributors_table}} function.
-#' The `contributors_table` must be based on the \code{\link{contributors_table_template}}.
+#' `contributors_table` validated with the [validate_contributors_table()] function.
+#' The `contributors_table` must be based on the [contributors_table_template()].
 #' 
 #' @section Warning:
 #' The function is primarily developed to be the part of a shiny app. As the

R/print_yaml.R

@@ -2,8 +2,8 @@
 #' 
 #' The function generates a YAML document containing the contributors information
 #' and contributions according to the CRediT taxonomy. The output is generated
-#' from an `contributors_table` validated with the \code{\link{validate_contributors_table}} function.
-#' The `contributors_table` must be based on the \code{\link{contributors_table_template}}.
+#' from an `contributors_table` validated with the [validate_contributors_table()] function.
+#' The `contributors_table` must be based on the [contributors_table_template()].
 #' 
 #' @section Warning:
 #' The function is primarily developed to be the part of a shiny app. As the

R/render_report.R

@@ -1,12 +1,12 @@
-#' Wrapper around \code{rmarkdown::render}
+#' Wrapper around `rmarkdown::render`
 #' 
-#' A wrapper function around \code{rmarkdown::render} in order
+#' A wrapper function around `rmarkdown::render` in order
 #' to call it in a different process in the modules.
 #' 
 #' @section Source:
-#' The function is based on the suggestion of Hadley Wickham \url{https://mastering-shiny.org/action-transfer.html}.
+#' The function is based on the suggestion of Hadley Wickham <https://mastering-shiny.org/action-transfer.html>.
 #' 
-#' @seealso \code{\link[rmarkdown]{render}}
+#' @seealso [rmarkdown::render()]
 #' 
 #' @param input path of the input RMD skeleton
 #' @param output path of the rendered output file
@@ -19,4 +19,4 @@ render_report <- function(input, output, format, params) {
                     params = params,
                     envir = new.env(parent = globalenv())
   )
-}
+}

R/utils-pipe.R

@@ -1,6 +1,6 @@
 #' Pipe operator
 #'
-#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#' See `magrittr::[\%>\%][magrittr::pipe]` for details.
 #'
 #' @name %>%
 #' @rdname pipe

R/validate_contributors_table.R

@@ -1,7 +1,7 @@
 #' Validating the contributors table
 #' 
 #' This function validates the `contributors_table` provided to it by checking whether the
-#' provided `contributors_table` is compatible with the \code{\link{contributors_table_template}}. The function
+#' provided `contributors_table` is compatible with the [contributors_table_template()]. The function
 #' early escapes only if the provided `contributors_table` is not a dataframe, the variable
 #' names that are present in the `contributors_table_template` are missing, or if the 
 #' `contributors_table` is empty.
@@ -11,13 +11,13 @@
 #'   \item error, the provided contributors_table is a dataframe
 #'   \item error, the provided contributors_table does not have the same column names as the template
 #'   \item error, the provided contributors_table is empty
-#'   \item error, \code{Firstname} variable has missing value for one of the contributors
-#'   \item error, \code{Surname} variable has a missing value for one of the contributors
+#'   \item error, `Firstname` variable has missing value for one of the contributors
+#'   \item error, `Surname` variable has a missing value for one of the contributors
 #'   \item warning, the contributors_table has duplicate names
 #'   \item warning, the contributors_table has names with duplicate initials
-#'   \item error, the \code{'Order in publication'} variable has missing values
-#'   \item error, the \code{'Order in publication'} variable has duplicate values
-#'   \item error, both \code{'Primary affiliation'} and \code{'Secondary affiliation'} variables
+#'   \item error, the `'Order in publication'` variable has missing values
+#'   \item error, the `'Order in publication'` variable has duplicate values
+#'   \item error, both `'Primary affiliation'` and `'Secondary affiliation'` variables
 #'     are missing for one contributor
 #'   \item warning, there is no corresponding author added
 #'   \item warning, email address is missing for the corresponding author
@@ -27,8 +27,8 @@
 #' @param contributors_table dataframe, filled out contributors_table
 #' 
 #' @return The function returns a list for each checked statement. Each list contains
-#'   a \code{type} vector that stores whether the statement passed the check "success"
-#'   or failed "warning" or "error", and a \code{message} vector that contains information
+#'   a `type` vector that stores whether the statement passed the check "success"
+#'   or failed "warning" or "error", and a `message` vector that contains information
 #'   about the nature of the check.
 #' @export 
 #' @examples
@@ -354,4 +354,4 @@ check_duplicate_initials <- function(contributors_table) {
       message = "There are no duplicate initials in the contributors_table."
     )
   }
-}
+}

_pkgdown.yml

@@ -34,7 +34,7 @@ news:
   one_page: true
 
 home:
-  strip_header: true
+  strip_header: false
   links:
-  - text: Shiny app
+  - text: Find the Shiny app
     href: http://tenzing.club/