Added more specific NAs in world error

Author: wburke24

R/GIS_read.R

@@ -185,11 +185,17 @@ GIS_read = function(maps_in, type, typepars, map_info = NULL, seq_patch_IDs = FA
 
     # Check for missing data (within world map mask) - no fix, just an error since I think this will break things if left unchecked
     cat("Checking for missing data within bounds of world map.\n")
-    if (!is.null("map_info") &
-        sum(is.na(raster::values(read_stack)[!is.na(raster::values(read_stack[[map_info[map_info[, 1] == "world", 2][[1]]]])),
-                                             !colnames(raster::values(read_stack)) %in% map_info[map_info[, 1] == "streams", 2]])) > 0) {
-      # Add in future? - which maps are missing data?
-      stop("Missing data within bounds of world level map. Check you input maps.")
+    if (!is.null("map_info")) {
+      wrld_vals = !is.na(raster::values(read_stack[[map_info[map_info[, 1] == "world", 2][[1]]]]))
+      NAs_in_wrld = lapply(as.data.frame(raster::values(read_stack)), function(X) {sum(is.na( X[wrld_vals]))})
+      if ("streams" %in% map_info[, 1]) {
+        NAs_in_wrld[[map_info[map_info[, 1] == "streams", 2]]] = NULL
+      }
+      if (any(NAs_in_wrld > 0) ) {
+        cat("One or more maps have NAs within the bounds of the world map, see maps and counts of NAs below:\n")
+        print(NAs_in_wrld[NAs_in_wrld > 0])
+        stop("See above and check your input maps.")
+      }
     }
 
     # Convert maps to SpatialGridDataFrame since world_gen.R expects that format

R/spatial_input_gen.R

@@ -36,6 +36,18 @@ spatial_input_gen = function(name,
 
   warning("Work in progress - May not work, output crs/proj is weird, optional args/fucntionality is broken, probably best to run line by line")
 
+  # maybe this will help
+  library(rgrass7)
+
+  basin = NULL
+  patch = FALSE
+  define_watershed = FALSE
+  easting = NULL
+  northing = NULL
+  gisDbase = NULL
+  location = NULL
+  mapset = NULL
+
   # check and convert file paths for args
 
 
@@ -74,7 +86,7 @@ spatial_input_gen = function(name,
   }
 
   # --- checking env and stuff ---
-  # gmeta()
+  # rgrass7::gmeta()
   # rgrass7::execGRASS(cmd = "g.mapset", flags = "p")
   # rgrass7::execGRASS(cmd = "g.mapset", flags = "l")
   # rgrass7::execGRASS(cmd = "g.list", flags = "p", type = "raster")

R/utils.R

@@ -12,38 +12,31 @@ init_defaults = function() {
 
 # run this is preprocess isn't working to check out if anything stands out with the maps
 # i'll try to add checks to this as needed.
-debug_spatial = function(template, typepars, streams) {
-
-  template = template_read(template = template)
-  maps = as.data.frame(unique(template[[5]]))
-  maps = rbind(maps, c("streams", streams))
-
-  map_paths = file.path(typepars, maps$Map)
-
-  maps$Exists = sapply(map_paths, file.exists)
-
-  library(raster)
-  # going to assume this might not work, tho this is how they are read normally
-  #map_stack = raster::stack(x = map_paths)
-  map_data = list()
-  for (i in seq_along(map_paths)) {
-    map_data[[i]] = raster(map_paths[i])
-
-    maps$extent = paste(map_data[[i]]@extent[1:4])
-    maps$cellsize = res(map_data[[i]])
-
-    maps$ncell = ncell(map_data[[i]])
-    maps$NAs = sum(is.na(values(map_data[[i]])))
-    maps$NULLs = sum(is.null(map_data[[i]]))
-    maps$proj = paste(crs(map_data[[i]]@crs))
-
-
-  }
-
-  prob = map_stack[values(map_stack$pch_30m1000.1) == 15660]
-
-
-
-
-
-}
+# debug_spatial = function(template, typepars, streams) {
+#
+#   template = template_read(template = template)
+#   maps = as.data.frame(unique(template[[5]]))
+#   maps = rbind(maps, c("streams", streams))
+#
+#   map_paths = file.path(typepars, maps$Map)
+#
+#   maps$Exists = sapply(map_paths, file.exists)
+#
+#   library(raster)
+#   # going to assume this might not work, tho this is how they are read normally
+#   #map_stack = raster::stack(x = map_paths)
+#   map_data = list()
+#   for (i in seq_along(map_paths)) {
+#     map_data[[i]] = raster(map_paths[i])
+#
+#     maps$extent = paste(map_data[[i]]@extent[1:4])
+#     maps$cellsize = res(map_data[[i]])
+#
+#     maps$ncell = ncell(map_data[[i]])
+#     maps$NAs = sum(is.na(values(map_data[[i]])))
+#     maps$NULLs = sum(is.null(map_data[[i]]))
+#     maps$proj = paste(crs(map_data[[i]]@crs))
+#
+#   }
+#
+# }