Fix documentation

Addressing package check warnings for "Rd files with duplicated alias" and "Undocumented arguments in Rd file":

- remove duplicate aliases for EcologicalDroughtMetrics2023_annual/Clim and RR2022predictors_annual/Clim
- link to general "metrics" documentation for EcologicalDroughtMetrics2023_annual/Clim and RR2022predictors_annual/Clim
- use links to individual metrics in general "metrics" documentation

R/Functions_Metrics_002_newRR.R

@@ -2178,14 +2178,16 @@ get_RR2022predictors_annual <- function(
 #' means, standard deviations, or coefficients of variation of
 #' annual values.
 #'
+#' @inheritParams metrics
+#'
 #' @references Chambers et al. (2023)
 #' New indicators of ecological resilience and invasion resistance to support
 #' prioritization and management in the sagebrush biome, United States.
 #' Frontiers in Ecology and Evolution, 10, 1–17.
 #' \url{https://doi.org/10.3389/fevo.2022.1009268}
 #'
-#' @seealso [RR2022predictors_annualClim()] and
-#' [metric_RR2022predictors_annual()]
+#' @seealso [RR2022predictors_annualClim()];
+#' see [metrics] for a complete list of available metric functions.
 #'
 #' @name RR2022predictors_annual
 #' @md
@@ -2226,6 +2228,8 @@ metric_RR2022predictors_annual <- function(
 #' means, standard deviations, or coefficients of variation of
 #' annual values (see `metric_RR2022predictors_annual()`).
 #'
+#' @inheritParams metrics
+#'
 #' @return A return object where `group` contains the following annual
 #' variables:
 #'    * `"Tmean_mean"`
@@ -2259,8 +2263,8 @@ metric_RR2022predictors_annual <- function(
 #' Frontiers in Ecology and Evolution, 10, 1–17.
 #' \url{https://doi.org/10.3389/fevo.2022.1009268}
 #'
-#' @seealso [RR2022predictors_annual()] and
-#' [metric_RR2022predictors_annualClim()]
+#' @seealso [RR2022predictors_annual()];
+#' see [metrics] for a complete list of available metric functions.
 #'
 #' @name RR2022predictors_annualClim
 #' @md
@@ -2796,13 +2800,15 @@ get_EcologicalDroughtMetrics2023_annual <- function(
 
 #' Annual time series of ecological drought metrics
 #'
+#' @inheritParams metrics
+#'
 #' @references Chenoweth et al. (2023)
 #' Ecologically relevant moisture and temperature metrics for assessing
 #' dryland ecosystem dynamics.
 #' Ecohydrology, 16(3), e2509. \url{https://doi.org/10.1002/eco.2509}
 #'
-#' @seealso [EcologicalDroughtMetrics2023_annualClim()] and
-#' [metric_EcologicalDroughtMetrics2023_annual()]
+#' @seealso [EcologicalDroughtMetrics2023_annualClim()];
+#' see [metrics] for a complete list of available metric functions.
 #'
 #' @section Details:
 #' The following functions produce all metrics used by Chenoweth et al.:
@@ -2926,8 +2932,10 @@ metric_EcologicalDroughtMetrics2023_annual <- function(
 #' annual values of metrics used by Chenoweth et al.
 #' (see `metric_EcologicalDroughtMetrics2023_annual()`).
 #'
-#' @seealso [EcologicalDroughtMetrics2023_annual()] and
-#' [metric_EcologicalDroughtMetrics2023_annualClim()]
+#' @inheritParams metrics
+#'
+#' @seealso [EcologicalDroughtMetrics2023_annual()];
+#' see [metrics] for a complete list of available metric functions.
 #'
 #' @return A return object where `group` contains the following climatologies of
 #' annual variables summarized across years by means `mean`,

R/rSW2metrics-package.R

@@ -62,34 +62,46 @@ rSW2_glovars <- new.env()
 #' @exportPattern "^metric_[^\\.]"
 
 
-rd_alias_metrics <- function() {
+md_aliases_of_metrics <- function() {
   tmp <- list_all_metrics()
 
-  # Remove `metric_SW2toTable_daily()` because it has it's own documentation
-  exclude_metrics <- "metric_SW2toTable_daily"
+  # Remove metrics that have their own dedicated documentation
+  exclude_metrics <- c(
+    "metric_SW2toTable_daily",
+    "EcologicalDroughtMetrics2023_annual",
+    "EcologicalDroughtMetrics2023_annualClim",
+    "RR2022predictors_annual",
+    "RR2022predictors_annualClim"
+  )
+
   ids_remove <- unique(unlist(lapply(
     exclude_metrics,
     FUN = grep,
     x = basename(tmp)
   )))
-  tmp <- tmp[-ids_remove]
+
+  if (length(ids_remove) > 0L) {
+    tmp <- tmp[-ids_remove]
+  }
 
   paste("@aliases", paste(tmp, collapse = " "))
 }
 
-rd_section_listing_metrics <- function() {
+rd_section_list_metrics <- function() {
   paste(
     "\\section{List of currently available metrics:}{\n",
     "\\itemize{\n",
     paste(
       "  \\item", # nolint: nonportable_path_linter.
-      paste0("\\var{", list_all_metrics(), "}"),
+      paste0("\\code{\\link{", list_all_metrics(), "}}"),
       collapse = "\n"
     ),
     "\n}}"
   )
 }
 
+
+
 #' End-user functions that calculate a specific `metric`
 #'
 #' These functions have a name that starts with `metric_`.
@@ -171,9 +183,10 @@ rd_section_listing_metrics <- function() {
 #' a different type of output, i.e., spreadsheets of the most important
 #' daily `SOILWAT2` variables, see [`SW2toTable`].
 #'
-#' @evalRd rd_section_listing_metrics()
+#' @evalRd rd_section_list_metrics()
+#'
+#' @eval md_aliases_of_metrics()
 #'
-#' @eval rd_alias_metrics()
 #' @name metrics
 NULL