From b75771d703835fc8d40ef8a76e0d48810fdca2e4 Mon Sep 17 00:00:00 2001
From: Andrea Manica <am315@cam.ac.uk>
Date: Fri, 20 Oct 2023 17:22:27 +0100
Subject: [PATCH] Update combining costs

---
 R/combineCosts.R               | 53 ++++++++++++------------
 R/setCosts.R                   | 74 ++++++++++++++++------------------
 man/buffer.Rd                  | 34 ++++++++--------
 man/closestNode.Rd             | 17 ++++----
 man/combineCosts.Rd            |  4 +-
 man/dijkstra-methods.Rd        | 15 ++++---
 man/dropDeadEdges.Rd           |  3 +-
 man/extractFromLayer.Rd        | 12 +++---
 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/plot-gData.Rd              | 19 +++++----
 man/plot-gGraph.Rd             | 19 +++++----
 man/setCosts.Rd                |  8 ++--
 man/setDistCosts.Rd            | 22 +++++-----
 man/worldgraph.Rd              | 15 ++++---
 man/zoom.Rd                    | 11 +++--
 tests/testthat/test_setCosts.R |  5 ++-
 vignettes/geograph.Rmd         |  2 +-
 29 files changed, 208 insertions(+), 225 deletions(-)

diff --git a/R/combineCosts.R b/R/combineCosts.R
index fb96217..7bb563b 100644
--- a/R/combineCosts.R
+++ b/R/combineCosts.R
@@ -8,11 +8,11 @@
 #' Note that costs are inversely proportional to connectivity between edges:
 #' the larger the cost associated to an edge, the lower the connectivity
 #' between the two concerned nodes.\cr
-#' 
+#'
 #' Also note that 'costs' defined in \code{geoGraph} are equivalent to
 #' 'weights' as defined in \code{graph} and \code{RBGL} packages.
-#' 
-#' @param x1 The firt gGraph (which will be used as a template to build the combined gGraph )
+#'
+#' @param x1 The firt gGraph (which will be used as a template to build the combined gGraph)
 #' @param x2 The second gGraph from which costs will be combined
 #' @param method a character string indicating which method should be used to
 #' combined edge cost from the two gGraph. Currently available options are 'sum',
@@ -27,8 +27,10 @@
 #' data("worldgraph.40k")
 #' # new graph with custom cost function
 #' exp.cost <- function(x1, x2, cost.coeff) {
-#'  exp(-abs(x1 - x2) * cost.coeff)
+#'   exp(-abs(x1 - x2) * cost.coeff)
 #' }
+#' # create a set of node costs
+#' worldgraph.40k@nodes.attr$meanProd <- runif(n = 40962)
 #' new_costs_graph <-
 #'   setCosts(
 #'     worldgraph.40k,
@@ -38,51 +40,50 @@
 #'     cost.coeff = 0.5
 #'   )
 #' # combine costs from the original graph with the new costs
-#' combine_costs_graph<- combineCosts(worldgraph.40k, new_costs_graph, method="sum")
-
+#' combine_costs_graph <- combineCosts(worldgraph.40k, new_costs_graph, method = "sum")
 ###############
 ## combineCosts
 ###############
-combineCosts <- function(x1, x2, method=c("sum", "product", "function"), FUN=NULL,...){
+combineCosts <- function(x1, x2, method = c("sum", "product", "function"), FUN = NULL, ...) {
   ## some checks + argument handling
-  if(!is.gGraph(x1)) stop("x1 is not a valid gGraph object")
-  if(!is.gGraph(x2)) stop("x2 is not a valid gGraph object")
-  if(!hasCosts(x1)) stop("x1 is does not have costs; use setCosts to set the costs first")
-  if(!hasCosts(x2)) stop("x1 is does not have costs; use setCosts to set the costs first")
+  if (!is.gGraph(x1)) stop("x1 is not a valid gGraph object")
+  if (!is.gGraph(x2)) stop("x2 is not a valid gGraph object")
+  if (!hasCosts(x1)) stop("x1 is does not have costs; use setCosts to set the costs first")
+  if (!hasCosts(x2)) stop("x1 is does not have costs; use setCosts to set the costs first")
   method <- match.arg(method)
 
