Merge pull request #20 from emlab-ucsb/dev

Fix #17

DESCRIPTION

@@ -1,12 +1,14 @@
 Package: spatialgridr
 Title: Grid spatial data for conservation planning purposes
-Version: 0.0.0.9000
+Version: 0.0.0.9001
 Authors@R: person(given = "Jason", family = "Flower", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-6731-8182"))
 Description: An R package that allows easy gridding of spatial data. Principally intended for spatial conservation planning uses.
 License: GPL (>= 3) + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+Depends: 
+    R (>= 3.5.0)
 Imports: 
     dplyr,
     exactextractr,

R/sf_to_grid.R

@@ -27,52 +27,96 @@ sf_to_grid <- function(dat, spatial_grid, matching_crs, name, feature_names, ant
       {if(antimeridian) sf::st_shift_longitude(.) else .}
 
     dat_cropped <- dat %>%
-      {if(antimeridian & !unique(sf::st_geometry_type(.)) %in% c("POINT", "MULTIPOINT")) {
+      {if(all(antimeridian & !(c("POINT", "MULTIPOINT") %in% unique(sf::st_geometry_type(.))))) {
         sf::st_break_antimeridian(., lon_0 = 180) %>% sf::st_shift_longitude()}
-        else if(antimeridian & unique(sf::st_geometry_type(.)) %in% c("POINT", "MULTIPOINT")){
+        else if(all(antimeridian & (c("POINT", "MULTIPOINT") %in% unique(sf::st_geometry_type(.))))){
           sf::st_shift_longitude(.)} else .} %>%
       sf::st_crop(grid_temp) %>%
       sf::st_transform(sf::st_crs(spatial_grid))
   }
 
-  if(nrow(dat_cropped) == 0) stop("No data in grid.")
-
   if(is.null(feature_names)){
     if(is.null(name)) name <- "data"
 
+    if(nrow(dat_cropped) == 0){
+      message("No ", name, " in grid")
+      if(is_raster){
+        return(spatial_grid %>%
+                 terra::subst(1,0) %>%
+                 setNames(name))
+      } else{
+        return(spatial_grid %>%
+                 dplyr::mutate({{name}} := 0, .before = ncol(.)))
+      }
+    }
+
     dat_grouped <- dat_cropped %>%
       dplyr::mutate({{name}} := 1, .before = 1) %>%
       dplyr::group_by({{name}}) %>%
       dplyr::summarise() %>%
       dplyr::ungroup() %>%
-      {if(sf::st_geometry_type(., by_geometry = FALSE) == "GEOMETRY") sf::st_cast(., to = "MULTIPOLYGON") else .}
+      {if(all(c("POLYGON", "MULTIPOLYGON") %in% (sf::st_geometry_type(.) %>% unique() %>% as.character()))) sf::st_cast(., to = "MULTIPOLYGON") else .}
 
   }  else {
+    if(nrow(dat_cropped) == 0){
+      message("No data in grid")
+
+      layer_names <- unique(dat[[feature_names]])
+
+      if(is_raster){
+        return(spatial_grid %>%
+                 terra::subst(1,0) %>%
+                 rep(length(layer_names)) %>%
+                 setNames(layer_names))
+      } else{
+        new_cols <- data.frame(matrix(data = 0, ncol= length(layer_names), nrow=nrow(spatial_grid), dimnames=list(NULL, layer_names)))
+        return(spatial_grid %>%
+                 dplyr::bind_cols(new_cols))
+      }
+    }
+
     dat_grouped <- dat_cropped %>%
       dplyr::group_by(.data[[feature_names]]) %>%
       dplyr::summarise() %>%
       dplyr::ungroup() %>%
-      {if(sf::st_geometry_type(., by_geometry = FALSE) == "GEOMETRY") sf::st_cast(., to = "MULTIPOLYGON") else .}
+      {if(all(c("POLYGON", "MULTIPOLYGON") %in% (sf::st_geometry_type(.) %>% unique() %>% as.character()))) sf::st_cast(., to = "MULTIPOLYGON") else .}
   }
-
   if(is_raster){
+
     nms <- dat_grouped[[1]]
 
