From 6abc877942e31e476fa072244a4b6f2ccfa44bf7 Mon Sep 17 00:00:00 2001
From: Luuk van der Meer <luukvandermeer@live.nl>
Date: Wed, 22 Mar 2023 14:51:14 +0100
Subject: [PATCH 1/6] refactor: Make sf S3 methods consistent

---
 R/sf.R           | 49 ++++++++++++++++++++++++------------------------
 man/as.linnet.Rd |  2 +-
 man/sf.Rd        | 17 +++++++++++------
 3 files changed, 36 insertions(+), 32 deletions(-)

diff --git a/R/sf.R b/R/sf.R
index 1f36fd16..16caac49 100644
--- a/R/sf.R
+++ b/R/sf.R
@@ -16,6 +16,8 @@ is.sfg = function(x) {
 #'
 #' @param x An object of class \code{\link{sfnetwork}}.
 #'
+#' @param obj An object of class \code{\link{sfnetwork}}.
+#'
 #' @param y An object of class \code{\link[sf]{sf}}, or directly convertible to
 #' it using \code{\link[sf]{st_as_sf}}. In some cases, it can also be an object
 #' of \code{\link[sf:st]{sfg}} or \code{\link[sf:st_bbox]{bbox}}. Always look
@@ -30,6 +32,9 @@ is.sfg = function(x) {
 #' @param value The value to be assigned. See the documentation of the
 #' corresponding sf function for details.
 #'
+#' @param precision The precision to be assigned. See
+#' \code{\link[sf]{st_precision}} for details.
+#'
 #' @return The \code{sfnetwork} method for \code{\link[sf]{st_as_sf}} returns
 #' the active element of the network as object of class \code{\link[sf]{sf}}.
 #' The \code{sfnetwork} and \code{morphed_sfnetwork} methods for
@@ -118,8 +123,8 @@ st_as_s2.sfnetwork = function(x, active = NULL, ...) {
 #'
 #' @importFrom sf st_geometry
 #' @export
-st_geometry.sfnetwork = function(x, active = NULL, ...) {
-  pull_geom(x, active)
+st_geometry.sfnetwork = function(obj, active = NULL, ...) {
+  pull_geom(obj, active)
 }
 
 #' @name sf
@@ -149,12 +154,12 @@ st_drop_geometry.sfnetwork = function(x, ...) {
 #'
 #' @importFrom sf st_bbox st_geometry
 #' @export
-st_bbox.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
+st_bbox.sfnetwork = function(obj, active = NULL, ...) {
+  if (is.null(active)) active = attr(obj, "active")
   switch(
     active,
-    nodes = st_bbox(pull_node_geom(x), ...),
-    edges = st_bbox(pull_edge_geom(x), ...),
+    nodes = st_bbox(pull_node_geom(obj), ...),
+    edges = st_bbox(pull_edge_geom(obj), ...),
     raise_unknown_input(active)
   )
 }
@@ -226,27 +231,21 @@ st_crs.sfnetwork = function(x, active = NULL, ...) {
 #' @name sf
 #' @importFrom sf st_precision
 #' @export
-st_precision.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
-  switch(
-    active,
-    nodes = st_precision(pull_node_geom(x), ...),
-    edges = st_precision(pull_edge_geom(x), ...),
-    raise_unknown_input(active)
-  )
+st_precision.sfnetwork = function(x) {
+  st_precision(pull_geom(x))
 }
 
 #' @name sf
 #' @importFrom sf st_set_precision st_precision<-
 #' @export
-st_set_precision.sfnetwork = function(x, value) {
+st_set_precision.sfnetwork = function(x, precision) {
   if (attr(x, "active") == "edges" || has_explicit_edges(x)) {
     geom = pull_edge_geom(x)
-    st_precision(geom) = value
+    st_precision(geom) = precision
     x = mutate_edge_geom(x, geom)
   }
   geom = pull_node_geom(x)
-  st_precision(geom) = value
+  st_precision(geom) = precision
   mutate_node_geom(x, geom)
 }
 