   ## get the edges and weights from teh two graphs
   myGraph1 <- getGraph(x1)
   edgeW1 <- edgeWeights(myGraph1)
   edgeL1 <- edgeL(myGraph1)
-  
+
   myGraph2 <- getGraph(x2)
   edgeW2 <- edgeWeights(myGraph2)
   edgeL2 <- edgeL(myGraph2)
-  
+
   # test that the two graphs have the same edges
-  if (!all(unlist(edgeL1)==unlist(edgeL2))){
+  if (!all(unlist(edgeL1) == unlist(edgeL2))) {
     stop("the graphs differ in the edges they have")
   }
-  
+
   newEdgeL <- list()
-  for(i in 1:length(edgeL1)){
+  for (i in 1:length(edgeL1)) {
     newEdgeL[[i]] <- list()
     newEdgeL[[i]]$edges <- edgeL1[[i]]$edges
-    if (method=="sum"){
-      newEdgeL[[i]]$weights <- edgeW1[[i]]+edgeW2[[i]]
-    } else if (method=="product"){
-      newEdgeL[[i]]$weights <- edgeW1[[i]]*edgeW2[[i]]
-    } else if (method=="function"){
+    if (method == "sum") {
+      newEdgeL[[i]]$weights <- edgeW1[[i]] + edgeW2[[i]]
+    } else if (method == "product") {
+      newEdgeL[[i]]$weights <- edgeW1[[i]] * edgeW2[[i]]
+    } else if (method == "function") {
       newEdgeL[[i]]$weights <- FUN(edgeW1[[i]], edgeW2[[i]], ...)
     }
   }
-  
+
   names(newEdgeL) <- nodes(myGraph1) # items of the list must be named
-  
-  newGraph <- new("graphNEL", nodes=nodes(myGraph1), edgeL=newEdgeL)
+
+  newGraph <- new("graphNEL", nodes = nodes(myGraph1), edgeL = newEdgeL)
   res <- x1
   res@graph <- newGraph
-  
+
   return(res)
-} # end combineCosts
\ No newline at end of file
+} # end combineCosts
diff --git a/R/setCosts.R b/R/setCosts.R
index fe00575..4edf052 100644
--- a/R/setCosts.R
+++ b/R/setCosts.R
@@ -11,7 +11,7 @@
 #' for the chosen attribute, which is associated to a costs (a friction). The
 #' cost of an edge is computed as a function (see argument \code{method}) of
 #' the costs of its nodes.\cr
-#' 
+#'
 #' Note that costs are inversely proportional to connectivity between edges:
 #' the larger the cost associated to an edge, the lower the connectivity
 #' between the two concerned nodes.\cr
@@ -55,35 +55,30 @@
 #' x <- setCosts(x, attr.name = "habitat")
 #' plot(x, edges = TRUE)
 #' title("costs defined by habitat (land/land=1, other=100)")
-#' 
-#' 
-setCosts <- function(x, attr.name=NULL, node.costs=NULL, method=c("mean", "product", "function"), FUN=NULL,...){
-    ## some checks + argument handling
-    if(!is.gGraph(x)) stop("x is not a valid gGraph object")
-    method <- match.arg(method)
-    if ((method=="function") && (is.null(FUN))){
-        stop("if method='function', FUN needs to be defined.")
-    }
+#'
+setCosts <- function(x, attr.name = NULL, node.costs = NULL, method = c("mean", "product", "function"), FUN = NULL, ...) {
+  ## some checks + argument handling
+  if (!is.gGraph(x)) stop("x is not a valid gGraph object")
+  method <- match.arg(method)
+  if ((method == "function") && (is.null(FUN))) {
+    stop("if method='function', FUN needs to be defined.")
+  }
 
-    ## assign costs to vertices
-    if(is.null(node.costs)){ # costs from a node attribute
-        nodeAttr <- unlist(getNodesAttr(x, attr.name=attr.name))
-        if(!is.null(x@meta$costs)){
-            if(!any(attr.name %in% colnames(x@meta$costs))) {
-                stop("attr.name is not documented in x@meta$costs.")
-            }
-            nodeCosts <- as.character(nodeAttr)
-            rules <- x@meta$costs
-            for(i in 1:nrow(x@meta$costs)){
-                nodeCosts[nodeCosts==rules[i,attr.name]] <- rules[i,ncol(rules)]
-            }
-            nodeCosts <- as.numeric(nodeCosts)
-        } else stop("x@meta does not contain a 'costs' component.")
-    } else{ # cost directly provided
-        if(!is.numeric(node.costs)) stop("Provided 'node.costs' not numeric.")
-        node.costs <- rep(node.costs, length=length(getNodes(x))) # recycling node costs
-        nodeCosts <- node.costs
-        ## might add some more checks here...
+  ## assign costs to vertices
+  if (is.null(node.costs)) { # costs from a node attribute
+    nodeAttr <- unlist(getNodesAttr(x, attr.name = attr.name))
+    if (!is.null(x@meta$costs)) {
+      if (!any(attr.name %in% colnames(x@meta$costs))) {
+        stop("attr.name is not documented in x@meta$costs.")
+      }
+      nodeCosts <- as.character(nodeAttr)
+      rules <- x@meta$costs
+      for (i in 1:nrow(x@meta$costs)) {
+        nodeCosts[nodeCosts == rules[i, attr.name]] <- rules[i, ncol(rules)]
+      }
+      nodeCosts <- as.numeric(nodeCosts)
+    } else {
+      stop("x@meta does not contain a 'costs' component.")
     }
   } else { # cost directly provided
     if (!is.numeric(node.costs)) stop("Provided 'node.costs' not numeric.")
@@ -92,7 +87,6 @@ setCosts <- function(x, attr.name=NULL, node.costs=NULL, method=c("mean", "produ
     ## might add some more checks here...
   }
 
