From aa7819c9a4fe5005f731cc2dc8b7c9deed685220 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 13:55:23 +0000
Subject: [PATCH 01/19] Modernise tests for classes

---
 tests/testthat/test_classes.R | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index e019f46..03fcc06 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -1,10 +1,8 @@
 library("geoGraph")
-context("Test classes")
 
 test_that("Empty constructors work", {
-  skip_on_cran()
   x <- new("gGraph")
+  expect_true(inherits(x,"gGraph"))
   y <- new("gData")
-  expect_is(x, "gGraph")
-  expect_is(y, "gData")
+  expect_true(inherits(y,"gData"))
 })

From e099cbde52551555348515f2417deceea30f4f65 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 14:07:28 +0000
Subject: [PATCH 02/19] add test for findLand

---
 tests/testthat/test_classes.R  | 1 -
 tests/testthat/test_findLand.R | 8 ++++++++
 2 files changed, 8 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/test_findLand.R

diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index 03fcc06..3797600 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -1,4 +1,3 @@
-library("geoGraph")
 
 test_that("Empty constructors work", {
   x <- new("gGraph")
diff --git a/tests/testthat/test_findLand.R b/tests/testthat/test_findLand.R
new file mode 100644
index 0000000..a7f5951
--- /dev/null
+++ b/tests/testthat/test_findLand.R
@@ -0,0 +1,8 @@
+test_that("find land correctly",{
+  # create a gGraph with one sea node and one land node
+  myCoords <- data.frame(long = c(-24, 37), lat =  c(31,55))
+  obj <- new("gGraph", coords = myCoords)
+  obj <- findLand(obj) 
+  # check that we classified the nodes correctly
+  expect_true(all(obj@nodes.attr$habitat==c("sea","land")))
+})
\ No newline at end of file

From 18a6da0af55a231b15b5a44529be4c9ed60dd4f8 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 14:12:06 +0000
Subject: [PATCH 03/19] check error messag for incorrect class

---
 tests/testthat/test_findLand.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/testthat/test_findLand.R b/tests/testthat/test_findLand.R
index a7f5951..4caebda 100644
--- a/tests/testthat/test_findLand.R
+++ b/tests/testthat/test_findLand.R
@@ -5,4 +5,8 @@ test_that("find land correctly",{
   obj <- findLand(obj) 
   # check that we classified the nodes correctly
   expect_true(all(obj@nodes.attr$habitat==c("sea","land")))
+  
+  # error if we pass an incorrect class
+  expect_error(findLand("blah"),
+               "unable to find an inherited method")
 })
\ No newline at end of file

From 774eaae0ade3e78739674ee54cf69d675a74834e Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 21:01:39 +0000
Subject: [PATCH 04/19] quick overlap algorithm

---
 R/extractFromLayer.R | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
index 6d3a3e7..c4a6f7b 100644
--- a/R/extractFromLayer.R
+++ b/R/extractFromLayer.R
@@ -95,35 +95,46 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
 
   ## Load default shapefile ##
   if (is.character(layer) && layer[1] == "world") {
-    layer <- worldshape
+    # layer <- worldshape
+    layer <- sf::st_read(system.file("files/shapefiles/world-countries.shp", package = "geoGraph"))
   }
 
   ## TODO if the layer is null, we should throw an error!!!
   if (!is.null(layer)) {
     if (!inherits(layer, "SpatialPolygonsDataFrame")) {
-      stop("Layer must be a SpatialPolygonsDataFrame object \n(see st_read and as_Spatial in sf to import such data from a GIS shapefile).")
+#      stop("Layer must be a SpatialPolygonsDataFrame object \n(see st_read and as_Spatial in sf to import such data from a GIS shapefile).")
     }
   }
 
   ## search attr in data ##
   if (attr[1] == "all") {
-    selAttr <- 1:ncol(layer@data)
+    selAttr <- 1:ncol(layer)
   } else {
-    selAttr <- match(attr, colnames(layer@data)) # selected attributes
+    selAttr <- match(attr, colnames(layer)) # selected attributes
     if (any(is.na(selAttr))) { # attribute not found in layer@data
       cat("\nSome requested attribute (attr) not found in the layer.\n")
       cat("\nAvailable data are:\n")
-      print(utils::head(layer@data))
+      print(utils::head(layer))
       return(NULL) # return NULL if attr not found, not generate an error
     }
   }
 
+  # create an sf point object from the coordinates
+  locations_st <- x %>% as.data.frame %>%sf::st_as_sf(coords=c(1,2))
+  points_within <- sf::st_within(locations_st, layer)
+  points_within <- sf::st_join(locations_st, layer, join = sf::st_within)
+  points_within <- sf::st_intersects(layer, locations_st)
+  points_within <- data.frame(x = unlist(points_within), 
+                              polygon = rep(seq_along(lengths(points_within)), lengths(points_within)))
+  
+  
+  
   ## variables and initialization ##
   long <- unlist(x[, 1]) # unlist needed when nrow==1
   lat <- unlist(x[, 2])
   n.poly.list <- length(layer@polygons) # number of lists of Polygons obj.
   res <- NULL
-  dat <- layer@data
+  dat <- layer
   layerId <- rep(NA, length(long)) # stores the id of matching polygon for each location
 
 

From 8bbe459f4bf85cf0d1d7c91e6237eb8df31ec234 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 21:25:37 +0000
Subject: [PATCH 05/19] Use sf for extractFromLayer

---
 R/extractFromLayer.R | 55 ++++++++------------------------------------
 1 file changed, 9 insertions(+), 46 deletions(-)

diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
index c4a6f7b..26e1111 100644
--- a/R/extractFromLayer.R
+++ b/R/extractFromLayer.R
@@ -49,15 +49,9 @@
 #'
 #' plot(worldgraph.10k, reset = TRUE)
 #'
-#'
-#' ## see what info is available
-#' names(worldshape@data)
-#' unique(worldshape@data$CONTINENT)
-#'
-#'
 #' ## retrieve continent info for all nodes
 #' ## (might take a few seconds)
-#' x <- extractFromLayer(worldgraph.10k, layer = worldshape, attr = "CONTINENT")
+#' x <- extractFromLayer(worldgraph.10k, layer = "world", attr = "CONTINENT")
 #' x
 #' table(getNodesAttr(x, attr.name = "CONTINENT"))
 #'
@@ -121,47 +115,16 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
 
   # create an sf point object from the coordinates
   locations_st <- x %>% as.data.frame %>%sf::st_as_sf(coords=c(1,2))
-  points_within <- sf::st_within(locations_st, layer)
-  points_within <- sf::st_join(locations_st, layer, join = sf::st_within)
+  # now find points in polygons
   points_within <- sf::st_intersects(layer, locations_st)
   points_within <- data.frame(x = unlist(points_within), 
                               polygon = rep(seq_along(lengths(points_within)), lengths(points_within)))
-  
-  
-  
-  ## variables and initialization ##
-  long <- unlist(x[, 1]) # unlist needed when nrow==1
-  lat <- unlist(x[, 2])
-  n.poly.list <- length(layer@polygons) # number of lists of Polygons obj.
-  res <- NULL
-  dat <- layer
-  layerId <- rep(NA, length(long)) # stores the id of matching polygon for each location
-
-
-  ## main computations ##
-
-  ## browsing elements of @polygons
-  ## each is a list with a @Polygons slot
-  for (i in 1:n.poly.list) {
-    this.poly.list <- layer@polygons[[i]]
-    n.polys <- length(this.poly.list@Polygons)
-    points.in.this.poly <- rep(0, length(long))
-
-    ## browsing elements of @Polygons
-    for (j in 1:n.polys) { ##
-      this.poly <- this.poly.list@Polygons[[j]]
-      points.in.this.poly <- points.in.this.poly +
-        sp::point.in.polygon(long, lat, this.poly@coords[, 1], this.poly@coords[, 2])
-
-      points.in.this.poly <- as.logical(points.in.this.poly)
-
-      if (any(points.in.this.poly)) {
-        layerId[points.in.this.poly] <- this.poly.list@ID
-      }
-    } # end for j
-  } # end for i
-
-  res <- dat[layerId, selAttr, drop = FALSE]
+  points_assignment <- data.frame(x=seq(1, nrow(x)), polygon = NA)
+  # add missing points for which we have no information
+  points_assignment[points_within$x,"polygon"]<-points_within$polygon
+
+  dat <- layer %>% sf::st_drop_geometry()
+  res <- dat[points_assignment$polygon, selAttr, drop = FALSE]
   row.names(res) <- rownames(x)
 
   return(res)
@@ -248,4 +211,4 @@ setMethod("extractFromLayer", "gData", function(x, layer = "world", attr = "all"
   }
 
   return(x)
-}) # end findLand
+})

From 08af23d77a78a652595328111dfc0ecfea25dd4f Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 21:43:47 +0000
Subject: [PATCH 06/19] Fix use of rnaturalearth

---
 R/extractFromLayer.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
index 26e1111..3a95eda 100644
--- a/R/extractFromLayer.R
+++ b/R/extractFromLayer.R
@@ -84,6 +84,8 @@ setGeneric("extractFromLayer", function(x, ...) {
 #' @rdname extractFromLayer
 #' @export
 setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all", ...) {
+  sf::sf_use_s2(FALSE)
+  
   ## This functions automatically assigns to land all points overlapping the country polygons
   # if(!require(maptools)) stop("maptools package is required.")
 
