Fix missing package targets in documentation

R/AllClasses.R

@@ -90,7 +90,7 @@ NULL
 #' Aoristic Sum
 #'
 #' An S4 class to represent an aoristic analysis results.
-#' @slot breaks A [`RataDie-class`] vector giving the date break between
+#' @slot breaks An [`aion::RataDie-class`] vector giving the date break between
 #'  time-blocks.
 #' @slot weights A [`numeric`] vector.
 #' @slot groups A [`character`] vector to store the group names (if any).

R/AllGenerics.R

@@ -59,8 +59,9 @@ NULL
 #'  * `sigma()` extracts the residual standard deviation (see [stats::sigma()]).
 #'  * `terms()` extracts model terms (see [stats::terms()]).
 #' @param x,object An [`EventDate-class`] object.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]). If `NULL` (the default), *rata die* are returned.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]). If `NULL` (the default), *rata die* are
+#'  returned.
 #' @param ... Currently not used.
 #' @example inst/examples/ex-event.R
 #' @author N. Frerebeau
@@ -74,8 +75,9 @@ NULL
 #'
 #' Get the times at which a time series was sampled.
 #' @param x An \R object.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]). If `NULL` (the default), *rata die* are returned.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]). If `NULL` (the default), *rata die* are
+#'  returned.
 #' @return
 #'  A [`numeric`] vector.
 #' @author N. Frerebeau
@@ -89,8 +91,8 @@ NULL
 #' Coerce to a Data Frame
 #'
 #' @param x An object.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]). If `NULL`, *rata die* are returned.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]). If `NULL`, *rata die* are returned.
 #' @param row.names,optional Currently not used.
 #' @param ... Further parameters to be passed to [data.frame()].
 #' @return
@@ -115,8 +117,8 @@ NULL
 #' @param nsim A non-negative [`integer`] specifying the number of simulations.
 #' @param f A [`function`] that takes a single numeric vector (the result of
 #'  the resampling procedure) as argument.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]).
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]).
 #' @return
 #'  If `f` is `NULL`, `bootstrap()` and `jackknife()` return a [`data.frame`]
 #'  with the following elements (else, returns the result of `f` applied to the
@@ -197,8 +199,8 @@ NULL
 #'  individuals for each category, i.e. a contingency table). A [`data.frame`]
 #'  will be coerced to a `numeric` `matrix` via [data.matrix()].
 #' @param dates A length-\eqn{p} [`numeric`] vector of dates expressed in years.
-#' @param calendar A [`TimeScale-class`] object specifying the calendar of
-#'  `dates` (see [calendar()]). Defaults to Gregorian Common Era.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the calendar
+#'  of `dates` (see [calendar()]). Defaults to Gregorian Common Era.
 #' @param ... Currently not used.
 #' @details
 #'  The Mean Ceramic Date (MCD) is a point estimate of the occupation of an
@@ -246,8 +248,8 @@ setGeneric(
 #'  axes corresponding to at least 60% of the inertia will be used.
 #' @param sup_row A [`numeric`] or [`logical`] vector specifying the indices of
 #'  the supplementary rows.
-#' @param calendar A [`TimeScale-class`] object specifying the calendar of
-#'  `dates` (see [calendar()]). Defaults to Gregorian Common Era.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the calendar
+#'  of `dates` (see [calendar()]). Defaults to Gregorian Common Era.
 #' @param ... Further arguments to be passed to internal methods.
 #' @details
 #'  This is an implementation of the chronological modeling method proposed by
@@ -319,8 +321,9 @@ setGeneric(
 #'  will be coerced to a `numeric` `matrix` via [data.matrix()].
 #' @param data A `numeric` [`matrix`] or a [`data.frame`] of count data
 #'  (absolute frequencies) for which to predict event and accumulation dates.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]). If `NULL` (the default), *rata die* are returned.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]). If `NULL` (the default), *rata die* are
+#'  returned.
 #' @param level A length-one [`numeric`] vector giving the confidence level.
 #' @param margin A [`numeric`] vector giving the subscripts which the prediction
 #'  will be applied over: `1` indicates rows, `2` indicates columns.
@@ -383,8 +386,8 @@ setGeneric(
 #'  window.
 #' @param end A length-one [`numeric`] vector giving the end of the time
 #'  window.
-#' @param calendar A [`TimeScale-class`] object specifying the calendar of
-#'  `x` and `y` (see [calendar()]). Defaults to Gregorian Common Era.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the calendar
+#'  of `x` and `y` (see [calendar()]). Defaults to Gregorian Common Era.
 #' @param weight A [`logical`] scalar: should the aoristic sum be weighted by
 #'  the length of periods (default). If `FALSE` the aoristic sum is the number
 #'  of elements within a time block.
@@ -534,8 +537,8 @@ setGeneric(
 #'  individuals for each category, i.e. a contingency table). A [`data.frame`]
 #'  will be coerced to a `numeric` `matrix` via [data.matrix()].
 #' @param dates A length-\eqn{m} [`numeric`] vector of dates.
-#' @param calendar A [`TimeScale-class`] object specifying the calendar of
-#'  `dates` (see [calendar()]). Defaults to Gregorian Common Era.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the calendar
+#'  of `dates` (see [calendar()]). Defaults to Gregorian Common Era.
 #' @param level A length-one [`numeric`] vector giving the confidence level.
 #' @param roll A [`logical`] scalar: should each time series be subsetted to
 #'  look for episodes of selection?
@@ -578,8 +581,8 @@ setGeneric(
 #'  individuals for each category, i.e. a contingency table). A [`data.frame`]
 #'  will be coerced to a `numeric` `matrix` via [data.matrix()].
 #' @param dates A [`numeric`] vector of dates.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]).
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]).
 #' @param ... Further parameters to be passed to [aion::plot()].
 #' @return
 #'   `plot_time()` is called it for its side-effects: it results in a graphic
@@ -598,6 +601,8 @@ setGeneric(
 #' Plot Aoristic Analysis
 #'
 #' @param x An [`AoristicSum-class`] object.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]).
 #' @param type A [`character`] string specifying whether bar or density should
 #'  be plotted? It must be one of "`bar`" or "`density`". Any unambiguous
 #'  substring can be given.
@@ -615,12 +620,12 @@ setGeneric(
 #' @rdname plot_aoristic
 NULL
 
