Convert documentation to use roxygen markdown

DESCRIPTION

@@ -66,3 +66,4 @@ Remotes:
     r-lib/covr,
     r-lib/rcmdcheck
 RoxygenNote: 6.1.0
+Roxygen: list(markdown = TRUE)

R/R.r

@@ -3,8 +3,8 @@
 #' Devtools sets a number of environmental variables to ensure consistent
 #' between the current R session and the new session, and to ensure that
 #' everything behaves the same across systems. It also suppresses a common
-#' warning on windows, and sets \code{NOT_CRAN} so you can tell that your
-#' code is not running on CRAN. If \code{NOT_CRAN} has been set externally, it
+#' warning on windows, and sets `NOT_CRAN` so you can tell that your
+#' code is not running on CRAN. If `NOT_CRAN` has been set externally, it
 #' is not overwritten.
 #'
 #' @keywords internal

R/bash.r

@@ -1,7 +1,7 @@
 #' Open bash shell in package directory.
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information
+#'   [as.package()] for more information
 #' @export
 bash <- function(pkg = ".") {
   pkg <- as.package(pkg)

R/build-manual.R

@@ -1,11 +1,11 @@
 #' Create package pdf manual
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information.
+#'   [as.package()] for more information.
 #' @param path path in which to produce package manual.
-#'   If \code{NULL}, defaults to the parent directory of the package.
+#'   If `NULL`, defaults to the parent directory of the package.
 #'
-#' @seealso \code{\link{Rd2pdf}}
+#' @seealso [Rd2pdf()]
 #' @export
 build_manual <- function(pkg = ".", path = NULL) {
   pkg <- as.package(pkg)

R/check-devtools.r

@@ -1,10 +1,10 @@
 #' Custom devtools release checks.
 #'
 #' This function performs additional checks prior to release. It is called
-#' automatically by \code{\link{release}()}.
+#' automatically by [release()].
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information.
+#'   [as.package()] for more information.
 #' @keywords internal
 #' @export
 release_checks <- function(pkg = ".", built_path = NULL) {

R/check-doc.r

@@ -1,12 +1,12 @@
-#' Check documentation, as \code{R CMD check} does.
+#' Check documentation, as `R CMD check` does.
 #'
 #' This function attempts to run the documentation related checks in the
-#' same way that \code{R CMD check} does. Unfortunately it can't run them
+#' same way that `R CMD check` does. Unfortunately it can't run them
 #' all because some tests require the package to be loaded, and the way
 #' they attempt to load the code conflicts with how devtools does it.
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information
+#'   [as.package()] for more information
 #' @return Nothing. This function is called purely for it's side effects: if
 #   no errors there will be no output.
 #' @export

R/check-git.r

@@ -1,10 +1,10 @@
 #' Git checks.
 #'
 #' This function performs Git checks checks prior to release. It is called
-#' automatically by \code{\link{release}()}.
+#' automatically by [release()].
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information.
+#'   [as.package()] for more information.
 #' @keywords internal
 git_checks <- function(pkg = ".") {
   pkg <- as.package(pkg)

R/check-results.R

@@ -106,17 +106,17 @@ trunc_middle <- function(x, n_max = 25, n_top = 10, n_bottom = 10) {
 
 #' Parses R CMD check log file for ERRORs, WARNINGs and NOTEs
 #'
-#' Extracts check messages from the \code{00check.log} file generated by
-#' \code{R CMD check}.
+#' Extracts check messages from the `00check.log` file generated by
+#' `R CMD check`.
 #'
-#' @param path check path, e.g., value of the \code{check_dir} argument in a
-#'   call to \code{\link{check}}
+#' @param path check path, e.g., value of the `check_dir` argument in a
+#'   call to [check()]
 #' @param error,warning,note logical, indicates if errors, warnings and/or
 #'   notes should be returned
 #' @return a character vector with the relevant messages, can have length zero
 #'   if no messages are found
 #'
-#' @seealso \code{\link{check}}, \code{\link{revdep_check}}
+#' @seealso [check()], [revdep_check()]
 #' @export
 check_failures <- function(path, error = TRUE, warning = TRUE, note = TRUE) {
   check_dir <- file.path(path, "00check.log")

