Fix doc

R/bbt_delete_temp_files.R

@@ -1,5 +1,6 @@
 #' Delete all the temporary files created by \link{bbt_run_from_model}
 #' @inheritParams default_params_doc
+#' @return Nothing.
 #' @examples
 #' if (beautier::is_on_ci() && is_beast2_installed()) {
 #'   beastier::remove_beaustier_folders()

R/bbt_self_test.R

@@ -1,5 +1,6 @@
 #' Do a self test to verify \link{babette} that works correctly.
 #' @inheritParams default_params_doc
+#' @return Nothing. Will raise an exception if something is wrong.
 #' @author Richèl J.C. Bilderbeek
 #' @export
 #' @examples

R/check_beast2_pkgs.R

@@ -4,6 +4,7 @@
 #' For example, to use a Nested Sampling MCMC, the 'BEAST2' 'NS' package
 #' needs to be installed.
 #' @inheritParams default_params_doc
+#' @return Nothing.
 #' @examples
 #' if (beautier::is_on_ci() && is_beast2_installed()) {
 #'   beastier::remove_beaustier_folders()

R/create_test_ns_output.R

@@ -2,6 +2,7 @@
 #'
 #' Create testing output similar to when running a 'BEAST2' run
 #' with nested sampling
+#' @return a text of type character vector.
 #' @author Richèl J.C. Bilderbeek
 #' @seealso Use \link{parse_beast2_output_to_ns} to parse
 #' this output to a Nested Sampling result.

R/prepare_file_creation.R

@@ -4,6 +4,7 @@
 #' to sub-sub-sub folders. Create those folders and test
 #' if these folders can be written to
 #' @inheritParams default_params_doc
+#' @return Nothing.
 #' @examples
 #' # This example will fail on the CRAN
 #' # r-oldrel-macos-x86_64 platform

R/update_babette.R

@@ -6,6 +6,7 @@
 #' See \url{https://github.com/richelbilderbeek/babetteinstall}
 #' how to do this.
 #' @param upgrade Deprecated.
+#' @return Nothing.
 #' @author Giovanni Laudanno, Richèl J.C. Bilderbeek
 #' @export
 update_babette <- function(upgrade = "default") {

scripts/find_functions_with_missing_rd_tags.R

@@ -0,0 +1,50 @@
+#!/bin/env Rscript
+#
+# Find function that are not completely documented
+#
+# Usage:
+#
+#   ./find_functions_with_missing_rd_tags
+#   ./find_functions_with_missing_rd_tags [package_name]
+#
+# Examples:
+#
+#   ./find_functions_with_missing_rd_tags
+#   ./find_functions_with_missing_rd_tags babette
+#
+# From https://stat.ethz.ch/pipermail/r-package-devel/2021q2/007106.html
+
+library(tools)
+
+pkg_of_interest <- "babette"
+
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) == 1) pkg_of_interest <- args[1]
+print(paste("Find functions in package", pkg_of_interest))
+
+db <- Rd_db(pkg_of_interest)
+
+name <- lapply(db, tools:::.Rd_get_metadata, "name")
+alias <- lapply(db, tools:::.Rd_get_metadata, "alias")
+value <- lapply(db, tools:::.Rd_get_metadata, "value")
+
+n_aliases <- lengths(alias)
+df <- data.frame(
+    file_name = rep(names(db), n_aliases),
+    name = rep(unlist(name, use.names = FALSE), n_aliases),
+    alias = unlist(alias, use.names = FALSE),
+    has_value = rep(lengths(value) > 0, n_aliases)
+)
+
+# Create subsets of the database, and find the aliases that have no values. 
+# This is trying to allow for the possibility that an alias occurs in more than 
+# one help file (is this allowed?)
+
+alias_with_value <- subset(df, has_value)
+alias_without_value <- subset(df, !has_value)    
+no_value <- subset(alias_without_value, !alias %in% alias_with_value$alias)
+
+# Find all the exports in the package, and subset the help pages to just those.
+
+exports <- getNamespaceExports(pkg_of_interest)
+subset(no_value, alias %in% exports)