Initial commit

Author: ecknight

gis/DataExtentSmoothing.R

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+###############################################
+# title: "Smoothing data range extent layer"
+# author: Elly Knight
+# date: August 8, 2025
+##################################################
+
+#This code takes the NA tif output from "Probable_Range_Extent.R" and smooths it for masking packaged outputs to the area of available survey data.
+
+#PREAMBLE############################
+
+#1. Load packages----
+
+library(tidyverse) #basic data wrangling
+library(sf) #read in & handle study area
+library(terra) #raster management
+
+#2. Set root path for data on google drive----
+root <- "G:/Shared drives/BAM_NationalModels5"
+
+#3. Get tif----
+na1 <- rast(file.path(root, "MosaicWeighting", "Range", "ABS_NA_Layer450.tiff"))
+
+#4. Get Canada extent----
+can <- read_sf(file.path(root, "Regions", "BAM_BCR_NationalModel_Unbuffered_Canada.shp")) |> 
+  st_union() |> 
+  st_transform(crs(na1)) |> 
+  vect()
+
+#5. Crop ----
+na2 <- na1 |> crop(can, mask=TRUE)
+
+#6. Smooth it ----
+w <- matrix(1, 299, 299)
+na3 <- focal(na2, w=w, fun=mean, na.policy="omit", expand=TRUE)
+
+#7. Rebinarize ----
+na4 <- na3 > 0.5
+
+#8. Fix boundary ----
+na5 <- resample(na4, na2)
+na5[is.na(na5)] <- 0
+na6 <- sum(na5, na2)
+na6[values(na6) > 0] <- 1
+
+#8. Plot ----
+plot(na6)
+
+#9. Save ----
+writeRaster(na6, file.path(root, "gis", "DataLimitationsMask.tif"))
+