R/check-win.r

@@ -1,17 +1,17 @@
 #' Build windows binary package.
 #'
 #' This function works by bundling source package, and then uploading to
-#' \url{http://win-builder.r-project.org/}.  Once building is complete you'll
+#' <http://win-builder.r-project.org/>.  Once building is complete you'll
 #' receive a link to the built package in the email address listed in the
 #' maintainer field.  It usually takes around 30 minutes. As a side effect,
-#' win-build also runs \code{R CMD check} on the package, so \code{build_win}
+#' win-build also runs `R CMD check` on the package, so `build_win`
 #' is also useful to check that your package is ok on windows.
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information
+#'   [as.package()] for more information
 #' @inheritParams pkgbuild::build
-#' @param quiet If \code{TRUE}, suppresses output.
-#' @param ... Additional arguments passed to \code{\link[pkgbuild]{build}}.
+#' @param quiet If `TRUE`, suppresses output.
+#' @param ... Additional arguments passed to [pkgbuild::build()].
 #' @family build functions
 #' @name check_win
 NULL

R/check.r

@@ -1,15 +1,15 @@
 #' Build and check a package, cleaning up automatically on success.
 #'
-#' \code{check} automatically builds and checks a source package, using all
-#' known best practices. \code{check_built} checks an already built package.
+#' `check` automatically builds and checks a source package, using all
+#' known best practices. `check_built` checks an already built package.
 #'
-#' Passing \code{R CMD check} is essential if you want to submit your package
+#' Passing `R CMD check` is essential if you want to submit your package
 #' to CRAN: you must not have any ERRORs or WARNINGs, and you want to ensure
 #' that there are as few NOTEs as possible.  If you are not submitting to CRAN,
 #' at least ensure that there are no ERRORs or WARNINGs: these typically
 #' represent serious problems.
 #'
-#' \code{check} automatically builds a package before calling \code{check_built}
+#' `check` automatically builds a package before calling `check_built`
 #' as this is the recommended way to check packages.  Note that this process
 #' runs in an independent realisation of R, so nothing in your current
 #' workspace will affect the process.
@@ -22,34 +22,34 @@
 #' \itemize{
 #'
 #'  \item The standard environment variables set by devtools:
-#'    \code{\link{r_env_vars}}. Of particular note for package tests is the
-#'    \code{NOT_CRAN} env var which lets you know that your tests are not
+#'    [r_env_vars()]. Of particular note for package tests is the
+#'    `NOT_CRAN` env var which lets you know that your tests are not
 #'    running on cran, and hence can take a reasonable amount of time.
 #'
 #'  \item Debugging flags for the compiler, set by
 #'    \code{\link{compiler_flags}(FALSE)}.
 #'
-#'  \item If \code{aspell} is found \code{_R_CHECK_CRAN_INCOMING_USE_ASPELL_}
-#'   is set to \code{TRUE}. If no spell checker is installed, a warning is
+#'  \item If `aspell` is found `_R_CHECK_CRAN_INCOMING_USE_ASPELL_`
+#'   is set to `TRUE`. If no spell checker is installed, a warning is
 #'   issued.)
 #'
-#'  \item env vars set by arguments \code{incoming}, \code{remote} and
-#'    \code{force_suggests}
+#'  \item env vars set by arguments `incoming`, `remote` and
+#'    `force_suggests`
 #' }
 #'
 #' @return An object containing errors, warnings, and notes.
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information
-#' @param document If \code{NA} and the package uses roxygen2, will
-#'   rerun \code{\link{document}} prior to checking. Use \code{TRUE}
-#'   and \code{FALSE} to override this default.
-#' @param build_args Additional arguments passed to \code{R CMD build}
+#'   [as.package()] for more information
+#' @param document If `NA` and the package uses roxygen2, will