-## MeanDate ---------------------------------------------------------------------
+## MeanDate --------------------------------------------------------------------
 #' MCD Plot
 #'
 #' @param x A [`MeanDate-class`] object.
-#' @param calendar A [`TimeScale-class`] object specifying the target calendar
-#'  (see [calendar()]).
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]).
 #' @param interval A [`character`] string giving the type of confidence
 #'  interval to be returned. It must be one "`student`" (the default),
 #'  "`normal`", "`percentiles`" or "`range`" (min-max).
@@ -659,6 +664,8 @@ NULL
 #'
 #' Produces an activity or a tempo plot.
 #' @param x An [`EventDate-class`] object.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]).
 #' @param type A [`character`] string indicating the type of plot.
 #'  It must be one of "`activity`" (default) or "`tempo`" (see details).
 #'  Any unambiguous substring can be given.
@@ -719,6 +726,8 @@ NULL
 #'
 #' Produces an abundance *vs* time diagram.
 #' @param x An [`IncrementTest-class`] object to be plotted.
+#' @param calendar An [`aion::TimeScale-class`] object specifying the target
+#'  calendar (see [calendar()]).
 #' @param col.neutral,col.selection,col.roll A vector of colors.
 #' @inheritParams aion::plot
 #' @details

cran-comments.md

@@ -1,13 +1,14 @@
 ## Test environments
-* Local R installation: R 4.3.2
+* Local R installation: R 4.4.1
 * Ubuntu (on GitHub Actions): R devel, release, oldrel
 * Windows (on GitHub Actions and win-builder): R devel, release, oldrel
 * MacOS (on GitHub Actions): R release
 
 ## R CMD check results
 
-0 errors | 0 warnings | 0 note
+0 errors | 0 warnings | 1 note
 
+* Rd `\link{}` targets missing package have been fixed (r-devel).
 * Some links in the documentation point to articles behind paywalls that may return an error.
 
 ## revdepcheck results