From 8439190fb0688348598d97bcaffb481c880d630b Mon Sep 17 00:00:00 2001
From: Josie Hughes <josie.hughes@canada.ca>
Date: Thu, 14 Mar 2024 11:39:50 -0400
Subject: [PATCH] fix error

---
 R/projectRoads.R    |  4 ++--
 man/projectRoads.Rd | 23 +++++++++++++++--------
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/R/projectRoads.R b/R/projectRoads.R
index 6e507b8..b720e8b 100644
--- a/R/projectRoads.R
+++ b/R/projectRoads.R
@@ -150,7 +150,7 @@ setGeneric('projectRoads', function(landings = NULL,
                                     plotRoads = FALSE,
                                     mainTitle = "",
                                     neighbourhood = "octagon",
-                                    weightFunction=function(x1,x2) (x1+x2)/2
+                                    weightFunction=function(x1,x2) (x1+x2)/2,
                                     sim = NULL,
                                     roadsOut = NULL,
                                     roadsInCost = TRUE,
@@ -277,7 +277,7 @@ setMethod(
 setMethod(
   'projectRoads', signature(sim = "list"),
   function(landings, cost, roads, roadMethod, plotRoads, mainTitle,
-           neighbourhood, sim, roadsOut, roadsInCost, ordering) {
+           neighbourhood, weightFunction,sim, roadsOut, roadsInCost, ordering) {
 
     # If roads in are raster return as raster
     if((is(sim$roads, "Raster") || is(sim$roads, "SpatRaster")) && is.null(roadsOut) ){
diff --git a/man/projectRoads.Rd b/man/projectRoads.Rd
index e74f3ac..87b1fea 100644
--- a/man/projectRoads.Rd
+++ b/man/projectRoads.Rd
@@ -2,8 +2,8 @@
 % Please edit documentation in R/projectRoads.R
 \name{projectRoads}
 \alias{projectRoads}
-\alias{projectRoads,ANY,ANY,ANY,ANY,ANY,ANY,ANY,missing-method}
-\alias{projectRoads,ANY,ANY,ANY,ANY,ANY,ANY,ANY,list-method}
+\alias{projectRoads,ANY,ANY,ANY,ANY,ANY,ANY,ANY,ANY,missing-method}
+\alias{projectRoads,ANY,ANY,ANY,ANY,ANY,ANY,ANY,ANY,list-method}
 \title{Project road network}
 \usage{
 projectRoads(
@@ -14,13 +14,14 @@ projectRoads(
   plotRoads = FALSE,
   mainTitle = "",
   neighbourhood = "octagon",
+  weightFunction = function(x1, x2) (x1 + x2)/2,
   sim = NULL,
   roadsOut = NULL,
   roadsInCost = TRUE,
   ordering = "closest"
 )
 
-\S4method{projectRoads}{ANY,ANY,ANY,ANY,ANY,ANY,ANY,missing}(
+\S4method{projectRoads}{ANY,ANY,ANY,ANY,ANY,ANY,ANY,ANY,missing}(
   landings = NULL,
   cost = NULL,
   roads = NULL,
@@ -28,13 +29,14 @@ projectRoads(
   plotRoads = FALSE,
   mainTitle = "",
   neighbourhood = "octagon",
+  weightFunction = function(x1, x2) (x1 + x2)/2,
   sim = NULL,
   roadsOut = NULL,
   roadsInCost = TRUE,
   ordering = "closest"
 )
 
-\S4method{projectRoads}{ANY,ANY,ANY,ANY,ANY,ANY,ANY,list}(
+\S4method{projectRoads}{ANY,ANY,ANY,ANY,ANY,ANY,ANY,ANY,list}(
   landings = NULL,
   cost = NULL,
   roads = NULL,
@@ -42,6 +44,7 @@ projectRoads(
   plotRoads = FALSE,
   mainTitle = "",
   neighbourhood = "octagon",
+  weightFunction = function(x1, x2) (x1 + x2)/2,
   sim = NULL,
   roadsOut = NULL,
   roadsInCost = TRUE,
@@ -72,6 +75,10 @@ should be considered adjacent. 'octagon' option is a modified version of
 the queen's 8 cell neighbourhood in which diagonals weights are 2^0.5x
 higher than horizontal/vertical weights.}
 
+\item{weightFunction}{function. Method for calculating the weight of an edge between two nodes
+from the value of the cost raster at each of those nodes (x1 and x2). Default is the mean.
+Functions should be symmetric, meaning that the value returned does not depend on the ordering of x1 and x2.}
+
 \item{sim}{list. Returned from a previous iteration of \code{projectRoads}.
 cost, roads, and \code{roadMethod} are ignored if a \code{sim} list is provided.}
 
@@ -101,8 +108,8 @@ a list with components:
 \item{roadMethod: }{the road simulation method used.}
 \item{landings: }{the landings used in the simulation.}
 \item{g: }{the graph that describes the cost of paths between each cell in the
-      cost raster. This is updated based on the new roads so that vertices 
-      were connected by new roads now have a cost of 0. This can be used to 
+      cost raster. This is updated based on the new roads so that vertices
+      were connected by new roads now have a cost of 0. This can be used to
       avoid recomputing the graph in a simulation with multiple time steps.}
 }
 }
@@ -134,7 +141,7 @@ doPlots <- interactive()
 
 projectRoads(CLUSexample$landings, CLUSexample$cost, CLUSexample$roads,
              "lcp", plotRoads = doPlots, mainTitle = "CLUSexample")
-                         
+
 
 # More realistic examples that take longer to run
 \donttest{
@@ -167,7 +174,7 @@ prRes <- projectRoads(land.rLyr, scen$cost.rast, scen$road.line, "mst",
 scen <- demoScen[[2]]
 
 # landing set 5 of scenario 2, as matrix:
-land.mat  <- scen$landings.points[scen$landings.points$set==5,] |> 
+land.mat  <- scen$landings.points[scen$landings.points$set==5,] |>
   sf::st_coordinates()
 
 prRes <- projectRoads(land.mat, scen$cost.rast, scen$road.rast, "snap",