Merge branch 'dev' into main

EvolEcolGroup · Dec 8, 2023 · 6cd7ee5 · 6cd7ee5
2 parents 3bf64b7 + 93d5956
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -2,7 +2,7 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, fix_check]
+    branches: [main, fix_check]
   pull_request:
     branches: [main, master]
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, dev]
+    branches: [main, dev]
   pull_request:
-    branches: [main, master, dev]
+    branches: [main, dev]
   release:
     types: [published]
   workflow_dispatch:

diff --git a/R/accessors.R b/R/accessors.R
@@ -63,7 +63,7 @@ setMethod("getGraph", "gData", function(x, ...) {
 #' @param \dots other arguments passed to other methods (currently unused).
 #' @return A data.frame with the requested nodes attributes. Nodes are
 #' displayed in rows, variables in columns.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso Most other accessors are documented in \linkS4class{gGraph} and
 #' \linkS4class{gData} manpages.\cr
 #' @keywords utilities methods
@@ -221,7 +221,7 @@ setMethod("getNodes", "gData", function(x, ...) {
 #'
 #' - \code{matId}: a matrix with two columns giving couples of node indices
 #' forming edges.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso Most other accessors are documented in \linkS4class{gGraph}
 #' manpage.\cr
 #'
@@ -305,7 +305,7 @@ setMethod("getEdges", "gGraph", function(x, res.type = c("asIs", "matNames", "ma
 #' \code{costs[i]} is the weight of the i-th edge.
 #' @param \dots other arguments passed to other methods (currently unused).
 #' @return A \linkS4class{gGraph} object with newly added or removed edges.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso \code{\link{geo.add.edges}} and \code{\link{geo.remove.edges}} to
 #' interactively add or remove edges in a \linkS4class{gGraph} object. \cr
 #'
@@ -400,7 +400,7 @@ setMethod("setEdges", "gGraph", function(x, add = NULL, remove = NULL, costs = N
 #'
 #' - \code{vector}: a vector of weights; this output matches matrix outputs of
 #' \code{\link{getEdges}}.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso Most other accessors are documented in \linkS4class{gGraph}
 #' manpage.\cr
 #' @keywords utilities methods
@@ -517,7 +517,7 @@ setMethod("getData", "gData", function(x, ...) {
 #' with different colors. See details.
 #' @param \dots other arguments passed to other methods.
 #' @return A vector of characters being valid colors.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @export
 #' @examples

diff --git a/R/auxil.R b/R/auxil.R
@@ -26,7 +26,7 @@
 #' \code{segments} function.
 #' @return For \code{hasCost}, a logical value is returned. \code{geo.segments}
 #' returns NULL.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @name auxiliary
 #' @examples

diff --git a/R/buffer.R b/R/buffer.R
@@ -27,7 +27,7 @@
 #'
 #' - \code{gData}: a \linkS4class{gData} object including all the nodes of the
 #' buffers.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @name buffer
 #' @examples

diff --git a/R/classes.R b/R/classes.R
@@ -47,7 +47,7 @@ NULL
 #'
 #' Note that none of these is mandatory: \code{new("gGraph")} would work, and
 #' create an empty \code{gGraph} object.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso Related classes are:\cr % - \code{\linkS4class{graphNEL}}
 #' (graph package): slot \code{@graph} in \code{gGraph}.\cr
 #' @keywords classes spatial graphs
@@ -139,7 +139,7 @@ setClass(
 #' an empty \code{gGraph} object. Also note that a finer matching of locations
 #' against the nodes of a \code{gGraph} object can be achieved after creating
 #' the object, for instance using the \code{closestNode} method.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso Related class:\cr - \code{\linkS4class{gGraph}}\cr
 #' @examples
 #'

diff --git a/R/closestNode.R b/R/closestNode.R
@@ -38,7 +38,7 @@
 #' If \code{x} is a \linkS4class{gData} object: a \linkS4class{gData} object
 #' with matching nodes stored in the \code{@nodes.id} slot. Note that previous
 #' content of \code{@nodes.id} will be erased.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso \code{\link{geo.add.edges}} and \code{\link{geo.remove.edges}} to
 #' interactively add or remove edges in a \linkS4class{gGraph} object.
 #' @keywords utilities methods

diff --git a/R/connectivity.R b/R/connectivity.R
@@ -50,7 +50,7 @@
 #'
 #' - \code{isConnected}: a single logical value, being TRUE if nodes of the
 #' object form a connected set.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @name connectivity
 #' @examples

diff --git a/R/dijkstra.R b/R/dijkstra.R
@@ -47,7 +47,7 @@
 #' \code{sp.between} function (see \code{?sp.between}), with a class attribute
 #' set to "gPath", and an additional slot 'xy' containing geographic
 #' coordinates of the nodes involved in the paths.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords methods spatial
 #' @examples
 #' \dontrun{

diff --git a/R/dropDead.R b/R/dropDead.R
@@ -20,7 +20,7 @@
 #' @param thres a numeric value indicating the threshold cost for an edge to be
 #' removed. All costs strictly greater than \code{thres} will be removed.
 #' @return A \linkS4class{gGraph} object.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @export
 #' @examples

diff --git a/R/extractFromLayer.R b/R/extractFromLayer.R
@@ -40,7 +40,7 @@
 #' - \code{gData}: a \linkS4class{gData} object with new data associated to
 #' locations (\code{@data} slot). New information is merge to older information
 #' according to the type of data being stored. \cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso \code{\link{findLand}}, to find which locations are on land.
 #' @keywords utilities methods
 #' @name extractFromLayer