@@ -288,12 +287,12 @@ st_zm.sfnetwork = function(x, ...) {
 #' @name sf
 #' @importFrom sf st_geometry st_m_range
 #' @export
-st_m_range.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
+st_m_range.sfnetwork = function(obj, active = NULL, ...) {
+  if (is.null(active)) active = attr(obj, "active")
   switch(
     active,
-    nodes = st_m_range(pull_node_geom(x), ...),
-    edges = st_m_range(pull_edge_geom(x), ...),
+    nodes = st_m_range(pull_node_geom(obj), ...),
+    edges = st_m_range(pull_edge_geom(obj), ...),
     raise_unknown_input(active)
   )
 }
@@ -301,12 +300,12 @@ st_m_range.sfnetwork = function(x, active = NULL, ...) {
 #' @name sf
 #' @importFrom sf st_geometry st_z_range
 #' @export
-st_z_range.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
+st_z_range.sfnetwork = function(obj, active = NULL, ...) {
+  if (is.null(active)) active = attr(obj, "active")
   switch(
     active,
-    nodes = st_z_range(pull_node_geom(x), ...),
-    edges = st_z_range(pull_edge_geom(x), ...),
+    nodes = st_z_range(pull_node_geom(obj), ...),
+    edges = st_z_range(pull_edge_geom(obj), ...),
     raise_unknown_input(active)
   )
 }
diff --git a/man/as.linnet.Rd b/man/as.linnet.Rd
index a4c61239..ac814f8b 100644
--- a/man/as.linnet.Rd
+++ b/man/as.linnet.Rd
@@ -5,7 +5,7 @@
 \alias{as.linnet.sfnetwork}
 \title{Convert a sfnetwork into a linnet}
 \usage{
-as.linnet.sfnetwork(X, ...)
+\method{as.linnet}{sfnetwork}(X, ...)
 }
 \arguments{
 \item{X}{An object of class \code{\link{sfnetwork}} with a projected CRS.}
diff --git a/man/sf.Rd b/man/sf.Rd
index 8f70a2f8..9b6698ba 100644
--- a/man/sf.Rd
+++ b/man/sf.Rd
@@ -46,13 +46,13 @@
 
 \method{st_as_s2}{sfnetwork}(x, active = NULL, ...)
 
-\method{st_geometry}{sfnetwork}(x, active = NULL, ...)
+\method{st_geometry}{sfnetwork}(obj, active = NULL, ...)
 
 \method{st_geometry}{sfnetwork}(x) <- value
 
 \method{st_drop_geometry}{sfnetwork}(x, ...)
 
-\method{st_bbox}{sfnetwork}(x, active = NULL, ...)
+\method{st_bbox}{sfnetwork}(obj, active = NULL, ...)
 
 \method{st_coordinates}{sfnetwork}(x, active = NULL, ...)
 
@@ -64,9 +64,9 @@
 
 \method{st_crs}{sfnetwork}(x) <- value
 
-\method{st_precision}{sfnetwork}(x, active = NULL, ...)
+\method{st_precision}{sfnetwork}(x)
 
-\method{st_set_precision}{sfnetwork}(x, value)
+\method{st_set_precision}{sfnetwork}(x, precision)
 
 \method{st_shift_longitude}{sfnetwork}(x, ...)
 
@@ -78,9 +78,9 @@
 
 \method{st_zm}{sfnetwork}(x, ...)
 
-\method{st_m_range}{sfnetwork}(x, active = NULL, ...)
+\method{st_m_range}{sfnetwork}(obj, active = NULL, ...)
 
-\method{st_z_range}{sfnetwork}(x, active = NULL, ...)
+\method{st_z_range}{sfnetwork}(obj, active = NULL, ...)
 
 \method{st_agr}{sfnetwork}(x, active = NULL, ...)
 