+#'   rerun [document()] prior to checking. Use `TRUE`
+#'   and `FALSE` to override this default.
+#' @param build_args Additional arguments passed to `R CMD build`
 #' @param check_dir the directory in which the package is checked
-#'   compatibility. \code{args = "--output=/foo/bar"} can be used to change the
+#'   compatibility. `args = "--output=/foo/bar"` can be used to change the
 #'   check directory.
-#' @param ... Additional arguments passed on to \code{\link[pkgbuild]{build}()}.
+#' @param ... Additional arguments passed on to [pkgbuild::build()].
 #' @param cleanup Deprecated.
-#' @seealso \code{\link{release}} if you want to send the checked package to
+#' @seealso [release()] if you want to send the checked package to
 #'   CRAN.
 #' @export
 check <- function(pkg = ".",
@@ -131,24 +131,24 @@ check <- function(pkg = ".",
 #' @export
 #' @rdname check
 #' @param path Path to built package.
-#' @param cran if \code{TRUE} (the default), check using the same settings as
+#' @param cran if `TRUE` (the default), check using the same settings as
 #'   CRAN uses.
-#' @param remote Sets \code{_R_CHECK_CRAN_INCOMING_REMOTE_} env var.
-#'   If \code{TRUE}, performs a number of CRAN incoming checks that require
+#' @param remote Sets `_R_CHECK_CRAN_INCOMING_REMOTE_` env var.
+#'   If `TRUE`, performs a number of CRAN incoming checks that require
 #'   remote access.
-#' @param incoming Sets \code{_R_CHECK_CRAN_INCOMING_} env var.
-#'   If \code{TRUE}, performs a number of CRAN incoming checks.
-#' @param force_suggests Sets \code{_R_CHECK_FORCE_SUGGESTS_}. If
-#'   \code{FALSE} (the default), check will proceed even if all suggested
+#' @param incoming Sets `_R_CHECK_CRAN_INCOMING_` env var.
+#'   If `TRUE`, performs a number of CRAN incoming checks.
+#' @param force_suggests Sets `_R_CHECK_FORCE_SUGGESTS_`. If
+#'   `FALSE` (the default), check will proceed even if all suggested
 #'   packages aren't found.
-#' @param run_dont_test Sets \code{--run-donttest} so that tests surrounded in
+#' @param run_dont_test Sets `--run-donttest` so that tests surrounded in
 #'   \code{\\dontest\{\}} are also tested. This is important for CRAN
 #'   submission.
-#' @param manual If \code{FALSE}, don't build and check manual
-#'   (\code{--no-manual}).
-#' @param args Additional arguments passed to \code{R CMD check}
-#' @param env_vars Environment variables set during \code{R CMD check}
-#' @param quiet if \code{TRUE} suppresses output from this function.
+#' @param manual If `FALSE`, don't build and check manual
+#'   (`--no-manual`).
+#' @param args Additional arguments passed to `R CMD check`
+#' @param env_vars Environment variables set during `R CMD check`
+#' @param quiet if `TRUE` suppresses output from this function.
 #' @inheritParams rcmdcheck::rcmdcheck
 check_built <- function(path = NULL, cran = TRUE,
                         remote = FALSE, incoming = remote, force_suggests = FALSE,

R/dev-mode.r

@@ -1,14 +1,14 @@
 #' Activate and deactivate development mode.
 #'
-#' When activated, \code{dev_mode} creates a new library for storing installed
-#' packages. This new library is automatically created when \code{dev_mode} is
+#' When activated, `dev_mode` creates a new library for storing installed
+#' packages. This new library is automatically created when `dev_mode` is
 #' activated if it does not already exist.
 #' This allows you to test development packages in a sandbox, without
 #' interfering with the other packages you have installed.
 #'
-#' @param on turn dev mode on (\code{TRUE}) or off (\code{FALSE}).  If omitted
-#'  will guess based on whether or not \code{path} is in
-#'  \code{\link{.libPaths}}
+#' @param on turn dev mode on (`TRUE`) or off (`FALSE`).  If omitted
+#'  will guess based on whether or not `path` is in
+#'  [.libPaths()]
 #' @param path directory to library.
 #' @export
 #' @examples