diff --git a/R/findLand.R b/R/findLand.R
@@ -28,7 +28,7 @@
 #' - \code{gGraph}: a \linkS4class{gGraph} object with a new node attribute,
 #' possibly added to previously existing node attributes (\code{@nodes.attr}
 #' slot).\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso \code{\link{extractFromLayer}}, to retrieve any information from a
 #' GIS shapefile.
 #' @keywords utilities methods

diff --git a/R/interact.R b/R/interact.R
@@ -28,7 +28,7 @@ NULL
 #' a character string can be provided, corresponding to one of the following
 #' datasets: 'rawgraph.10k', rawgraph.40k'.
 #' @return A \linkS4class{gGraph} object with newly added or removed edges.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso \code{\link{setEdges}} to non-interactively add or remove edges in
 #' a \linkS4class{gGraph} object.
 #' @keywords utilities
@@ -276,7 +276,7 @@ geo.remove.edges <- function(x, mode = c("points", "area")) {
 #' reference when re-adding edges. If a character string is provided, it must
 #' match one of the following dataset: 'rawgraph.10k', 'rawgraph.40k'.
 #' @return A \linkS4class{gGraph} object with modified node attributes.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities
 #' @examples
 #' \dontrun{

diff --git a/R/isInArea.R b/R/isInArea.R
@@ -34,7 +34,7 @@
 #'
 #' - \code{character}: a vector of characters corresponding to the names of the
 #' nodes falling within the area.\cr
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @export
 #' @examples

diff --git a/R/makeGrid.R b/R/makeGrid.R
@@ -21,7 +21,7 @@
 #' @param lon.range,lat.range vectors of length two giving the range covered by
 #' the grid, in longitude and latitude, respectively.
 #' @return A \linkS4class{gGraph} object.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @keywords utilities methods
 #' @export
 #' @examples

diff --git a/R/plot.R b/R/plot.R
@@ -57,7 +57,7 @@
 #' \code{reset=TRUE} will prevent points to be redrawn.
 #' @param \dots further arguments passed to the generic methods (plot, points,
 #' and segments, respectively).
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso - Different functions to explore these plots:\cr
 #' \code{\link{geo.zoomin}}, \code{\link{geo.zoomout}},
 #' \code{\link{geo.slide}}, \code{\link{geo.back}}.\cr
@@ -563,7 +563,7 @@ plotEdges <- function(x, useCosts = NULL, col = "black", lwd = 1,
 #' when replotting (TRUE, default), or not (FALSE). In any case,
 #' \code{reset=TRUE} will prevent points to be redrawn.
 #' @param \dots further arguments passed to \code{points}.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso - Different functions to explore these plots:\cr
 #' \code{\link{geo.zoomin}}, \code{\link{geo.zoomout}},
 #' \code{\link{geo.slide}}, \code{\link{geo.back}}, \code{\link{geo.bookmark}},

diff --git a/R/setCosts.R b/R/setCosts.R
@@ -34,7 +34,7 @@
 #' @param \dots additional parameters to be passed to \code{FUN}.
 #' @return A \linkS4class{gGraph} object with the newly defined costs used as
 #' weightings of edges.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso \code{\link{dropDeadEdges}}, to get rid of edge whose cost is below
 #' a given threshold. \code{\link{geo.add.edges}} to add edges to a
 #' \linkS4class{gGraph} object.

diff --git a/R/setDistCosts.R b/R/setDistCosts.R
@@ -17,7 +17,7 @@
 #' @return For the \linkS4class{gGraph} method, a \linkS4class{gGraph} object
 #' with appropriate weights. Note that former weights will be removed from the
 #' object.
-#' @author Thibaut Jombart (\email{t.jombart@@imperial.ac.uk})
+
 #' @seealso The \code{\link{getCosts}} accessor, returning costs of the edges
 #' of a \linkS4class{gGraph} object in different ways.\cr
 #' @keywords utilities methods

diff --git a/README.md b/README.md
@@ -30,7 +30,7 @@ You can install the development version of `geoGraph` from [GitHub](https://gith
 
 ``` r
 install.packages("devtools")
-devtools::install_github("thibautjombart/geoGraph")
+devtools::install_github("EvolEcolGroup/geograph/")
 ```
 
 ## How the package works

diff --git a/man/auxiliary.Rd b/man/auxiliary.Rd
diff --git a/man/buffer.Rd b/man/buffer.Rd
diff --git a/man/closestNode.Rd b/man/closestNode.Rd
diff --git a/man/combineCosts.Rd b/man/combineCosts.Rd
diff --git a/man/connectivity.Rd b/man/connectivity.Rd
diff --git a/man/dijkstra-methods.Rd b/man/dijkstra-methods.Rd
diff --git a/man/dropDeadEdges.Rd b/man/dropDeadEdges.Rd
diff --git a/man/extractFromLayer.Rd b/man/extractFromLayer.Rd
diff --git a/man/findLand.Rd b/man/findLand.Rd
diff --git a/man/gData-class.Rd b/man/gData-class.Rd
diff --git a/man/gGraph-class.Rd b/man/gGraph-class.Rd
diff --git a/man/geo.add.edges.Rd b/man/geo.add.edges.Rd
diff --git a/man/geo.change.attr.Rd b/man/geo.change.attr.Rd
diff --git a/man/getColors.Rd b/man/getColors.Rd
diff --git a/man/getCosts.Rd b/man/getCosts.Rd
diff --git a/man/getEdges.Rd b/man/getEdges.Rd