Examples are now in inst/doc folder

atero18 · Sep 23, 2023 · 9b48a69 · 9b48a69
1 parent ece144d
commit 9b48a69
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Showing 18 changed files with 12 additions and 103 deletions.
diff --git a/.gitignore b/.gitignore
@@ -50,6 +50,6 @@ po/*~
 # RStudio Connect folder
 rsconnect/
 
-core
+*core
 docs
 inst/doc
diff --git a/R/AHR_grid.R b/R/AHR_grid.R
@@ -106,7 +106,7 @@
 #' the connected component.
 #' @name AHR
 #' @details `r badge('experimental')`
-#' @example inst/examples/AHR.R
+#' @example inst/doc/ex_AHR.R
 #' @export
 #' @seealso [merge_cc_partitions()]
 #' @seealso [stats::hclust()] if you don't have any constraint.

diff --git a/R/arguments.R b/R/arguments.R
@@ -351,7 +351,7 @@ testContiguityMatrix <- makeTestFunction(checkContiguityMatrix)
 #' @name checkContiguityGraph
 #' @rdname checkContiguityGraph
 #' @family arguments checkers
-#' @example inst/examples/checkContiguityGraph.R
+#' @example inst/doc/ex_checkContiguityGraph.R
 #' @export
 #' @importFrom igraph is_igraph is.simple is.directed gorder gsize
 checkContiguityGraph <- function(g, n = gorder(g))
@@ -413,7 +413,7 @@ testContiguityGraph <- makeTestFunction(checkContiguityGraph)
 #' @inherit check_general details
 #' @family arguments checkers
 #' @export
-#' @example inst/examples/checkDistanceMatrix.R
+#' @example inst/doc/ex_checkDistanceMatrix.R
 #' @importFrom checkmate checkMatrix
 checkDistanceMatrix <- function(x, # nolint: cyclocomp_linter
                                 isComplete = TRUE,
@@ -498,7 +498,7 @@ testDistanceMatrix <- makeTestFunction(checkDistanceMatrix)
 #' @inherit check_general details
 #' @family arguments checkers
 #' @export
-#' @example inst/examples/checkPartition.R
+#' @example inst/doc/ex_checkPartition.R
 
 #' @importFrom checkmate checkIntegerish
 checkPartition <- function(x, n = length(x))
@@ -549,7 +549,7 @@ testPartition <- makeTestFunction(checkPartition)
 #' @inherit check_general return
 #' @inherit check_general details
 #' @family arguments checkers
-#' @example inst/examples/checkRegionalisation.R
+#' @example inst/doc/ex_checkRegionalisation.R
 #' @export
 #' @importFrom igraph gorder is_igraph
 checkRegionalisation <- function(regionalisation, contiguity)

diff --git a/R/contiguity.R b/R/contiguity.R
@@ -101,7 +101,7 @@ setGeneric("is_connected", igraph::is_connected)
 #' @returns TRUE if the set is connected, FALSE otherwise.
 #' @seealso [igraph::is_connected()]
 #' @keywords internal
-#' @example inst/examples/is_connected.R
+#' @example inst/doc/ex_is_connected.R
 #' @export
 #' @importFrom igraph is_connected
 setMethod(

diff --git a/R/medoids.R b/R/medoids.R
@@ -14,7 +14,7 @@ NULL
 #' @param byName `TRUE` if the returned result should be the row name
 #' corresponding to the medoid, `FALSE` if it should be the row number.
 #' Ignored if `distances` is not named. (flag)
-#' @example inst/examples/medoid.R
+#' @example inst/doc/ex_medoid.R
 #' @export
 medoid <- function(distances, byName = FALSE)
 {

diff --git a/R/partition_tools.R b/R/partition_tools.R
@@ -74,7 +74,7 @@ setGeneric("nbSingletons")
 #' @details This form is also used by [stats::cutree()].
 #' @details Two partitions are equivalent if and only if their
 #' standardised forms are equal.
-#' @example inst/examples/standardize_partition.R
+#' @example inst/doc/ex_standardize_partition.R
 standardize_partition <- function(partition)
 {
   clustersIDs <- clustersIDs(partition)
@@ -96,7 +96,7 @@ standardize_partition <- function(partition)
 #' @importFrom checkmate assertVector
 #' @export
 #'
-#' @example inst/examples/equivalent_partitions.R
+#' @example inst/doc/ex_equivalent_partitions.R
 equivalent_partitions <- function(partition1, partition2)
 {
   assertVector(partition1, min.len = 1L,

diff --git a/R/resolver.R b/R/resolver.R
@@ -12,7 +12,7 @@
 #' @param maxItTransfers positive integer indicating the maximum number
 #' of elements can be transferred.
 #' @param ... used for development.
-#' @example inst/examples/resolve_unfeasible.R
+#' @example inst/doc/ex_resolve_unfeasible.R
 #' @export
 #' @importFrom checkmate assertFlag
 resolve_unfeasible <- function(distances = NULL, contiguity = NULL,

diff --git a/inst/examples/AHR.R b/inst/examples/AHR.R
diff --git a/inst/examples/checkContiguityGraph.R b/inst/examples/checkContiguityGraph.R
diff --git a/inst/examples/checkDistanceMatrix.R b/inst/examples/checkDistanceMatrix.R
diff --git a/inst/examples/checkPartition.R b/inst/examples/checkPartition.R
diff --git a/inst/examples/checkRegionalisation.R b/inst/examples/checkRegionalisation.R
diff --git a/inst/examples/equivalent_partitions.R b/inst/examples/equivalent_partitions.R
diff --git a/inst/examples/is_connected.R b/inst/examples/is_connected.R
diff --git a/inst/examples/medoid.R b/inst/examples/medoid.R
diff --git a/inst/examples/resolve_unfeasible.R b/inst/examples/resolve_unfeasible.R
diff --git a/inst/examples/standardize_partition.R b/inst/examples/standardize_partition.R
diff --git a/inst/exclusions_lintr.R b/inst/exclusions_lintr.R
@@ -24,7 +24,7 @@ make_exclusions_lintr <- function()
   # Remove some linters for example files
   for (exampleFile in exampleFilenames)
   {
-    pathFile <- file.path("inst/examples/", exampleFile)
+    pathFile <- file.path("inst/doc/", exampleFile)
     exclusions_list[[pathFile]] <- list(implicit_integer_linter = Inf,
                                         commented_code_linter = Inf,
                                         undesirable_function_linter = Inf)