@@ -114,7 +116,9 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
   }
 
   # create an sf point object from the coordinates
-  locations_st <- x %>% as.data.frame %>%sf::st_as_sf(coords=c(1,2))
+  locations_st <- x %>% as.data.frame %>% 
+    sf::st_as_sf(coords=c(1,2)) %>%
+    sf::st_set_crs(sf::st_crs(layer))
   # now find points in polygons
   points_within <- sf::st_intersects(layer, locations_st)
   points_within <- data.frame(x = unlist(points_within), 

From 8f5c729ad288ca4bc6d46d449f59d7fa98dc1835 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Wed, 1 Nov 2023 21:48:34 +0000
Subject: [PATCH 07/19] how to use rnaturalearth

---
 R/extractFromLayer.R | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
index 3a95eda..06d45ab 100644
--- a/R/extractFromLayer.R
+++ b/R/extractFromLayer.R
@@ -91,14 +91,15 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
 
   ## Load default shapefile ##
   if (is.character(layer) && layer[1] == "world") {
-    # layer <- worldshape
+    # use rnaturalearth instead of the inbuilt dataset
+    # layer <- rnaturalearth::ne_countries(scale="medium", returnclass = "sf")
     layer <- sf::st_read(system.file("files/shapefiles/world-countries.shp", package = "geoGraph"))
   }
 
   ## TODO if the layer is null, we should throw an error!!!
   if (!is.null(layer)) {
-    if (!inherits(layer, "SpatialPolygonsDataFrame")) {
-#      stop("Layer must be a SpatialPolygonsDataFrame object \n(see st_read and as_Spatial in sf to import such data from a GIS shapefile).")
+    if (!inherits(layer, "sf")) {
+      stop("Layer must be a sf object \n(see st_read in sf to import such data from a GIS shapefile).")
     }
   }
 

From 6323e5fd47465c50ad9f1b0c8205d4c21b0a81ad Mon Sep 17 00:00:00 2001
From: Evie Carter <eviecarter41@outlook.com>
Date: Wed, 8 Nov 2023 06:56:59 +0000
Subject: [PATCH 08/19] Starting notes for test of NA values

---
 tests/testthat/test_findLand.R | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test_findLand.R b/tests/testthat/test_findLand.R
index 4caebda..397253b 100644
--- a/tests/testthat/test_findLand.R
+++ b/tests/testthat/test_findLand.R
@@ -9,4 +9,30 @@ test_that("find land correctly",{
   # error if we pass an incorrect class
   expect_error(findLand("blah"),
                "unable to find an inherited method")
-})
\ No newline at end of file
+
+})
+
+
+#Test whether findLand generates an error with invalid object
+test_that("co-ordinate format",{
+  #Create co-ordinates
+  obj <- matrix(c(-24, 31, 37, 55), nrow=2,ncol=2, byrow=TRUE)
+  obj <- findLand(obj) 
+  
+  #check for factor output
+  expect_is(obj,"factor")
+  #check for correct output
+  expect_equal(obj,factor(c('sea','land')))
+  
+  #obj1 <- matrix(c(-24, NA, 37, 55), nrow=2,ncol=2, byrow=TRUE)
+  #NA entries in matrix do not produce error
+  #expect_error(findLand(obj1))
+  
+  
+  
+  #obj2 <- data.frame(long = c(-24, 37), lat =  c(31,55))
+  #expect_error(obj2 <- findLand())
+})
+
+
+

From d6f704a06c02dfa603686585de67df6ad7a2139e Mon Sep 17 00:00:00 2001
From: Evie Carter <eviecarter41@outlook.com>
Date: Tue, 14 Nov 2023 12:00:09 +0000
Subject: [PATCH 09/19] Adding NA test and an if NA statement to findLand
 function

---
 R/findLand.R                   |  4 ++++
 tests/testthat/test_findLand.R | 27 ++++++++++++++++++++-------
 2 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/R/findLand.R b/R/findLand.R
index a187d40..d5ade2c 100644
--- a/R/findLand.R
+++ b/R/findLand.R
@@ -91,6 +91,10 @@ setMethod("findLand", "matrix", function(x, shape = "world", ...) {
     }
   }
 
+  if (any(is.na(x))) {
+    stop("Matrix contains NA values.")
+  }
+  
   long <- x[, 1]
   lat <- x[, 2]
   n.country <- length(shape@polygons)
diff --git a/tests/testthat/test_findLand.R b/tests/testthat/test_findLand.R
index 397253b..73af25a 100644
--- a/tests/testthat/test_findLand.R
+++ b/tests/testthat/test_findLand.R
@@ -9,13 +9,24 @@ test_that("find land correctly",{
   # error if we pass an incorrect class
   expect_error(findLand("blah"),
                "unable to find an inherited method")
+  
+  #Create gGraph with NA's
+  NACoords <- data.frame(long = c(-24, NA), lat =  c(31,55))
+  NA_gGraph <- new("gGraph", coords = NACoords)
+  
+  #NA entries are recognised and produce error in plot
+  expect_error(plot(NA_gGraph))
+  
+  #NA produces error in findLand
+  expect_error(findLand(NA_gGraph))
+  
 
 })
 
 
-#Test whether findLand generates an error with invalid object
+#Test whether findLand generates an error with invalid matrix object
 test_that("co-ordinate format",{
-  #Create co-ordinates
+  #Create co-ordinates matrix
   obj <- matrix(c(-24, 31, 37, 55), nrow=2,ncol=2, byrow=TRUE)
   obj <- findLand(obj) 
   
@@ -24,14 +35,16 @@ test_that("co-ordinate format",{
   #check for correct output
   expect_equal(obj,factor(c('sea','land')))
   
-  #obj1 <- matrix(c(-24, NA, 37, 55), nrow=2,ncol=2, byrow=TRUE)
-  #NA entries in matrix do not produce error
-  #expect_error(findLand(obj1))
+  #Create co-ordinates matrix with NA
+  NA_matrix <- matrix(c(-24, NA, 37, 55), nrow=2,ncol=2, byrow=TRUE)
+  #NA entries are recognised and produce error in plot 
+  expect_true(is.na(NA_matrix[1,2]))
+  expect_error(plotEdges(NA_matrix))
   
+  #NA produces error in findLand
+  expect_error(findLand(NA_matrix))
   
   
-  #obj2 <- data.frame(long = c(-24, 37), lat =  c(31,55))
-  #expect_error(obj2 <- findLand())
 })
 
 

From 8d5d5f8af5d2fcd6711a701ae6e74d9b47a677c9 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 14 Nov 2023 13:41:00 +0000
Subject: [PATCH 10/19] Update version

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

diff --git a/DESCRIPTION b/DESCRIPTION
index 9ad1686..679bfed 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: geoGraph
 Type: Package
 Title: Walking through the geographic space using graphs
-Version: 1.1.1.9001
+Version: 1.1.1.9002
 Author: Thibaut Jombart,
   Andrea Manica
 Maintainer: Andrea Manica <am315@cam.ac.uk>

From 8009b3fd91d7dbcd70f732c7f325289ee62eaebb Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 28 Nov 2023 14:05:23 +0000
Subject: [PATCH 11/19] check for NAs in gGraph constructor

---
 R/classes.R                    | 10 +++++++++-
 tests/testthat/test_classes.R  |  8 ++++++++
 tests/testthat/test_findLand.R | 13 +++++--------
 3 files changed, 22 insertions(+), 9 deletions(-)

diff --git a/R/classes.R b/R/classes.R
index 48a9da7..77ef972 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -289,7 +289,15 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
       input$coords <- as.matrix(input$coords)
     }
 
-    if (nrow(input$coords) > 0 && !is.numeric(input$coords)) stop("Argument coords has to be numeric.")
+    if (nrow(input$coords) > 0 && !is.numeric(input$coords)) {
+      stop("Argument coords has to be numeric.")
+      }
+    
+    ## NAs in coords
+    if (any(is.na(input$coords))) {
+      stop("Argument coords includes NAs")
+    }
+    
 