R/document.r

@@ -1,14 +1,14 @@
 #' Use roxygen to document a package.
 #'
-#' This function is a wrapper for the \code{\link[roxygen2]{roxygenize}()}
+#' This function is a wrapper for the [roxygen2::roxygenize()]
 #' function from the roxygen2 package. See the documentation and vignettes of
 #' that package to learn how to use roxygen.
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information
+#'   [as.package()] for more information
 #' @inheritParams roxygen2::roxygenise
-#' @seealso \code{\link[roxygen2]{roxygenize}},
-#'   \code{browseVignettes("roxygen2")}
+#' @seealso [roxygen2::roxygenize()],
+#'   `browseVignettes("roxygen2")`
 #' @export
 document <- function(pkg = ".", roclets = NULL) {
   check_suggested("roxygen2")

R/github.R

@@ -84,7 +84,7 @@ github_tag <- function(username, repo, ref = "master") {
 #' Retrieve Github personal access token.
 #'
 #' A github personal access token
-#' Looks in env var \code{GITHUB_PAT}
+#' Looks in env var `GITHUB_PAT`
 #'
 #' @keywords internal
 #' @export

R/install.r

@@ -1,58 +1,58 @@
 #' Install a local development package.
 #'
-#' Uses \code{R CMD INSTALL} to install the package. Will also try to install
+#' Uses `R CMD INSTALL` to install the package. Will also try to install
 #' dependencies of the package from CRAN, if they're not already installed.
 #'
 #' By default, installation takes place using the current package directory.
 #' If you have compiled code, this means that artefacts of compilation will be
-#' created in the \code{src/} directory. If you want to avoid this, you can
-#' use \code{build = TRUE} to first build a package bundle and then install
+#' created in the `src/` directory. If you want to avoid this, you can
+#' use `build = TRUE` to first build a package bundle and then install
 #' it from a temporary directory. This is slower, but keeps the source
 #' directory pristine.
 #'
 #' If the package is loaded, it will be reloaded after installation. This is
-#' not always completely possible, see \code{\link{reload}} for caveats.
+#' not always completely possible, see [reload()] for caveats.
 #'
-#' To install a package in a non-default library, use \code{\link[withr]{with_libpaths}}.
+#' To install a package in a non-default library, use [withr::with_libpaths()].
 #'
 #' @param pkg package description, can be path or package name.  See
-#'   \code{\link{as.package}} for more information
-#' @param reload if \code{TRUE} (the default), will automatically reload the
+#'   [as.package()] for more information
+#' @param reload if `TRUE` (the default), will automatically reload the
 #'   package after installing.
-#' @param quick if \code{TRUE} skips docs, multiple-architectures,
+#' @param quick if `TRUE` skips docs, multiple-architectures,
 #'   demos, and vignettes, to make installation as fast as possible.
-#' @param build if \code{TRUE} \code{\link[pkgbuild]{build}}s the package first:
+#' @param build if `TRUE` [pkgbuild::build()]s the package first:
 #'   this ensures that the installation is completely clean, and prevents any
-#'   binary artefacts (like \file{.o}, \code{.so}) from appearing in your local
+#'   binary artefacts (like \file{.o}, `.so`) from appearing in your local
 #'   package directory, but is considerably slower, because every compile has
 #'   to start from scratch.
 #' @param args An optional character vector of additional command line
-#'   arguments to be passed to \code{R CMD INSTALL}. This defaults to the
-#'   value of the option \code{"devtools.install.args"}.
-#' @param quiet if \code{TRUE} suppresses output from this function.
-#' @param dependencies \code{logical} indicating to also install uninstalled
-#'   packages which this \code{pkg} depends on/links to/suggests. See
-#'   argument \code{dependencies} of \code{\link{install.packages}}.
-#' @param upgrade If \code{TRUE}, the default, will also update
+#'   arguments to be passed to `R CMD INSTALL`. This defaults to the
+#'   value of the option `"devtools.install.args"`.
+#' @param quiet if `TRUE` suppresses output from this function.
+#' @param dependencies `logical` indicating to also install uninstalled
+#'   packages which this `pkg` depends on/links to/suggests. See
+#'   argument `dependencies` of [install.packages()].
+#' @param upgrade If `TRUE`, the default, will also update
 #'   any out of date dependencies.
-#' @param build_vignettes if \code{TRUE}, will build vignettes. Normally it is
-#'   \code{build} that's responsible for creating vignettes; this argument makes
+#' @param build_vignettes if `TRUE`, will build vignettes. Normally it is
+#'   `build` that's responsible for creating vignettes; this argument makes
 #'   sure vignettes are built even if a build never happens (i.e. because
-#'   \code{local = TRUE}).
-#' @param keep_source If \code{TRUE} will keep the srcrefs from an installed
+#'   `local = TRUE`).
+#' @param keep_source If `TRUE` will keep the srcrefs from an installed
 #'   package. This is useful for debugging (especially inside of RStudio).
-#'   It defaults to the option \code{"keep.source.pkgs"}.
+#'   It defaults to the option `"keep.source.pkgs"`.
 #' @param threads number of concurrent threads to use for installing
 #'   dependencies.
-#'   It defaults to the option \code{"Ncpus"} or \code{1} if unset.
+#'   It defaults to the option `"Ncpus"` or `1` if unset.
 #' @param force whether to force installation of dependencies even if they
 #'   have not been updated from the previously installed version.
-#' @param ... additional arguments passed to \code{\link{install.packages}}
-#'   when installing dependencies. \code{pkg} is installed with
-#'   \code{R CMD INSTALL}.
+#' @param ... additional arguments passed to [install.packages()]
+#'   when installing dependencies. `pkg` is installed with
+#'   `R CMD INSTALL`.
 #' @family package installation
-#' @seealso \code{\link{update_packages}} to update installed packages from the
-#' source location and \code{\link{with_debug}} to install packages with
+#' @seealso [update_packages()] to update installed packages from the
+#' source location and [with_debug()] to install packages with
 #' debugging flags set.
 #' @export
 install <-

