Version bump and small zoning-related fixes added #121

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ibis.iSDM
 Type: Package
 Title: Modelling framework for integrated biodiversity distribution scenarios
-Version: 0.1.4
+Version: 0.1.5
 Authors@R: 
     c(person(given = "Martin",
            family = "Jung",

NEWS.md

@@ -1,4 +1,11 @@
-# ibis.iSDM 0.1.4 (current dev branch)
+# ibis.iSDM 0.1.5 (current dev branch)
+
+#### New features
+
+#### Minor improvements and bug fixes
+* Minor :bug: fix related to misaligned thresholds and negative expontential kernels.
+
+# ibis.iSDM 0.1.4 
 
 #### New features
 * Support for carnying over latent spatial effects (`add_latent_spatial()`) to `scenario()` projections.

R/add_constraint.R

@@ -382,8 +382,11 @@ methods::setMethod(
   # Divide alpha values by 2
   alpha <- value/2
 
+  # Scale value for different projections
+  value_scale <- ifelse(terra::is.lonlat(baseline_threshold), terra::res(baseline_threshold)[1] * 10000, 1)
+
   # Grow baseline raster by using an exponentially weighted kernel
-  ras_dis <- terra::gridDist(baseline_threshold, target = 1)
+  ras_dis <- terra::gridDist(baseline_threshold, target = 1, scale = value_scale)
   # Normalized (with a constant) negative exponential kernel
   ras_dis <- terra::app(ras_dis, fun = function(x) (1 / (2 * pi * value ^ 2)) * exp(-x / value) )
   # Equivalent to alpha = 1/value and

R/project.R

@@ -236,6 +236,9 @@ methods::setMethod(
                               msg = "Model predictors are missing from the scenario predictor!")
     }
 
+    # Create a template for use
+    template <- emptyraster( new_preds$get_data() )
+
     # Get constraints, threshold values and other parameters
     scenario_threshold <- mod$get_threshold()
     if(!is.Waiver(scenario_threshold)){
@@ -264,8 +267,13 @@ methods::setMethod(
         baseline_threshold <- baseline_threshold[[grep(layer, names(baseline_threshold))]]
       }
 
-      # Set all NA values to 0 (and then mask by background?)
-      baseline_threshold[is.na(baseline_threshold)]<-0
+      # Set all NA values to 0
+      baseline_threshold[is.na(baseline_threshold)] <- 0
+      # Align with newpreds extend and
+      if(!terra::compareGeom(baseline_threshold, template, stopOnError = FALSE)){
+        baseline_threshold <- terra::extend(baseline_threshold, template)
+        baseline_threshold <- terra::crop(baseline_threshold, template)
+      }
 
     } else {
       baseline_threshold <- new_waiver()
@@ -275,9 +283,6 @@ methods::setMethod(
     scenario_constraints <- mod$get_constraints()
     scenario_simulations <- mod$get_simulation()
 
-    # Create a template for use
-    template <- emptyraster( new_preds$get_data() )
-
     #  --- Check that everything is there ---
     # Check that thresholds are set for constrains
     if("dispersal" %in% names(scenario_constraints)){
@@ -455,6 +460,7 @@ methods::setMethod(
         scenario_threshold <- scenario_threshold[[1]]
         out_thresh <- out
         out_thresh[out_thresh < scenario_threshold] <- 0; out_thresh[out_thresh >= scenario_threshold] <- 1
+        out_thresh[is.na(out_thresh)] <- 0 # Added to avoid unnecessary clipping
         names(out_thresh) <- "threshold"
 
         # Apply minimum size constraint if set