     ## names of the matrix
     colnames(input$coords) <- c("lon", "lat")
diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index 3797600..8263dc2 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -5,3 +5,11 @@ test_that("Empty constructors work", {
   y <- new("gData")
   expect_true(inherits(y,"gData"))
 })
+
+test_that("Contructors fails with invalid coordinates",{
+  NACoords <- data.frame(long = c(-24, NA), lat =  c(31,55))
+  #Create gGraph with NA's
+  expect_error(new("gGraph", coords = NACoords),
+               "Argument coords includes NAs")
+
+})
\ No newline at end of file
diff --git a/tests/testthat/test_findLand.R b/tests/testthat/test_findLand.R
index 73af25a..a8c85d2 100644
--- a/tests/testthat/test_findLand.R
+++ b/tests/testthat/test_findLand.R
@@ -10,16 +10,13 @@ test_that("find land correctly",{
   expect_error(findLand("blah"),
                "unable to find an inherited method")
   
-  #Create gGraph with NA's
+  # tests error for NAs as coordinates (this only applies to matrices and data.frames)
+  # gGraph objects should fail when creted with NA coordinates
   NACoords <- data.frame(long = c(-24, NA), lat =  c(31,55))
-  NA_gGraph <- new("gGraph", coords = NACoords)
-  
-  #NA entries are recognised and produce error in plot
-  expect_error(plot(NA_gGraph))
-  
-  #NA produces error in findLand
-  expect_error(findLand(NA_gGraph))
+  expect_error(findLand(NACoords),
+               "Matrix contains NA")
   
+ 
 
 })
 

From 244938b91c306b9a5e6c3a40dcd6fb51ad2b620a Mon Sep 17 00:00:00 2001
From: m-colucci <margherita.col@gmail.com>
Date: Mon, 4 Dec 2023 21:06:48 +0100
Subject: [PATCH 12/19] check numeric coordinates and ncol

---
 R/classes.R                   |  4 ++++
 tests/testthat/test_classes.R | 18 +++++++++++++++++-
 2 files changed, 21 insertions(+), 1 deletion(-)

diff --git a/R/classes.R b/R/classes.R
index 77ef972..fff4b82 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -281,6 +281,10 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
 
   ## handle @coords ##
   if (!is.null(input$coords)) {
+    if (is.list(input$coords) && length(input$coords) > 2) {
+      stop("Argument coords must include only two columns (longitude and latitude).")
+    }
+
     if (is.list(input$coords) && length(input$coords) == 2) {
       input$coords <- as.data.frame(input$coords)
     }
diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index 8263dc2..d6c0513 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -12,4 +12,20 @@ test_that("Contructors fails with invalid coordinates",{
   expect_error(new("gGraph", coords = NACoords),
                "Argument coords includes NAs")
 
-})
\ No newline at end of file
+})
+
+test_that("Contructors fails with invalid matrix dimensions",{
+  extra_coords <- data.frame(long = c(-24, 37), lat =  c(31,55), x = c(31,31))
+  #Create gGraph with three columns
+  expect_error(new("gGraph", coords = extra_coords),
+               "Argument coords must include")
+
+})
+
+test_that("Contructors fails with invalid non-numeric matrix",{
+  non_num_coords <- data.frame(long = c("lon1", 37), lat =  c(31,55))
+  #Create gGraph with non numeric elements
+  expect_error(new("gGraph", coords = non_num_coords),
+               "Argument coords has to be numeric")
+  
+})

From 293371a0a72edecb8543856a50835f649f91eb99 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 5 Dec 2023 13:08:25 +0000
Subject: [PATCH 13/19] docs fixes

---
 DESCRIPTION             | 14 +++++++++-----
 NAMESPACE               |  2 ++
 R/extractFromLayer.R    |  9 +++++++--
 R/utils-pipe.R          | 14 ++++++++++++++
 man/buffer.Rd           | 34 +++++++++++++++++-----------------
 man/closestNode.Rd      | 17 ++++++++---------
 man/dijkstra-methods.Rd | 15 +++++++--------
 man/dropDeadEdges.Rd    |  3 +--
 man/extractFromLayer.Rd | 18 +++++-------------
 man/findLand.Rd         |  7 +++----
 man/gData-class.Rd      | 11 +++++------
 man/gGraph-class.Rd     | 15 +++++++--------
 man/geo.add.edges.Rd    |  9 ++++-----
 man/geo.change.attr.Rd  | 15 +++++++--------
 man/geoGraph-package.Rd | 13 ++++++-------
 man/getColors.Rd        |  3 +--
 man/getCosts.Rd         |  4 ++--
 man/getEdges.Rd         |  4 ++--
 man/getNodesAttr.Rd     |  1 -
 man/hgdp.Rd             | 18 +++++++++---------
 man/isInArea.Rd         | 10 +++++-----
 man/makeGrid.Rd         | 10 ++++++----
 man/pipe.Rd             | 20 ++++++++++++++++++++
 man/plot-gData.Rd       | 19 +++++++++----------
 man/plot-gGraph.Rd      | 19 +++++++++----------
 man/setCosts.Rd         |  9 ++++-----
 man/setDistCosts.Rd     | 22 +++++++++++-----------
 man/worldgraph.Rd       | 15 +++++++--------
 man/zoom.Rd             | 11 +++++------
 29 files changed, 192 insertions(+), 169 deletions(-)
 create mode 100644 R/utils-pipe.R
 create mode 100644 man/pipe.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index c524be3..e85deb0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,14 +17,17 @@ Depends:
   methods,
   graph
 Imports:
-  fields,
-  RBGL,
-  sp
+    fields,
+    RBGL,
+    rnaturalearth,
+    rnaturalearthdata,
+    sp,
+    sf,
+    magrittr
 Suggests: 
   testthat, 
   knitr, 
-  rmarkdown,
-  sf
+  rmarkdown
 RoxygenNote: 7.2.3
 Collate: 
     'classes.R'
@@ -48,5 +51,6 @@ Collate:
     'rebuild.R'
     'setCosts.R'
     'setDistCosts.R'
+    'utils-pipe.R'
     'zoom.R'
     'zzz.R'
diff --git a/NAMESPACE b/NAMESPACE
index 243f0ad..03aae94 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(plot,gPath)
+export("%>%")
 export()
 export(.gData.valid)
 export(.gGraph.valid)
@@ -76,3 +77,4 @@ import(sp)
 importFrom(graphics,identify)
 importFrom(graphics,locator)
 importFrom(graphics,segments)
+importFrom(magrittr,"%>%")
diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
index 06d45ab..5f0b6a3 100644
--- a/R/extractFromLayer.R
+++ b/R/extractFromLayer.R
@@ -84,7 +84,7 @@ setGeneric("extractFromLayer", function(x, ...) {
 #' @rdname extractFromLayer
 #' @export
 setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all", ...) {
-  sf::sf_use_s2(FALSE)
+  
   
   ## This functions automatically assigns to land all points overlapping the country polygons
   # if(!require(maptools)) stop("maptools package is required.")
@@ -93,13 +93,18 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
   if (is.character(layer) && layer[1] == "world") {
     # use rnaturalearth instead of the inbuilt dataset
     # layer <- rnaturalearth::ne_countries(scale="medium", returnclass = "sf")
+    # sf::sf_use_s2(FALSE)
     layer <- sf::st_read(system.file("files/shapefiles/world-countries.shp", package = "geoGraph"))
   }
 
   ## TODO if the layer is null, we should throw an error!!!
   if (!is.null(layer)) {
     if (!inherits(layer, "sf")) {
-      stop("Layer must be a sf object \n(see st_read in sf to import such data from a GIS shapefile).")
+      if (inherits(layer, "SpatialPolygonsDataFrame")){
+        layer <- sf::st_as_sf(layer)
+      } else {
+        stop("Layer must be a sf object \n(see st_read in sf to import such data from a GIS shapefile).")
+      }
     }
   }
 
diff --git a/R/utils-pipe.R b/R/utils-pipe.R
new file mode 100644
index 0000000..fd0b1d1
--- /dev/null
+++ b/R/utils-pipe.R
@@ -0,0 +1,14 @@
+#' Pipe operator
+#'
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @rdname pipe
+#' @keywords internal
+#' @export
+#' @importFrom magrittr %>%
+#' @usage lhs \%>\% rhs
+#' @param lhs A value or the magrittr placeholder.
+#' @param rhs A function call using the magrittr semantics.
+#' @return The result of calling `rhs(lhs)`.
+NULL
diff --git a/man/buffer.Rd b/man/buffer.Rd
index 82699b6..c7220ff 100644
--- a/man/buffer.Rd
+++ b/man/buffer.Rd
@@ -50,33 +50,33 @@ location they surround.
 