@@ -127,9 +127,14 @@ the given network. Defaults to \code{NULL}.}
 
 \item{...}{Arguments passed on the corresponding \code{sf} function.}
 
+\item{obj}{An object of class \code{\link{sfnetwork}}.}
+
 \item{value}{The value to be assigned. See the documentation of the
 corresponding sf function for details.}
 
+\item{precision}{The precision to be assigned. See
+\code{\link[sf]{st_precision}} for details.}
+
 \item{y}{An object of class \code{\link[sf]{sf}}, or directly convertible to
 it using \code{\link[sf]{st_as_sf}}. In some cases, it can also be an object
 of \code{\link[sf:st]{sfg}} or \code{\link[sf:st_bbox]{bbox}}. Always look

From d6870d19b62be5a7f56fe3e98d804d90996c71d7 Mon Sep 17 00:00:00 2001
From: Luuk van der Meer <luukvandermeer@live.nl>
Date: Wed, 22 Mar 2023 14:56:40 +0100
Subject: [PATCH 2/6] refactor: Make st_crs consistent with st_precision
 :construction:

---
 R/sf.R    | 10 ++--------
 man/sf.Rd |  2 +-
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/R/sf.R b/R/sf.R
index 16caac49..733888f7 100644
--- a/R/sf.R
+++ b/R/sf.R
@@ -204,14 +204,8 @@ st_is_valid.sfnetwork = function(x, ...) {
 #'
 #' @importFrom sf st_crs
 #' @export
-st_crs.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
-  switch(
-    active,
-    nodes = st_crs(pull_node_geom(x), ...),
-    edges = st_crs(pull_edge_geom(x), ...),
-    raise_unknown_input(active)
-  )
+st_crs.sfnetwork = function(x, ...) {
+  st_crs(pull_geom(x), ...)
 }
 
 #' @name sf
diff --git a/man/sf.Rd b/man/sf.Rd
index 9b6698ba..dc060d87 100644
--- a/man/sf.Rd
+++ b/man/sf.Rd
@@ -60,7 +60,7 @@
 
 \method{st_is_valid}{sfnetwork}(x, ...)
 
-\method{st_crs}{sfnetwork}(x, active = NULL, ...)
+\method{st_crs}{sfnetwork}(x, ...)
 
 \method{st_crs}{sfnetwork}(x) <- value
 

From bf6651edc8dad3e390949af80a938f0794823e5c Mon Sep 17 00:00:00 2001
From: Luuk van der Meer <luukvandermeer@live.nl>
Date: Wed, 22 Mar 2023 15:07:36 +0100
Subject: [PATCH 3/6] refactor: Tidy sf script :construction:

---
 R/sf.R | 76 +++++++++++++---------------------------------------------
 1 file changed, 17 insertions(+), 59 deletions(-)

diff --git a/R/sf.R b/R/sf.R
index 733888f7..a83b7192 100644
--- a/R/sf.R
+++ b/R/sf.R
@@ -100,13 +100,7 @@ edges_as_sf = function(x, ...) {
 #' @importFrom sf st_as_s2
 #' @export
 st_as_s2.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
-  switch(
-    active,
-    nodes = st_as_s2(pull_node_geom(x), ...),
-    edges = st_as_s2(pull_edge_geom(x), ...),
-    raise_unknown_input(active)
-  )
+  st_as_s2(pull_geom(x, active), ...)
 }
 
 # =============================================================================
@@ -152,45 +146,31 @@ st_drop_geometry.sfnetwork = function(x, ...) {
 #' # Get bbox of the active network element.
 #' st_bbox(net)
 #'
-#' @importFrom sf st_bbox st_geometry
+#' @importFrom sf st_bbox
 #' @export
 st_bbox.sfnetwork = function(obj, active = NULL, ...) {
-  if (is.null(active)) active = attr(obj, "active")
-  switch(
-    active,
-    nodes = st_bbox(pull_node_geom(obj), ...),
-    edges = st_bbox(pull_edge_geom(obj), ...),
-    raise_unknown_input(active)
-  )
+  st_bbox(pull_geom(obj, active), ...)
 }
 
 #' @name sf
-#' @importFrom sf st_coordinates st_geometry
+#' @importFrom sf st_coordinates
 #' @export
 st_coordinates.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
-  switch(
-    active,
-    nodes = st_coordinates(pull_node_geom(x), ...),
-    edges = st_coordinates(pull_edge_geom(x), ...),
-    raise_unknown_input(active)
-  )
+  st_coordinates(pull_geom(x, active), ...)
 }
 
 #' @name sf
 #' @importFrom sf st_is
 #' @export
 st_is.sfnetwork = function(x, ...) {
-  active = attr(x, "active")
-  st_is(pull_geom(x, active), ...)
+  st_is(pull_geom(x), ...)
 }
 