R/lint.r

@@ -1,18 +1,18 @@
 #' Lint all source files in a package.
 #'
 #' The default lintings correspond to the style guide at
-#' \url{http://r-pkgs.had.co.nz/r.html#style}, however it is possible to
-#' override any or all of them using the \code{linters} parameter.
+#' <http://r-pkgs.had.co.nz/r.html#style>, however it is possible to
+#' override any or all of them using the `linters` parameter.
 #' @param pkg package description, can be path or package name. See
-#'   \code{\link{as.package}} for more information
+#'   [as.package()] for more information
 #' @param cache store the lint results so repeated lints of the same content
 #' use the previous results.
-#' @param ... additional arguments passed to \code{\link[lintr]{lint_package}}
-#' @seealso \code{\link[lintr]{lint_package}}, \code{\link[lintr]{lint}}
+#' @param ... additional arguments passed to [lintr::lint_package()]
+#' @seealso [lintr::lint_package()], [lintr::lint()]
 #' @details
-#' The lintr cache is by default stored in \code{~/.R/lintr_cache/} (this can
-#' be configured by setting \code{options(lintr.cache_directory)}).  It can be
-#' cleared by calling \code{\link[lintr]{clear_cache}}.
+#' The lintr cache is by default stored in `~/.R/lintr_cache/` (this can
+#' be configured by setting `options(lintr.cache_directory)`).  It can be
+#' cleared by calling [lintr::clear_cache()].
 #' @export
 lint <- function(pkg = ".", cache = TRUE, ...) {
   check_suggested("lintr")