 #### gGraph example ####
 ## zoom in to an area
-plot(worldgraph.10k, reset=TRUE)
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+plot(worldgraph.10k, reset = TRUE)
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 
 ## identify one node
-oneNodeXY <- c(getCoords(worldgraph.10k)[9299,1],getCoords(worldgraph.10k)[9299,2])
-points(oneNodeXY[1],  oneNodeXY[2], col="red")
+oneNodeXY <- c(getCoords(worldgraph.10k)[9299, 1], getCoords(worldgraph.10k)[9299, 2])
+points(oneNodeXY[1], oneNodeXY[2], col = "red")
 
 ## find some buffers
 buffer(worldgraph.10k, "9299", 100) # nothing around 100km
 buffer(worldgraph.10k, "9299", 500)
-buf500km <- buffer(worldgraph.10k, "9299", 500, res="gGraph")
-plot(buf500km, col.rules=buf500km@meta$buf.colors)
-buf1000km <- buffer(worldgraph.10k, "9299", 1000, res="gGraph")
-plot(buf1000km, col.rules=buf1000km@meta$buf.colors)
+buf500km <- buffer(worldgraph.10k, "9299", 500, res = "gGraph")
+plot(buf500km, col.rules = buf500km@meta$buf.colors)
+buf1000km <- buffer(worldgraph.10k, "9299", 1000, res = "gGraph")
+plot(buf1000km, col.rules = buf1000km@meta$buf.colors)
 
 
 #### gData example ####
 x <- hgdp[27:30] # retain a subset of hgdp
-plot(x, reset=TRUE, col.g="lightgrey", pch.node=20)
-buf.200 <- buffer(x, 200, res="gData")
-buf.400 <- buffer(x, 400, res="gData")
-buf.600 <- buffer(x, 600, res="gData")
-buf.1000 <- buffer(x, 1000, res="gData")
-points(buf.1000, col.node="black")
-points(buf.600, col.node="yellow")
-points(buf.400, col.node="gold")
-points(buf.200, col.node="orange")
+plot(x, reset = TRUE, col.g = "lightgrey", pch.node = 20)
+buf.200 <- buffer(x, 200, res = "gData")
+buf.400 <- buffer(x, 400, res = "gData")
+buf.600 <- buffer(x, 600, res = "gData")
+buf.1000 <- buffer(x, 1000, res = "gData")
+points(buf.1000, col.node = "black")
+points(buf.600, col.node = "yellow")
+points(buf.400, col.node = "gold")
+points(buf.200, col.node = "orange")
 title("Different buffers for a gData \n(100km, 200km, 500km)")
 
 }
diff --git a/man/closestNode.Rd b/man/closestNode.Rd
index f7dffca..fe340a7 100644
--- a/man/closestNode.Rd
+++ b/man/closestNode.Rd
@@ -68,33 +68,32 @@ that it is not possible to specify node attributes (\code{attr.names} and
 
 }}
 \examples{
-
 \dontrun{
 ## interactive example ##
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 ## zooming in
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 ## click some locations
-myNodes <- closestNode(worldgraph.10k,locator(), attr.name="habitat", attr.value="land")
+myNodes <- closestNode(worldgraph.10k, locator(), attr.name = "habitat", attr.value = "land")
 myNodes
 
 ## here are the closestNodes
-points(getCoords(worldgraph.10k)[myNodes,], col="red")
+points(getCoords(worldgraph.10k)[myNodes, ], col = "red")
 }
 
 ## example with a gData object ##
-myLoc <- list(x=c(3, -8, 11, 28), y=c(50, 57, 71, 67)) # some locations
-obj <- new("gData", coords=myLoc) # new gData object
+myLoc <- list(x = c(3, -8, 11, 28), y = c(50, 57, 71, 67)) # some locations
+obj <- new("gData", coords = myLoc) # new gData object
 obj
 
 obj@gGraph.name <- "worldgraph.10k" # this could be done when creating obj
-obj <- closestNode(obj, attr.name="habitat", attr.value="land")
+obj <- closestNode(obj, attr.name = "habitat", attr.value = "land")
 
 ## plot the result (original location -> assigned node)
-plot(obj, method="both", reset=TRUE)
+plot(obj, method = "both", reset = TRUE)
 title("'x'=location, 'o'=assigned node")
 
 
diff --git a/man/dijkstra-methods.Rd b/man/dijkstra-methods.Rd
index 3ebc6eb..dd0bfe6 100644
--- a/man/dijkstra-methods.Rd
+++ b/man/dijkstra-methods.Rd
@@ -89,28 +89,27 @@ In 'dijkstraBetween', paths are seeked all possible pairs of nodes between
 'from' and 'to'.
 }
 \examples{
-
 \dontrun{
 
 ## plotting
 world <- worldgraph.40k
-par(mar=rep(.1,4))
-plot(world, reset=TRUE)
+par(mar = rep(.1, 4))
+plot(world, reset = TRUE)
 
 ## check connectivity
 isConnected(hgdp) # must be ok
 
 ## Lowest cost path from an hypothetical origin
-ori.coord <- list(33,10) # one given location long/lat
-points(data.frame(ori.coord), pch="x", col="black", cex=3) # an 'x' shows the putative origin
+ori.coord <- list(33, 10) # one given location long/lat
+points(data.frame(ori.coord), pch = "x", col = "black", cex = 3) # an 'x' shows the putative origin
 ori <- closestNode(world, ori.coord) # assign it the closest node
 
 myPath <- dijkstraFrom(hgdp, ori) # compute shortest path
 
 ## plotting
-plot(world,pch="") # plot the world
-points(hgdp, lwd=3) # plot populations
-points(data.frame(ori.coord), pch="x", col="black", cex=3) # add origin
+plot(world, pch = "") # plot the world
+points(hgdp, lwd = 3) # plot populations
+points(data.frame(ori.coord), pch = "x", col = "black", cex = 3) # add origin
 plot(myPath) # plot the path
 }
 
diff --git a/man/dropDeadEdges.Rd b/man/dropDeadEdges.Rd
index 7d2ba00..2dc8d97 100644
--- a/man/dropDeadEdges.Rd
+++ b/man/dropDeadEdges.Rd
@@ -28,9 +28,8 @@ Dead nodes are nodes that are not connected to any other node, thus not
 having any role in the connectivity of a graph.\cr
 }
 \examples{
-
 \dontrun{
-plot(worldgraph.10k,reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 x <- dropDeadNodes(worldgraph.10k)
 plot(x)
 }
diff --git a/man/extractFromLayer.Rd b/man/extractFromLayer.Rd
index 08fb2ed..c92db67 100644
--- a/man/extractFromLayer.Rd
+++ b/man/extractFromLayer.Rd
@@ -67,30 +67,22 @@ Nodes can be specified in different ways, including by providing a
 input formats.
 }
 \examples{
-
 \dontrun{
 
-plot(worldgraph.10k, reset=TRUE)
-
-
-## see what info is available
-names(worldshape@data)
-unique(worldshape@data$CONTINENT)
-
+plot(worldgraph.10k, reset = TRUE)
 
 ## retrieve continent info for all nodes
 ## (might take a few seconds)
-x <- extractFromLayer(worldgraph.10k, layer=worldshape, attr="CONTINENT")
+x <- extractFromLayer(worldgraph.10k, layer = "world", attr = "CONTINENT")
 x
-table(getNodesAttr(x, attr.name="CONTINENT"))
+table(getNodesAttr(x, attr.name = "CONTINENT"))
 
 
 ## subset Africa
-temp <- getNodesAttr(x, attr.name="CONTINENT")=="Africa"
+temp <- getNodesAttr(x, attr.name = "CONTINENT") == "Africa"
 temp[is.na(temp)] <- FALSE
 x <- x[temp]
-plot(x, reset=TRUE)
-
+plot(x, reset = TRUE)
 }
 
 }
diff --git a/man/findLand.Rd b/man/findLand.Rd
index cc298ea..a513acd 100644
--- a/man/findLand.Rd
+++ b/man/findLand.Rd
@@ -55,8 +55,8 @@ Nodes can be specified either as a matrix of geographic coordinates, or as a
 
 
 ## create a new gGraph with random coordinates
-myCoords <- data.frame(long=runif(1000,-180,180), lat=runif(1000,-90,90))
-obj <- new("gGraph", coords=myCoords)
+myCoords <- data.frame(long = runif(1000, -180, 180), lat = runif(1000, -90, 90))
+obj <- new("gGraph", coords = myCoords)
 obj # note: no node attribute
 plot(obj)
 
@@ -65,14 +65,13 @@ obj <- findLand(obj)
 obj # note: new node attribute
 
 ## define rules for colors
-temp <- data.frame(habitat=c("land","sea"), color=c("green","blue"))
+temp <- data.frame(habitat = c("land", "sea"), color = c("green", "blue"))
 temp
 obj@meta$color <- temp
 