 #' @name sf
 #' @importFrom sf st_is_valid
 #' @export
 st_is_valid.sfnetwork = function(x, ...) {
-  active = attr(x, "active")
-  st_is_valid(pull_geom(x, active), ...)
+  st_is_valid(pull_geom(x), ...)
 }
 
 # =============================================================================
@@ -279,29 +259,17 @@ st_zm.sfnetwork = function(x, ...) {
 }
 
 #' @name sf
-#' @importFrom sf st_geometry st_m_range
+#' @importFrom sf st_m_range
 #' @export
 st_m_range.sfnetwork = function(obj, active = NULL, ...) {
-  if (is.null(active)) active = attr(obj, "active")
-  switch(
-    active,
-    nodes = st_m_range(pull_node_geom(obj), ...),
-    edges = st_m_range(pull_edge_geom(obj), ...),
-    raise_unknown_input(active)
-  )
+  st_m_range(pull_geom(obj, active), ...)
 }
 
 #' @name sf
-#' @importFrom sf st_geometry st_z_range
+#' @importFrom sf st_z_range
 #' @export
 st_z_range.sfnetwork = function(obj, active = NULL, ...) {
-  if (is.null(active)) active = attr(obj, "active")
-  switch(
-    active,
-    nodes = st_z_range(pull_node_geom(obj), ...),
-    edges = st_z_range(pull_edge_geom(obj), ...),
-    raise_unknown_input(active)
-  )
+  st_z_range(pull_geom(obj, active), ...)
 }
 
 change_coords = function(x, op, ...) {
@@ -330,13 +298,7 @@ change_coords = function(x, op, ...) {
 #' @importFrom sf st_agr
 #' @export
 st_agr.sfnetwork = function(x, active = NULL, ...) {
-  if (is.null(active)) active = attr(x, "active")
-  switch(
-    active,
-    nodes = node_agr(x),
-    edges = edge_agr(x),
-    raise_unknown_input(active)
-  )
+  agr(x, active)
 }
 
 #' @name sf
@@ -772,11 +734,10 @@ find_indices_to_drop = function(x, y, ..., .operator = sf::st_filter) {
 #' @importFrom sf st_geometry st_intersects
 #' @export
 st_intersects.sfnetwork = function(x, y, ...) {
-  active = attr(x, "active")
   if (missing(y)) {
-    st_intersects(pull_geom(x, active), ...)
+    st_intersects(pull_geom(x), ...)
   } else {
-    st_intersects(pull_geom(x, active), st_geometry(y), ...)
+    st_intersects(pull_geom(x), st_geometry(y), ...)
   }
 }
 
@@ -784,22 +745,19 @@ st_intersects.sfnetwork = function(x, y, ...) {
 #' @importFrom sf st_as_sf st_sample
 #' @export
 st_sample.sfnetwork = function(x, ...) {
-  active = attr(x, "active")
-  st_sample(st_as_sf(x, active), ...)
+  st_sample(st_as_sf(x), ...)
 }
 
 #' @name sf
 #' @importFrom sf st_geometry st_nearest_points
 #' @export
 st_nearest_points.sfnetwork = function(x, y, ...) {
-  active = attr(x, "active")
-  st_nearest_points(pull_geom(x, active), st_geometry(y), ...)
+  st_nearest_points(pull_geom(x), st_geometry(y), ...)
 }
 
 #' @name sf
 #' @importFrom sf st_area
 #' @export
 st_area.sfnetwork = function(x, ...) {
-  active = attr(x, "active")
-  st_area(pull_geom(x, active), ...)
+  st_area(pull_geom(x), ...)
 }

From af490854744a3d4c396b451c4fe0a64d6f130c6f Mon Sep 17 00:00:00 2001
From: Luuk van der Meer <luukvandermeer@live.nl>
Date: Wed, 22 Mar 2023 15:13:37 +0100
Subject: [PATCH 4/6] release: Version bump to 0.6.3 :bookmark:

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 001c6e77..1b561ce2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: sfnetworks
 Title: Tidy Geospatial Networks
-Version: 0.6.2
+Version: 0.6.3
 Authors@R:
     c(person(given = "Lucas",
              family = "van der Meer",