-    exactextractr::coverage_fraction(spatial_grid, dat_grouped) %>%
+ temp_rast  <- exactextractr::coverage_fraction(spatial_grid, dat_grouped) %>%
       terra::rast() %>%
       setNames(nms) %>%
       terra::mask(spatial_grid) %>%
-      {if(apply_cutoff) terra::classify(., matrix(c(-1, cutoff, NA, cutoff, 1.2, 1), ncol = 3, byrow = TRUE), include.lowest = FALSE, right = FALSE) else .} %>%
-      .[[lapply(., function(x) !all(terra::values(x) == 0)) %>% unlist()]] #removes all zero layers and by default also all NA layers
+      {if(apply_cutoff) terra::classify(., matrix(c(-1, cutoff, 0, cutoff, 1.2, 1), ncol = 3, byrow = TRUE), include.lowest = FALSE, right = FALSE) else .}
+
+    #check if some features were cropped out; if so, need to add raster layers with zeroes in
+    if(is.null(feature_names)) {
+        return(temp_rast)
+      } else if(all(unique(dat[[feature_names]]) %in% nms)){
+        return(temp_rast)
+      }  else{
+        missing_feature_nms <- setdiff(unique(dat[[feature_names]]), nms)
+
+        missing_features_rast <- spatial_grid %>%
+          terra::subst(1,0) %>%
+          rep(length(missing_feature_nms)) %>%
+          setNames(missing_feature_nms)
+
+        return(c(temp_rast, missing_features_rast))
+      }
   } else{
 
     grid_has_extra_cols <- if(ncol(spatial_grid)>1) TRUE else FALSE
 
     if(grid_has_extra_cols) extra_cols <- sf::st_drop_geometry(spatial_grid)
 
-    spatial_grid_with_id <- spatial_grid %>%
+    spatial_grid_geom <- spatial_grid %>%
       sf::st_geometry() %>%
-      sf::st_sf() %>%
+      sf::st_sf()
+
+    spatial_grid_with_id <- spatial_grid_geom %>%
       dplyr::mutate(cellID = 1:nrow(.))
 
     spatial_grid_with_area <- spatial_grid_with_id %>%
@@ -86,12 +130,13 @@ sf_to_grid <- function(dat, spatial_grid, matching_crs, name, feature_names, ant
     intersected_data_list <- list()
 
     for (layer in layer_names) {
-      temp_intersection <- sf::st_intersection(spatial_grid_with_id, dat_list[[layer]])
+      temp_intersection <- sf::st_intersection(spatial_grid_with_id, dat_list[[layer]]) %>%
+        {if(all(sf::st_is_valid(.))) . else sf::st_make_valid(.)}
 
       if(nrow(temp_intersection)>0) {
         intersected_data_list[[layer]] <- temp_intersection %>%
           dplyr::mutate(area = as.numeric(sf::st_area(.))) %>%
-          sf::st_drop_geometry(.) %>%
+          sf::st_drop_geometry() %>%
           dplyr::full_join(spatial_grid_with_area, ., by = c("cellID")) %>%
           dplyr::mutate(perc_area = .data$area / .data$area_cell, .keep = "unused", .before = 1) %>%
           dplyr::mutate(perc_area = dplyr::case_when(is.na(.data$perc_area) ~ 0,
@@ -104,15 +149,32 @@ sf_to_grid <- function(dat, spatial_grid, matching_crs, name, feature_names, ant
             ) %>%
               dplyr::select({{layer}})
           }}
+      } else{
+        intersected_data_list[[layer]] <- spatial_grid_geom %>%
+          dplyr::mutate({{layer}} := 0, .before = 1)
       }
     }
+    intersected_data_df <- lapply(intersected_data_list, function(x) sf::st_drop_geometry(x)) %>%
+      do.call(cbind, .)
 
-    if(length(intersected_data_list) == 0) stop("No data in grid")
+    nms <- colnames(intersected_data_df)
 
-    lapply(intersected_data_list, function(x) sf::st_drop_geometry(x) %>% dplyr::select(dplyr::where(~any(. != 0)))) %>%
-      do.call(cbind, .) %>%
+    intersected_data_sf <- intersected_data_df %>%
       {if(grid_has_extra_cols) cbind(extra_cols, .) else .} %>%
       sf::st_set_geometry(sf::st_geometry(intersected_data_list[[1]])) %>%
       sf::st_set_geometry("geometry")
-  }
+
+    if(is.null(feature_names)) {
+      return(intersected_data_sf)
+    } else if(all(unique(dat[[feature_names]]) %in% nms)){
+      return(intersected_data_sf)
+    }  else{
+      missing_feature_nms <- setdiff(unique(dat[[feature_names]]), nms)
+
+      new_cols <- data.frame(matrix(data = 0, ncol= length(missing_feature_nms), nrow=nrow(spatial_grid), dimnames=list(NULL, missing_feature_nms)))
+      return(intersected_data_sf %>%
+               dplyr::bind_cols(new_cols))
+
+    }
+   }
   }