 ## plot object with new colors
 plot(obj)
 
-
 }
 \seealso{
 \code{\link{extractFromLayer}}, to retrieve any information from a
diff --git a/man/gData-class.Rd b/man/gData-class.Rd
index 42deaf9..fcd8fb7 100644
--- a/man/gData-class.Rd
+++ b/man/gData-class.Rd
@@ -63,16 +63,15 @@ arguments:
 hgdp
 
 ## plot data
-plot(worldgraph.40k, pch="")
+plot(worldgraph.40k, pch = "")
 points(hgdp)
 
 ## subset and plot data
-onlyNorth <- hgdp[hgdp@data$Latitude >0] # only northern populations
-
-plot(worldgraph.40k, reset=TRUE)
-abline(h=0) # equator
-points(onlyNorth, pch.node=20, cex=2, col.node="purple")
+onlyNorth <- hgdp[hgdp@data$Latitude > 0] # only northern populations
 
+plot(worldgraph.40k, reset = TRUE)
+abline(h = 0) # equator
+points(onlyNorth, pch.node = 20, cex = 2, col.node = "purple")
 
 }
 \seealso{
diff --git a/man/gGraph-class.Rd b/man/gGraph-class.Rd
index dde6eab..ec782b8 100644
--- a/man/gGraph-class.Rd
+++ b/man/gGraph-class.Rd
@@ -65,10 +65,10 @@ new("gGraph")
 
 
 ## plotting the object
-plot(rawgraph.10k, reset=TRUE)
+plot(rawgraph.10k, reset = TRUE)
 
 ## zooming in
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 ## to play interactively with graphics, use:
@@ -79,20 +79,19 @@ title("Europe")
 
 ## defining a new object restrained to visible nodes
 x <- rawgraph.10k[isInArea(rawgraph.10k)]
-plot(x,reset=TRUE, edges=TRUE)
+plot(x, reset = TRUE, edges = TRUE)
 title("x does just contain these visible nodes.")
 
 ## define weights for edges
-x <- setCosts(x, attr.name="habitat", method="prod")
-plot(x,edges=TRUE)
+x <- setCosts(x, attr.name = "habitat", method = "prod")
+plot(x, edges = TRUE)
 title("costs defined by habitat (land/land=1, other=100)")
 
 ## drop 'dead edges' (i.e. with weight 0)
-x <- dropDeadEdges(x, thres=10)
-plot(x,edges=TRUE)
+x <- dropDeadEdges(x, thres = 10)
+plot(x, edges = TRUE)
 title("after droping edges with null weight")
 
-
 }
 \seealso{
 Related classes are:\cr \% - \code{\linkS4class{graphNEL}}
diff --git a/man/geo.add.edges.Rd b/man/geo.add.edges.Rd
index 4d90b58..9197a72 100644
--- a/man/geo.add.edges.Rd
+++ b/man/geo.add.edges.Rd
@@ -33,21 +33,20 @@ edges (mode="points")\cr - select an area in which all edges from a
 reference graph are added (mode="area").\cr
 }
 \examples{
-
 \dontrun{
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 ## zooming in
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 ## remove edges
 geo.remove.edges(worldgraph.10k) # points mode
-geo.remove.edges(worldgraph.10k, mode="area") # area mode
+geo.remove.edges(worldgraph.10k, mode = "area") # area mode
 
 ## add edges
 geo.add.edges(worldgraph.10k) # points mode
-geo.add.edges(worldgraph.10k, mode="area") # area mode
+geo.add.edges(worldgraph.10k, mode = "area") # area mode
 }
 }
 \seealso{
diff --git a/man/geo.change.attr.Rd b/man/geo.change.attr.Rd
index 66e94b7..8c3eb7e 100644
--- a/man/geo.change.attr.Rd
+++ b/man/geo.change.attr.Rd
@@ -60,23 +60,22 @@ worldgraph.10k that are exclusively on land: this would be done by
 specifying \code{only.name="habitat"} and \code{only.value="land"}.
 }
 \examples{
-
 \dontrun{
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 ## have to click here for an area
 ## all nodes are modified in the area
-x <- geo.change.attr(worldgraph.10k, mode="area", attr.name="habitat", attr.value="fancy
-habitat", newCol="pink") # modify selected area
+x <- geo.change.attr(worldgraph.10k, mode = "area", attr.name = "habitat", attr.value = "fancy
+habitat", newCol = "pink") # modify selected area
 
-plot(x,reset=TRUE) # modification in the whole selected area
+plot(x, reset = TRUE) # modification in the whole selected area
 
 ## have to click here for an area
 ## only nodes on land are modified
-x <- geo.change.attr(x, mode="area", attr.name="habitat", attr.value="fancy2
-habitat", newCol="purple", only.name="habitat", only.value="land")
+x <- geo.change.attr(x, mode = "area", attr.name = "habitat", attr.value = "fancy2
+habitat", newCol = "purple", only.name = "habitat", only.value = "land")
 
-plot(x,reset=TRUE) # modification in the whole selected area
+plot(x, reset = TRUE) # modification in the whole selected area
 }
 
 }
diff --git a/man/geoGraph-package.Rd b/man/geoGraph-package.Rd
index a01dd39..3b888b3 100644
--- a/man/geoGraph-package.Rd
+++ b/man/geoGraph-package.Rd
@@ -89,10 +89,10 @@ To cite geoGraph, please use the reference given by
 worldgraph.10k
 
 ## plotting the object
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 ## zooming in
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 ## to play interactively with graphics, use:
@@ -103,20 +103,19 @@ title("Europe")
 
 ## defining a new object restrained to visible nodes
 x <- worldgraph.10k[isInArea(worldgraph.10k)]
-plot(x,reset=TRUE, edges=TRUE)
+plot(x, reset = TRUE, edges = TRUE)
 title("x does just contain these visible nodes.")
 
 ## define weights for edges
-x <- setCosts(x, attr.name="habitat", method="prod")
-plot(x,edges=TRUE)
+x <- setCosts(x, attr.name = "habitat", method = "prod")
+plot(x, edges = TRUE)
 title("connectivity defined by habitat (land/land=1, other=0)")
 
 ## drop 'dead edges' (i.e. with weight 0)
 x <- dropDeadEdges(x)
-plot(x,edges=TRUE)
+plot(x, edges = TRUE)
 title("after droping edges with null weight")
 
-
 }
 \keyword{manip}
 \keyword{spatial}
diff --git a/man/getColors.Rd b/man/getColors.Rd
index 03da00a..7eca63f 100644
--- a/man/getColors.Rd
+++ b/man/getColors.Rd
@@ -55,8 +55,7 @@ worldgraph.10k # there is a node attribute 'habitat'
 worldgraph.10k@meta$color
 
 head(getNodes(worldgraph.10k))
-head(getColors(worldgraph.10k,res.type="vector", attr.name="habitat"))
-
+head(getColors(worldgraph.10k, res.type = "vector", attr.name = "habitat"))
 
 }
 \author{
diff --git a/man/getCosts.Rd b/man/getCosts.Rd
index 41d103e..0d6df6d 100644
--- a/man/getCosts.Rd
+++ b/man/getCosts.Rd
@@ -66,8 +66,8 @@ connectivity there is between the couple of concerned nodes.
 }}
 \examples{
 
-head(getEdges(worldgraph.10k, res.type="matNames",unique=TRUE))
-head(getCosts(worldgraph.10k,res.type="vector",unique=TRUE))
+head(getEdges(worldgraph.10k, res.type = "matNames", unique = TRUE))
+head(getCosts(worldgraph.10k, res.type = "vector", unique = TRUE))
 
 
 }
diff --git a/man/getEdges.Rd b/man/getEdges.Rd
index 0f9b22d..2e6dfa7 100644
--- a/man/getEdges.Rd
+++ b/man/getEdges.Rd
@@ -47,8 +47,8 @@ object using different possible outputs.
 example(gGraph)
 
 getEdges(x)
-getEdges(x,res.type="matNames")
-getEdges(x,res.type="matId")
+getEdges(x, res.type = "matNames")
+getEdges(x, res.type = "matId")
 
 }
 \seealso{
diff --git a/man/getNodesAttr.Rd b/man/getNodesAttr.Rd
index 22167cf..737cea1 100644
--- a/man/getNodesAttr.Rd
+++ b/man/getNodesAttr.Rd
@@ -50,7 +50,6 @@ head(getNodesAttr(worldgraph.40k))
 ## gData method
 getNodesAttr(hgdp)
 