From 839dcabcecfa7ff3e8ba20fa228e7c6215718e25 Mon Sep 17 00:00:00 2001
From: Luuk van der Meer <luukvandermeer@live.nl>
Date: Wed, 22 Mar 2023 15:14:05 +0100
Subject: [PATCH 5/6] release: Update changelog and cran comments :bookmark:

---
 NEWS.md          |  8 ++++++++
 cran-comments.md | 11 +++++------
 2 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index fc1d64c7..0c969dd6 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,11 @@
+# sfnetworks v0.6.3
+
+### Bug fixes
+
+* Argument names of sfnetwork S3 methods for `sf::st_geometry()`, `sf::st_bbox()`, `sf::st_m_range()` and `sf::st_set_precision()` are updated to be consistent with their corresponding generic functions in sf.
+* Arguments `active` and `...` are removed from the sfnetwork S3 method for `sf::st_precision()` to be consistent with its corresponding generic function in sf.
+* Argument `active` is removed from the sfnetwork S3 method for `sf::st_crs()` to be consistent with the above-mentioned change regarding `sf::st_precision()` (since both CRS and precision can not differ between nodes and edges).
+
 # sfnetworks v0.6.2
 
 ### Bug fixes
diff --git a/cran-comments.md b/cran-comments.md
index bbc1137f..2143b65f 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,11 +1,10 @@
 In this release we have made the following changes:
 
-* The reference to `sf:::agr_levels` is removed, solving the note in the CRAN checks about the usage of the `:::` operator.
-* Unit tests that where failing after an igraph update now run successfully again. Refs [#232](https://github.com/luukvdmeer/sfnetworks/issues/232). This means the CRAN checks that where failing should now be passing successfully again.
-* Unit test stuck in an infinite loop caused by usage of `sf::st_sample()` on a polygon crossing the date line updated accordingly. See [this sf issue](https://github.com/r-spatial/sf/issues/1984) for details on the underlying problem.
-* The `to_spatial_contracted()` morpher now correctly handles cases for undirected networks in which only loop edges are created after contraction. Refs [#237](https://github.com/luukvdmeer/sfnetworks/issues/237).
-* The `to_spatial_contracted()` morpher now directly returns the original network when none of the contraction groups contain more than one node.
-* Umbrella packages tidyverse and spatstat are no longer suggested packages. Only individual members of these packages are now suggested packages.
+* Argument names of sfnetwork S3 methods for `sf::st_geometry()`, `sf::st_bbox()`, `sf::st_m_range()` and `sf::st_set_precision()` are updated to be consistent with their corresponding generic functions in sf.
+* Arguments `active` and `...` are removed from the sfnetwork S3 method for `sf::st_precision()` to be consistent with its corresponding generic function in sf.
+* Argument `active` is removed from the sfnetwork S3 method for `sf::st_crs()` to be consistent with the above-mentioned change regarding `sf::st_precision()` (since both CRS and precision can not differ between nodes and edges).
+
+These changes solve the warnings in the CRAN checks regarding S3 method consistency.
 
 ## R CMD check results
 

From d9b5ad2e2e1182be2aa53907bfbd197fb3a70870 Mon Sep 17 00:00:00 2001
From: Luuk van der Meer <luukvandermeer@live.nl>
Date: Wed, 22 Mar 2023 17:07:04 +0100
Subject: [PATCH 6/6] release: Update cran comments :bookmark:

---
 cran-comments.md | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/cran-comments.md b/cran-comments.md
index 2143b65f..802667c8 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -10,6 +10,15 @@ These changes solve the warnings in the CRAN checks regarding S3 method consiste
 
 0 errors | 0 warnings | 0 notes
 
+When running checks on R-hub, the following note occured only on Windows (Server 2022, R-devel 64-bit):
+
+```
+* checking for detritus in the temp directory ... NOTE
+Found the following files/directories:
+  'lastMiKTeXException'
+```
+As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this is a bug in R-hub rather than a bug in our package, and can likely be ignored.
+
 ## revdepcheck results
 
 We checked 1 reverse dependencies (0 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.