From 06418146bf3d1b11964cf214207bcaf00e4c6557 Mon Sep 17 00:00:00 2001
From: emilio-berti <emilio.berti90@gmail.com>
Date: Fri, 21 May 2021 09:08:05 +0200
Subject: [PATCH] Checks

---
 DESCRIPTION         | 3 ++-
 R/circuitscape.R    | 4 ++--
 R/en_path.R         | 6 ++++--
 R/enerscape.R       | 2 +-
 R/least-cost_path.R | 2 +-
 R/omniscape.R       | 4 ++--
 man/en_path.Rd      | 3 ++-
 man/enerscape.Rd    | 2 +-
 8 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 607adb9..469c1c0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: enerscape
 Type: Package
 Title: Compute Energy Landscapes
-Version: 0.1.0
+Version: 0.1.1
 Author: Emilio Berti
 Maintainer: Emilio Berti <emilio.berti@idiv.de>
 Description: Compute energy landscapes using a digital elevation model (DEM) 
@@ -13,6 +13,7 @@ Imports:
     raster,
     gdistance,
     rgdal,
+    rgeos,
     sp,
     Matrix
 Suggests:
diff --git a/R/circuitscape.R b/R/circuitscape.R
index aa95540..ada2540 100644
--- a/R/circuitscape.R
+++ b/R/circuitscape.R
@@ -22,8 +22,8 @@ circuitscape_skeleton <- function(
       stop("points are not data.frame or matrix")
     }
   }
-  pr <- raster::rasterize(points, en$rasters$Work, na.rm = TRUE)
-  raster::writeRaster(en$rasters$Work, file.path(path, "/work.tif"),
+  pr <- raster::rasterize(points, en$rasters$EnergyScape, na.rm = TRUE)
+  raster::writeRaster(en$rasters$EnergyScape, file.path(path, "/work.tif"),
                       overwrite = TRUE)
   raster::writeRaster(pr, file.path(path, "/loc.tif"),
                       overwrite = TRUE)
diff --git a/R/en_path.R b/R/en_path.R
index cbf50f4..e407730 100644
--- a/R/en_path.R
+++ b/R/en_path.R
@@ -16,7 +16,9 @@
 #' data("volcano")
 #' dem <- raster(volcano)
 #' en <- enerscape(dem, 10, unit = "kcal", neigh = 16)
-#' en_path(en, draw = TRUE, n = 10)
+# p <- coordinates(en$rasters$DEM)[sample(1:ncell(en$rasters$DEM), 5), ]
+# path <- sp::SpatialLines(list(sp::Lines(sp::Line(p), ID = "path")))
+# en_path(en, path)
 #' }
 #' @export
 #' @references Etten, J. van. (2017). R Package gdistance: Distances and Routes
@@ -51,7 +53,7 @@ en_path <- function(
   } else if (class(p)[1] != "SpatialLines") {
     stop("Path must be a SpatialLines object")
   }
-  w <- raster::extract(en$rasters$Work, p)[[1]]
+  w <- raster::extract(en$rasters$EnergyScape, p)[[1]]
   ans <- list(Path = p,
               Distance = sp::SpatialLinesLengths(p),
               Cost = sum(w))
diff --git a/R/enerscape.R b/R/enerscape.R
index e03f543..bc27ab5 100644
--- a/R/enerscape.R
+++ b/R/enerscape.R
@@ -14,7 +14,7 @@
 #'   Prampero et al. (1979).
 #' @param v speed of cyclist (km / h), only for \code{method = 'cycling'}.
 #' @return A list with elements a rasterStack of the digital elevation model,
-#'   slope, work, and conductance and the conductance as a transitionLayer for
+#'   slope, energy landscape, and conductance and the conductance as a transitionLayer for
 #'   path analysis.
 #' @details From the digital elevation model, transition slopes, energy costs
 #'   and conductances (1 / work) are computed based on the model described in
diff --git a/R/least-cost_path.R b/R/least-cost_path.R
index 4da4433..38fd5cf 100644
--- a/R/least-cost_path.R
+++ b/R/least-cost_path.R
@@ -33,7 +33,7 @@ en_lcp <- function(
     stop("en must be an enerscape object")
   } else {
     x <- en$rasters$DEM
-    work <- en$rasters$Work
+    work <- en$rasters$EnergyScape
     cond <- en$cond_tr
   }
   ans <- list() #initialize return value
diff --git a/R/omniscape.R b/R/omniscape.R
index 800b68d..a5b99e3 100644
--- a/R/omniscape.R
+++ b/R/omniscape.R
@@ -18,9 +18,9 @@ omniscape_skeleton <- function(
     stop("Missing mandatory input")
   }
   if (aggr_fact > 1) {
-    w <- raster::aggregate(en$rasters$Work, aggr_fact)
+    w <- raster::aggregate(en$rasters$EnergyScape, aggr_fact)
   } else {
-    w <- en$rasters$Work
+    w <- en$rasters$EnergyScape
   }
   raster::writeRaster(w, file.path(path, "/work.tif"),
                       overwrite = TRUE)
diff --git a/man/en_path.Rd b/man/en_path.Rd
index b9989e0..2eb39ce 100644
--- a/man/en_path.Rd
+++ b/man/en_path.Rd
@@ -26,8 +26,9 @@ Optionally, the path can be selected by specifying the number of nodes and
 clicking on the plot.
 }
 \examples{
-\dontrun{
+\donttest{
 library(raster)
+library(enerscape)
 data("volcano")
 dem <- raster(volcano)
 en <- enerscape(dem, 10, unit = "kcal", neigh = 16)
diff --git a/man/enerscape.Rd b/man/enerscape.Rd
index e96a9c8..a6b66b7 100644
--- a/man/enerscape.Rd
+++ b/man/enerscape.Rd
@@ -24,7 +24,7 @@ Prampero et al. (1979).}
 }
 \value{
 A list with elements a rasterStack of the digital elevation model,
-  slope, work, and conductance and the conductance as a transitionLayer for
+  slope, energy landscape, and conductance and the conductance as a transitionLayer for
   path analysis.
 }
 \description{