-
 }
 \seealso{
 Most other accessors are documented in \linkS4class{gGraph} and
diff --git a/man/hgdp.Rd b/man/hgdp.Rd
index 8a0c986..32341f9 100644
--- a/man/hgdp.Rd
+++ b/man/hgdp.Rd
@@ -37,24 +37,24 @@ plot(hgdp)
 ## results from Handley et al.
 \dontrun{
 ## Addis Ababa
-addis <- list(lon=38.74,lat=9.03)
-addis <- closestNode(worldgraph.40k,addis) # this takes a while
+addis <- list(lon = 38.74, lat = 9.03)
+addis <- closestNode(worldgraph.40k, addis) # this takes a while
 
 ## shortest path from Addis Ababa
 myPath <- dijkstraFrom(hgdp, addis)
 
 ## plot results
-plot(worldgraph.40k, col=0)
+plot(worldgraph.40k, col = 0)
 points(hgdp)
-points(worldgraph.40k[addis], psize=3,pch="x", col="black")
+points(worldgraph.40k[addis], psize = 3, pch = "x", col = "black")
 plot(myPath)
 
 ## correlations distance/genetic div.
-geo.dist <- sapply(myPath[-length(myPath)],function(e) e$length)
-gen.div <- getData(hgdp)[,"Genetic.Div"]
-plot(gen.div~geo.dist)
-lm1 <- lm(gen.div~geo.dist)
-abline(lm1, col="blue") # this regression is wrong
+geo.dist <- sapply(myPath[-length(myPath)], function(e) e$length)
+gen.div <- getData(hgdp)[, "Genetic.Div"]
+plot(gen.div ~ geo.dist)
+lm1 <- lm(gen.div ~ geo.dist)
+abline(lm1, col = "blue") # this regression is wrong
 summary(lm1)
 }
 
diff --git a/man/isInArea.Rd b/man/isInArea.Rd
index c8a5186..3f78143 100644
--- a/man/isInArea.Rd
+++ b/man/isInArea.Rd
@@ -89,10 +89,10 @@ the output are also available.
 }}
 \examples{
 
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 ## zooming in
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 
@@ -102,14 +102,14 @@ length(isInArea(worldgraph.10k))
 sum(isInArea(worldgraph.10k))
 head(which(isInArea(worldgraph.10k))) # which nodes are TRUE ?
 
-head(isInArea(worldgraph.10k, res.type="integer")) # node indices
+head(isInArea(worldgraph.10k, res.type = "integer")) # node indices
 
-head(isInArea(worldgraph.10k, res.type="character")) # node names
+head(isInArea(worldgraph.10k, res.type = "character")) # node names
 
 
 ## use isInArea to have a subset of visible nodes
 x <- worldgraph.10k[isInArea(worldgraph.10k)]
-plot(x, reset=TRUE)
+plot(x, reset = TRUE)
 
 }
 \author{
diff --git a/man/makeGrid.Rd b/man/makeGrid.Rd
index c0057d2..73c57a8 100644
--- a/man/makeGrid.Rd
+++ b/man/makeGrid.Rd
@@ -39,18 +39,20 @@ curvature of the surface of the earth can be neglected.
 
 ## zoom in to a smaller area
 plot(worldgraph.10k)
-geo.zoomin(c(-10,0, 50,54))
+geo.zoomin(c(-10, 0, 50, 54))
 
 
 ## make a new gGraph
 newGraph <- makeGrid(1e3)
 newGraph <- findLand(newGraph)
-newGraph@meta$colors <- data.frame(habitat=c("sea","land"),
-color=c("blue","green"))
+newGraph@meta$colors <- data.frame(
+  habitat = c("sea", "land"),
+  color = c("blue", "green")
+)
 
 
 ## plot the new gGraph
-plot(newGraph, reset=TRUE, edge=TRUE)
+plot(newGraph, reset = TRUE, edge = TRUE)
 
 }
 \author{
diff --git a/man/pipe.Rd b/man/pipe.Rd
new file mode 100644
index 0000000..a648c29
--- /dev/null
+++ b/man/pipe.Rd
@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils-pipe.R
+\name{\%>\%}
+\alias{\%>\%}
+\title{Pipe operator}
+\usage{
+lhs \%>\% rhs
+}
+\arguments{
+\item{lhs}{A value or the magrittr placeholder.}
+
+\item{rhs}{A function call using the magrittr semantics.}
+}
+\value{
+The result of calling \code{rhs(lhs)}.
+}
+\description{
+See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+}
+\keyword{internal}
diff --git a/man/plot-gData.Rd b/man/plot-gData.Rd
index 7d7d08e..6b2675f 100644
--- a/man/plot-gData.Rd
+++ b/man/plot-gData.Rd
@@ -89,26 +89,25 @@ the \code{gData} plot.\cr
 \examples{
 
 
-myLoc <- list(x=c(3, -8, 11, 28), y=c(50, 57, 71, 67)) # some locations
-obj <- new("gData", coords=myLoc) # new gData object
+myLoc <- list(x = c(3, -8, 11, 28), y = c(50, 57, 71, 67)) # some locations
+obj <- new("gData", coords = myLoc) # new gData object
 obj
 
 obj@gGraph.name <- "worldgraph.10k"
-obj <- closestNode(obj, attr.name="habitat", attr.value="land")
+obj <- closestNode(obj, attr.name = "habitat", attr.value = "land")
 
 ## plot the result (original location -> assigned node)
-plot(obj, type="both",reset=TRUE)
+plot(obj, type = "both", reset = TRUE)
 title("'x'=location, 'o'=assigned node")
 
 ## using different parameters
-points(obj, type="both", pch.ori=2, col.ori="red", pch.nodes=20, col.nodes="pink")
+points(obj, type = "both", pch.ori = 2, col.ori = "red", pch.nodes = 20, col.nodes = "pink")
 
 ## only nodes, fancy plot
-plot(obj, col.nodes="red", cex=1, pch.node=20)
-points(obj, col.nodes="red", cex=2)
-points(obj, col.nodes="orange", cex=3)
-points(obj, col.nodes="yellow", cex=4)
-
+plot(obj, col.nodes = "red", cex = 1, pch.node = 20)
+points(obj, col.nodes = "red", cex = 2)
+points(obj, col.nodes = "orange", cex = 3)
+points(obj, col.nodes = "yellow", cex = 4)
 
 }
 \seealso{
diff --git a/man/plot-gGraph.Rd b/man/plot-gGraph.Rd
index 5444c7f..f181cca 100644
--- a/man/plot-gGraph.Rd
+++ b/man/plot-gGraph.Rd
@@ -88,32 +88,31 @@ specify \code{reset=TRUE} as argument to \code{plot}.
 
 
 ## just the background
-plot(worldgraph.10k,reset=TRUE,type="n")
+plot(worldgraph.10k, reset = TRUE, type = "n")
 
 ## basic plot
 plot(worldgraph.10k)
 
 ## zooming and adding edges
-geo.zoomin(list(x=c(90,150),y=c(0,-50)))
-plot(worldgraph.10k, edges=TRUE)
+geo.zoomin(list(x = c(90, 150), y = c(0, -50)))
+plot(worldgraph.10k, edges = TRUE)
 
 
 ## display edges differently
-plotEdges(worldgraph.10k, col="red", lwd=2)
+plotEdges(worldgraph.10k, col = "red", lwd = 2)
 
 
 ## replot points with different color
-points(worldgraph.10k, col="orange")
+points(worldgraph.10k, col = "orange")
 
 ## mask points in the sea
-inSea <- unlist(getNodesAttr(worldgraph.10k,attr.name="habitat"))=="sea"
+inSea <- unlist(getNodesAttr(worldgraph.10k, attr.name = "habitat")) == "sea"
 head(inSea)
-points(worldgraph.10k[inSea], col="white", sticky=TRUE) # this will stay
+points(worldgraph.10k[inSea], col = "white", sticky = TRUE) # this will stay
 
 ## but better, only draw those on land, and use a fancy setup
-par(bg="blue")
-plot(worldgraph.10k[!inSea], bg.col="darkgreen", col="purple", edges=TRUE)
-
+par(bg = "blue")
+plot(worldgraph.10k[!inSea], bg.col = "darkgreen", col = "purple", edges = TRUE)
 
 }
 \seealso{
diff --git a/man/setCosts.Rd b/man/setCosts.Rd
index 0cbf3ca..f6bcef6 100644
--- a/man/setCosts.Rd
+++ b/man/setCosts.Rd
@@ -43,21 +43,20 @@ Also note that 'costs' defined in \code{geoGraph} are equivalent to
 }
 \examples{
 
-plot(rawgraph.10k, reset=TRUE)
+plot(rawgraph.10k, reset = TRUE)
 