-
   ## find costs of edges as a function of terminating vertices
   EL <- getGraph(x)@edgeL
 
@@ -110,17 +104,17 @@ setCosts <- function(x, attr.name=NULL, node.costs=NULL, method=c("mean", "produ
     }
   }
 
-    ## method == function ##
-    if (method=="function"){
-        for(i in 1:length(EL)){
-            EL[[i]]$weights <- FUN(nodeCosts[i], nodeCosts[EL[[i]]$edges], ...)
-        }            
+  ## method == function ##
+  if (method == "function") {
+    for (i in 1:length(EL)) {
+      EL[[i]]$weights <- FUN(nodeCosts[i], nodeCosts[EL[[i]]$edges], ...)
     }
-    
-    ## return result
-    newGraph <- new("graphNEL", nodes=getNodes(x), edgeL=EL)
-    res <- x
-    res@graph <- newGraph
+  }
+
+  ## return result
+  newGraph <- new("graphNEL", nodes = getNodes(x), edgeL = EL)
+  res <- x
+  res@graph <- newGraph
 
   return(res)
 } # end setCosts
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/combineCosts.Rd b/man/combineCosts.Rd
index c2725aa..925e3ac 100644
--- a/man/combineCosts.Rd
+++ b/man/combineCosts.Rd
@@ -7,7 +7,7 @@
 combineCosts(x1, x2, method = c("sum", "product", "function"), FUN = NULL, ...)
 }
 \arguments{
-\item{x1}{The firt gGraph (which will be used as a template to build the combined gGraph )}
+\item{x1}{The firt gGraph (which will be used as a template to build the combined gGraph)}
 
 \item{x2}{The second gGraph from which costs will be combined}
 
@@ -44,6 +44,8 @@ data("worldgraph.40k")
 exp.cost <- function(x1, x2, cost.coeff) {
  exp(-abs(x1 - x2) * cost.coeff)
 }
+# create a set of node costs
+worldgraph.40k@nodes.attr$meanProd<-runif(n=40962)
 new_costs_graph <-
   setCosts(
     worldgraph.40k,
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..7eb940b 100644
--- a/man/extractFromLayer.Rd
+++ b/man/extractFromLayer.Rd
@@ -67,10 +67,9 @@ Nodes can be specified in different ways, including by providing a
 input formats.
 }
 \examples{
-
 \dontrun{
 
-plot(worldgraph.10k, reset=TRUE)
+plot(worldgraph.10k, reset = TRUE)
 
 
 ## see what info is available
@@ -80,17 +79,16 @@ 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 = worldshape, 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/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 1bd598e..8c90750 100644
--- a/man/setCosts.Rd
+++ b/man/setCosts.Rd
@@ -54,18 +54,18 @@ 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)")
 
 
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 !
diff --git a/tests/testthat/test_setCosts.R b/tests/testthat/test_setCosts.R
index ad633f4..299d65f 100644
--- a/tests/testthat/test_setCosts.R
+++ b/tests/testthat/test_setCosts.R
@@ -6,6 +6,7 @@ test_that("arbitrary function to set costs", {
   exp.cost <- function(x1, x2, cost.coeff) {
     exp(-abs(x1 - x2) * cost.coeff)
   }
+  worldgraph.40k@nodes.attr$meanProd <- runif(graph::numNodes(getGraph(worldgraph.40k)))
   my_coeff <- 0.5
   test_graph <-
     setCosts(
@@ -15,7 +16,7 @@ test_that("arbitrary function to set costs", {
       FUN = exp.cost,
       cost.coeff = my_coeff
     )
-  #now check that we have the right costs
+  # now check that we have the right costs
   sample_edge <- names(test_graph@graph@edgeData@data)[1]
   sample_nodes <- as.integer(strsplit(sample_edge, "|", fixed = TRUE)[[1]])
   sample_meanProd <- worldgraph.40k@nodes.attr$meanProd[sample_nodes]
@@ -23,4 +24,4 @@ test_that("arbitrary function to set costs", {
     test_graph@graph@edgeData@data[[1]]$weight,
     exp.cost(sample_meanProd[1], sample_meanProd[2], cost.coeff = my_coeff)
   )
-})
\ No newline at end of file
+})
diff --git a/vignettes/geograph.Rmd b/vignettes/geograph.Rmd
index cfe63a6..308f13d 100644
--- a/vignettes/geograph.Rmd
+++ b/vignettes/geograph.Rmd
@@ -11,7 +11,7 @@ vignette: >
 
 
 ```{r setup, echo=FALSE}
-#knitr::opts_chunk$set(fig.width = 7, fig.height = 6)
+# knitr::opts_chunk$set(fig.width = 7, fig.height = 6)
 options(digits = 4)
 ```