✅ Update tests

Author: mhesselbarth

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: shar
 Title: Species-Habitat Associations
-Version: 1.0.1
+Version: 1.1
 Authors@R: c(person("Maximillian H.K.", "Hesselbarth", email = "[email protected]",
              role = c("aut", "cre"), comment = c(ORCID = "0000-0003-1125-9918")),
              person("Marco", "Sciaini", email = "[email protected]",

NEWS.md

@@ -1,3 +1,8 @@
+# shar 1.1
+* Improvements
+  * Use energy_df to get energy for printing if available
+  + Updated tests
+
 # shar 1.0.1
 * Improvements
   * No calculation of energy for printig (too slow)

R/plot_energy.R

@@ -41,6 +41,12 @@ plot_energy <- function(pattern,
          call. = FALSE)
   }
 
+  if (all(pattern$energy_df == "NA")) {
+
+    stop("There is no 'energy_df' slot. Please use pattern reconstruction for valid input data.",
+         call. = FALSE)
+  }
+
   # get number of rows
   range_i <- range(vapply(X = pattern$energy_df,
                           FUN = function(x) range(x$i), FUN.VALUE = numeric(2)))
@@ -58,7 +64,7 @@ plot_energy <- function(pattern,
   graphics::plot(NULL,
                  xlim = range_i,
                  ylim = range_energy,
-                 main = "Energy over time",
+                 main = "Energy over iterations",
                  xlab = "Iterations",
                  ylab = "Energy")
 

R/print.rd_mar.R

@@ -46,6 +46,11 @@ print.rd_mar <- function(x,
     includes_observed <- "included"
   }
 
+  # get extent of window
+  extent_window <- paste0(c(x$randomized[[1]]$window$xrange,
+                            x$randomized[[1]]$window$yrange), collapse = " ")
+
+
   # get number of randomized patterns plus observed pattern
   number_patterns <- length(x$randomized) + number_patterns_obs
 
@@ -63,10 +68,25 @@ print.rd_mar <- function(x,
                              collapse = " ")
   }
 
+  # check if eneergy_df is available
+  if (is.list(x$energy_df)) {
+
+    mean_energy <- round(mean(vapply(x$energy_df, function(x) {
+
+      tail(x, n = 1)[, 2]
+    }, FUN.VALUE = numeric(1))), digits = digits)
+  }
+
+  else {
+    mean_energy <- "NA"
+  }
+
   # print result
   cat(paste0("No. of pattern: ", number_patterns, "\n",
              "Method: ", x$method, "\n",
              "Observed pattern: ", includes_observed, "\n",
              "Iterations (mean): ", mean_iterations, "\n",
-             "Stop criterion (no. of patterns): ", stop_criterion, "\n"), ...)
+             "Energy (mean): ", mean_energy, "\n",
+             "Stop criterion (no. of patterns): ", stop_criterion, "\n",
+             "Extent: ", extent_window, " (xmin, xmax, ymin, ymax) \n"), ...)
 }

R/print.rd_pat.R

@@ -51,6 +51,10 @@ print.rd_pat <- function(x,
     includes_observed <- "included"
   }
 
+  # get extent of window
+  extent_window <- paste0(c(x$randomized[[1]]$window$xrange,
+                            x$randomized[[1]]$window$yrange), collapse = " ")
+
   # get number of randomized patterns plus observed pattern
   number_patterns <- length(x$randomized) + number_patterns_obs
 
@@ -68,10 +72,25 @@ print.rd_pat <- function(x,
                              collapse = " ")
   }
 
+  # check if eneergy_df is available
+  if (is.list(x$energy_df)) {
+
+    mean_energy <- round(mean(vapply(x$energy_df, function(x) {
+
+      tail(x, n = 1)[, 2]
+    }, FUN.VALUE = numeric(1))), digits = digits)
+  }
+
+  else {
+    mean_energy <- "NA"
+  }
+
   # print result
   cat(paste0("No. of pattern: ", number_patterns, "\n",
              "Method: ", x$method, "\n",
              "Observed pattern: ", includes_observed, "\n",
              "Iterations (mean): ", mean_iterations, "\n",
-             "Stop criterion (no. of patterns): ", stop_criterion, "\n"), ...)
+             "Energy (mean): ", mean_energy, "\n",
+             "Stop criterion (no. of patterns): ", stop_criterion, "\n",
+             "Extent: ", extent_window, " (xmin, xmax, ymin, ymax) \n"), ...)
 }

R/print.rd_ras.R

@@ -43,14 +43,19 @@ print.rd_ras <- function(x,
     includes_observed <- "included"
   }
 
+  # get extent of window
+  extent_window <- paste0(c(raster::xmin(x$randomized[[1]]),
+                            raster::xmax(x$randomized[[1]]),
+                            raster::ymin(x$randomized[[1]]),
+                            raster::ymax(x$randomized[[1]])),
+                          collapse = " ")
+
   # get number of randomized patterns plus observed pattern
   number_raster <- length(x$randomized) + number_raster_obs
 
   # print result
   cat(paste0("No. of raster: ", number_raster, "\n",
-             # "Mean energy: ", energy, "\n",
              "Method: ", x$method, "\n",
-             "Observed pattern: ", includes_observed, "\n"),
-             # "Iterations (mean): ", mean_iterations, "\n"),
-      ...)
+             "Observed pattern: ", includes_observed, "\n",
+             "Extent: ", extent_window, " (xmin, xmax, ymin, ymax) \n"), ...)
 }