 ## zooming in
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 ## defining a new object restrained to visible nodes
 x <- rawgraph.10k[isInArea(rawgraph.10k)]
 
 ## define weights for edges
-x <- setCosts(x, attr.name="habitat")
-plot(x,edges=TRUE)
+x <- setCosts(x, attr.name = "habitat")
+plot(x, edges = TRUE)
 title("costs defined by habitat (land/land=1, other=100)")
 
-
 }
 \seealso{
 \code{\link{dropDeadEdges}}, to get rid of edge whose cost is below
diff --git a/man/setDistCosts.Rd b/man/setDistCosts.Rd
index 8e31a19..1005258 100644
--- a/man/setDistCosts.Rd
+++ b/man/setDistCosts.Rd
@@ -40,19 +40,19 @@ connectivity there is between the couple of concerned nodes.
 }}
 \examples{
 
-if(require(fields)){
-## load data
-plot(rawgraph.10k,reset=TRUE)
-geo.zoomin(list(x=c(110,150),y=c(-10,-40)))
-plotEdges(rawgraph.10k)
+if (require(fields)) {
+  ## load data
+  plot(rawgraph.10k, reset = TRUE)
+  geo.zoomin(list(x = c(110, 150), y = c(-10, -40)))
+  plotEdges(rawgraph.10k)
 
-## compute costs
-x <- rawgraph.10k[isInArea(rawgraph.10k)]
-x <- setDistCosts(x)
+  ## compute costs
+  x <- rawgraph.10k[isInArea(rawgraph.10k)]
+  x <- setDistCosts(x)
 
-## replot edges
-plotEdges(x) # no big differences can be seen
-head(getCosts(x))
+  ## replot edges
+  plotEdges(x) # no big differences can be seen
+  head(getCosts(x))
 }
 
 }
diff --git a/man/worldgraph.Rd b/man/worldgraph.Rd
index 5b91620..4ae5fc9 100644
--- a/man/worldgraph.Rd
+++ b/man/worldgraph.Rd
@@ -30,10 +30,10 @@ world, with respective resolutions of 10,242 and 40,962 vertices.\cr
 references.\cr
 
 'worldgraph's are 'rawgraph's that have been modified manually to rectify
-connectivity between edges at some places. The most noticable change is that
+connectivity between edges at some places. The most noticeable change is that
 all edges involving sea vertices have been removed.\cr
 
-'worldshape' is a shapefile of contries of the world (snapshot from 1994).
+'worldshape' is a shapefile of countries of the world (snapshot from 1994).
 }
 \examples{
 
@@ -41,24 +41,24 @@ all edges involving sea vertices have been removed.\cr
 worldgraph.10k
 
 ## plotting the object
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 title("Hello world")
 
 ## zooming in
-geo.zoomin(list(x=c(-12,45), y=c(33,75)))
+geo.zoomin(list(x = c(-12, 45), y = c(33, 75)))
 title("Europe")
-geo.zoomin(list(x=c(-12,2), y=c(50,60)))
+geo.zoomin(list(x = c(-12, 2), y = c(50, 60)))
 plotEdges(worldgraph.10k)
 title("United Kingdom")
 
 ## zooming out
 # geo.zoomout() # needs clicking on device
-geo.zoomin(list(x=c(-6,38), y=c(35,73)))
+geo.zoomin(list(x = c(-6, 38), y = c(35, 73)))
 title("Europe")
 
 ## defining the subset of visible points
 x <- worldgraph.10k[isInArea(worldgraph.10k)]
-plot(x,reset=TRUE, edges=TRUE)
+plot(x, reset = TRUE, edges = TRUE)
 title("One subsetted object.")
 
 \dontrun{
@@ -66,7 +66,6 @@ title("One subsetted object.")
 geo.zoomin()
 }
 
-
 }
 \references{
 === On the construction of the graph ===\cr Randall, D. A.;
diff --git a/man/zoom.Rd b/man/zoom.Rd
index 0eda369..c5b66cf 100644
--- a/man/zoom.Rd
+++ b/man/zoom.Rd
@@ -50,16 +50,15 @@ Whenever clicking is needed, a right-click will stop the function.
 }
 \examples{
 
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 ## zooming in
-x.ini <- c(-100,-60)
-y.ini <- c(-30,30)
-for(i in 0:3){
-geo.zoomin(list(x=x.ini + i*60, y=y.ini))
+x.ini <- c(-100, -60)
+y.ini <- c(-30, 30)
+for (i in 0:3) {
+  geo.zoomin(list(x = x.ini + i * 60, y = y.ini))
 }
 
-
 \dontrun{
 ## going back
 geo.back() # you have to click !

From 45e1aabd37ec9dacf479598b65bead77c972fe44 Mon Sep 17 00:00:00 2001
From: m-colucci <margherita.col@gmail.com>
Date: Tue, 5 Dec 2023 14:31:08 +0100
Subject: [PATCH 14/19] update column checks

---
 R/classes.R | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/classes.R b/R/classes.R
index fff4b82..29f3063 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -281,18 +281,20 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
 
   ## handle @coords ##
   if (!is.null(input$coords)) {
-    if (is.list(input$coords) && length(input$coords) > 2) {
-      stop("Argument coords must include only two columns (longitude and latitude).")
-    }
 
-    if (is.list(input$coords) && length(input$coords) == 2) {
+
+    if (is.list(input$coords)) {
       input$coords <- as.data.frame(input$coords)
     }
 
     if (is.data.frame(input$coords)) {
       input$coords <- as.matrix(input$coords)
     }
-
+    
+    if (ncol(input$coords)!=2){
+      stop("Argument coords must include only two columns (longitude and latitude).")
+    }
+    
     if (nrow(input$coords) > 0 && !is.numeric(input$coords)) {
       stop("Argument coords has to be numeric.")
       }

From 7fea0240541fbe93b3f6d2d6d2bfe7492c965077 Mon Sep 17 00:00:00 2001
From: Aramish Fatima <af686@cam.ac.uk>
Date: Wed, 6 Dec 2023 23:45:44 +0000
Subject: [PATCH 15/19] Added column name swap and test for column names

---
 R/classes.R                   |  4 ++++
 tests/testthat/test_classes.R | 12 ++++++++++++
 2 files changed, 16 insertions(+)

diff --git a/R/classes.R b/R/classes.R
index 29f3063..78ea285 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -304,6 +304,10 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
       stop("Argument coords includes NAs")
     }
     
+    if (identical(colnames(input$coords), c("lat", "lon"))) {
+      input$coords[ , c(1,2)] <- input$coords[ , c(2,1)]
+    }
+      
 
     ## names of the matrix
     colnames(input$coords) <- c("lon", "lat")
diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index d6c0513..a9f5ca3 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -29,3 +29,15 @@ test_that("Contructors fails with invalid non-numeric matrix",{
                "Argument coords has to be numeric")
   
 })
+
+test_that("Constructor checks column headings" , {
+  column_heading <- data.frame(lat = c(-24, 37), lon =  c(31,55)) 
+  #Create Ggraph with lat/lon headings
+  correct_heading <- new("gGraph", coords = column_heading)
+  column_heading <- data.frame(lon =  c(31,55), lat = c(-24, 37))
+  #Create Ggraph with lon/lat headings
+  swapped_heading <- new("gGraph", coords = column_heading)
+  expect_identical(correct_heading, swapped_heading,
+                  "Argument column names are not recognised")
+})
+  

From 7c220c9a811788daa041e8128849f4c73ae1de08 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 12 Dec 2023 14:02:09 +0000
Subject: [PATCH 16/19] Add simple test to extractFromLayer

---
 R/extractFromLayer.R                   | 2 ++
 tests/testthat/test_extractFromLayer.R | 8 ++++++++
 2 files changed, 10 insertions(+)
 create mode 100644 tests/testthat/test_extractFromLayer.R

diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
index 6d3a3e7..9207da9 100644
--- a/R/extractFromLayer.R
+++ b/R/extractFromLayer.R
@@ -105,6 +105,7 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
     }
   }
 
+
   ## search attr in data ##
   if (attr[1] == "all") {
     selAttr <- 1:ncol(layer@data)
@@ -150,6 +151,7 @@ setMethod("extractFromLayer", "matrix", function(x, layer = "world", attr = "all
     } # end for j
   } # end for i
 
+  # @TOFIX the line below will fail if layerId is all NAs (i.e. no points were assigned to a polygon)
   res <- dat[layerId, selAttr, drop = FALSE]
   row.names(res) <- rownames(x)
 
diff --git a/tests/testthat/test_extractFromLayer.R b/tests/testthat/test_extractFromLayer.R
new file mode 100644
index 0000000..b0cad72
--- /dev/null
+++ b/tests/testthat/test_extractFromLayer.R
@@ -0,0 +1,8 @@
+test_that("extractFromLayer assigns points correctly",
+          {
+            # create a matrix of locations including two continents and the sea
+            myCoords <- data.frame(long = c(-24, 71.5, -46.5), lat =  c(31, 30,-23.5))
+            # assign to continents
+            continents <- extractFromLayer(myCoords, layer = worldshape, attr = "CONTINENT")
+            expect_identical(as.character(continents$CONTINENT), c(NA,"Asia","South America"))
+          })
\ No newline at end of file

From e5598c634aac2546ae82314e5cd8c6f96aff012f Mon Sep 17 00:00:00 2001
From: Aramish Fatima <af686@cam.ac.uk>
Date: Tue, 19 Dec 2023 00:20:00 +0000
Subject: [PATCH 17/19] Added code to account for different lon/lat spelling
 and capitalisation

---
 R/classes.R                    | 26 ++++++++++++++++++++++++--
 tests/testthat/test_classes.R  | 17 ++++++++++++++++-
 tests/testthat/test_findLand.R |  2 +-
 3 files changed, 41 insertions(+), 4 deletions(-)

diff --git a/R/classes.R b/R/classes.R
index 78ea285..abf72b1 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -304,8 +304,30 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
       stop("Argument coords includes NAs")
     }
     
-    if (identical(colnames(input$coords), c("lat", "lon"))) {
-      input$coords[ , c(1,2)] <- input$coords[ , c(2,1)]
+    ## Convert all column names to lower case
+    colnames(input$coords) <- tolower(colnames(input$coords))
+    ## Create list of lon/lat column heading names
+    lonlist <- list("lon", "longitude", "x")
+    latlist <- list("lat", "latitude", "y")
+    ## Test first column name against list
+    if (is.element(colnames(input$coords)[1], lonlist)) {
+      reverse_column = FALSE
+    }  else if (is.element(colnames(input$coords)[1], latlist)) {
+      reverse_column = TRUE
+    }   else {
+      stop("Argument first column name not recognised")
+    }
+    ## Test second column name against list
+    if (is.element(colnames(input$coords)[2], latlist)) {
+      reverse_column = FALSE
+    }  else if (is.element(colnames(input$coords)[2], lonlist)) {
+      reverse_column = TRUE
+    }  else {
+      stop("Argument second column name not recognised")
+    }
+    
+    if (reverse_column) {
+      input$coords[, c(1, 2)] <- input$coords[, c(2, 1)]
     }
       
 
diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index a9f5ca3..f54ea72 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -30,6 +30,22 @@ test_that("Contructors fails with invalid non-numeric matrix",{
   
 })
 
+
+
+test_that("Constructor accounts for different column names" , {
+  columnheading_names <-
+    data.frame(longitude =  c(31, 55), Latitude = c(-24, 37))
+  columnheading_names <- new("gGraph", coords = columnheading_names)
+  new_columnheading_names <-
+    data.frame(lon = c(31, 55), lat =  c(-24, 37))
+  new_columnheading_names <-
+    new("gGraph", coords = new_columnheading_names)
+  expect_identical(columnheading_names,
+                   new_columnheading_names,
+                   "Argument column names not listed")
+  
+})
+
 test_that("Constructor checks column headings" , {
   column_heading <- data.frame(lat = c(-24, 37), lon =  c(31,55)) 
   #Create Ggraph with lat/lon headings
@@ -40,4 +56,3 @@ test_that("Constructor checks column headings" , {
   expect_identical(correct_heading, swapped_heading,
                   "Argument column names are not recognised")
 })
-  
diff --git a/tests/testthat/test_findLand.R b/tests/testthat/test_findLand.R
index a8c85d2..17af0be 100644
--- a/tests/testthat/test_findLand.R
+++ b/tests/testthat/test_findLand.R
@@ -1,6 +1,6 @@
 test_that("find land correctly",{
   # create a gGraph with one sea node and one land node
-  myCoords <- data.frame(long = c(-24, 37), lat =  c(31,55))
+  myCoords <- data.frame(lon = c(-24, 37), lat =  c(31,55))
   obj <- new("gGraph", coords = myCoords)
   obj <- findLand(obj) 
   # check that we classified the nodes correctly

From 034288037033436ebad4ed41aeaf9259d82ab097 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 19 Dec 2023 09:16:41 +0000
Subject: [PATCH 18/19] Simplify column name checks

---
 R/classes.R                   | 28 ++++++++--------------------
 tests/testthat/test_classes.R | 22 +++++++++++++++++-----
 2 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/R/classes.R b/R/classes.R
index abf72b1..f54805e 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -309,27 +309,15 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
     ## Create list of lon/lat column heading names
     lonlist <- list("lon", "longitude", "x")
     latlist <- list("lat", "latitude", "y")
-    ## Test first column name against list
-    if (is.element(colnames(input$coords)[1], lonlist)) {
-      reverse_column = FALSE
-    }  else if (is.element(colnames(input$coords)[1], latlist)) {
-      reverse_column = TRUE
-    }   else {
-      stop("Argument first column name not recognised")
-    }
-    ## Test second column name against list
-    if (is.element(colnames(input$coords)[2], latlist)) {
-      reverse_column = FALSE
-    }  else if (is.element(colnames(input$coords)[2], lonlist)) {
-      reverse_column = TRUE
-    }  else {
-      stop("Argument second column name not recognised")
-    }
-    
-    if (reverse_column) {
+    ## Test if the column order is inverted
+    if (is.element(colnames(input$coords)[1], latlist) & 
+        is.element(colnames(input$coords)[2], lonlist)) {
       input$coords[, c(1, 2)] <- input$coords[, c(2, 1)]
-    }
-      
+    } else if  (!(is.element(colnames(input$coords)[1], lonlist) & 
+                  is.element(colnames(input$coords)[2], latlist))){
+      message("The coordinate column names are not part of the standardised list;\n",
+      "we will use the order they were given in, make sure it corresponds to x and y!")
+    } # if neither of the if catches it, then the names are part of the lists and in the correct order
 
     ## names of the matrix
     colnames(input$coords) <- c("lon", "lat")
diff --git a/tests/testthat/test_classes.R b/tests/testthat/test_classes.R
index f54ea72..986a855 100644
--- a/tests/testthat/test_classes.R
+++ b/tests/testthat/test_classes.R
@@ -41,18 +41,30 @@ test_that("Constructor accounts for different column names" , {
   new_columnheading_names <-
     new("gGraph", coords = new_columnheading_names)
   expect_identical(columnheading_names,
-                   new_columnheading_names,
-                   "Argument column names not listed")
+                   new_columnheading_names)
   
 })
 
-test_that("Constructor checks column headings" , {
+test_that("Constructor reverses coord column order" , {
   column_heading <- data.frame(lat = c(-24, 37), lon =  c(31,55)) 
   #Create Ggraph with lat/lon headings
   correct_heading <- new("gGraph", coords = column_heading)
   column_heading <- data.frame(lon =  c(31,55), lat = c(-24, 37))
   #Create Ggraph with lon/lat headings
   swapped_heading <- new("gGraph", coords = column_heading)
-  expect_identical(correct_heading, swapped_heading,
-                  "Argument column names are not recognised")
+  expect_identical(correct_heading, swapped_heading)
 })
+
+test_that("we give message when columns are not recognised",{
+  column_heading <- data.frame(lon=  c(31,55), lat = c(-24, 37))
+  #Create Ggraph with lat/lon headings
+  correct_heading <- new("gGraph", coords = column_heading)
+  column_heading <- data.frame(blah=  c(31,55), lat = c(-24, 37))  
+  #Create Ggraph with lon/lat headings
+  expect_message(unrecognised_heading <- new("gGraph", coords = column_heading),
+                 "The coordinate column names are not part of the standardised list")
+  expect_identical(correct_heading, unrecognised_heading)
+}
+          
+          
+          )

From 03197d4e2a92c8e904e334355d8ee6ad8522626a Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Tue, 19 Dec 2023 13:20:26 +0000
Subject: [PATCH 19/19] Add long to accepted labels

---
 R/classes.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/classes.R b/R/classes.R
index f54805e..90db994 100644
--- a/R/classes.R
+++ b/R/classes.R
@@ -307,7 +307,7 @@ setMethod("initialize", "gGraph", function(.Object, ...) {
     ## Convert all column names to lower case
     colnames(input$coords) <- tolower(colnames(input$coords))
     ## Create list of lon/lat column heading names
-    lonlist <- list("lon", "longitude", "x")
+    lonlist <- list("lon", "long", "longitude", "x")
     latlist <- list("lat", "latitude", "y")
     ## Test if the column order is inverted
     if (is.element(colnames(input$coords)[1], latlist) &