CST-564 add preview_grid()

Author: KevCaz

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: SAVM
 Title: Submerged aquatic vegetation model
-Version: 0.0.1.9002
-Date: 2025-07-14
+Version: 0.0.1.9003
+Date: 2025-07-15
 Authors@R: c(
     person(given = "Kevin",
            family = "Cazelles",

NAMESPACE

@@ -1,10 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(preview_grid,sav_data)
 export(compute_fetch)
 export(invert_polygon)
 export(plot_sav_density)
 export(plot_sav_distribution)
 export(plot_sav_tmap)
+export(preview_grid)
 export(read_sav)
 export(read_sav_aoi)
 export(read_sav_csv)

NEWS.md

@@ -1,6 +1,7 @@
 # SAVM (devel)
 
+* `preview_grid()` allows to preview grid (see #8).
 * Add more guidance on reading shapefiles in the vignette (see #6). 
 * `invert_polygon()` has been added to invert polygon (see #6).
 * `compute_fetch()` has a new argument `n_bearings` that provides the number of bearings, it replaces `n_quad_seg` (see #4 and #5). 
-* `compute_fetch()` only compute the mean fetch for all bearings (see #4). 
+* `compute_fetch()` only compute the mean fetch for all bearings (see #4).

R/data_input.R

@@ -1,11 +1,17 @@
 #' Read SAV data from different formats
 #'
 #' @param file_path {`character`}\cr{} Path to the input file.
-#' @param spacing {`numeric`}\cr{} Spacing for grid generation (if AOI is used).
+#' @param spacing {`numeric`}\cr{}
+#' Spacing for grid generation. Used if an area of interest (AOI) is provided,
+#' ignored otherwise.
 #' @param layer {`character`}\cr{} Layer name for multi-layer spatial files (default: NULL).
-#' @param crs {`numeric`}\cr{} Coordinate Reference System (CRS) of the output data. Default is 32617.
-#' @param crs_input {`numeric`}\cr{} Coordinate Reference System (CRS) of the input data, used for CSV import. Default is 4326.
-#' @param export {`character`}\cr{} Optional. Folder path to export outputs as .gpkg.
+#' @param crs {`numeric`}\cr{}
+#' Coordinate Reference System (CRS) of the output data. Default is 32617.
+#' @param crs_input {`numeric`}\cr{}
+#' Coordinate Reference System (CRS) of the input data, used for CSV import.
+#' Default is 4326.
+#' @param export {`character`}\cr{}
+#' Optional. Folder path to export outputs as .gpkg.
 #'
 #' @return A list with `points` (sf object) and `polygon` (sf object).
 #'
@@ -52,12 +58,15 @@ read_sav <- function(file_path, spacing = 500, layer = NULL, crs = 32617, crs_in
     file_ext <- tools::file_ext(file_path)
 
     if (file_ext == "csv") {
+        sav_msg_info("csv detected")
         points_sf <- read_sav_csv(file_path, crs = crs)
         polygon_sf <- sf::st_sf(geometry = sf::st_union(points_sf) |> sf::st_convex_hull())
     } else if (file_ext %in% c("shp", "geojson", "gpkg", "gbd")) {
         if (file_ext == "gbd") {
+            sav_msg_info("gdb detected")
             sf_obj <- sf::st_read(file_path, layer = layer, quiet = TRUE)
         } else {
+            sav_msg_info("spatial file detected")
             sf_obj <- sf::st_read(file_path, quiet = TRUE)
         }
 
@@ -83,7 +92,12 @@ read_sav <- function(file_path, spacing = 500, layer = NULL, crs = 32617, crs_in
         sav_msg_success("Exported outputs to {export}.")
     }
 
-    return(list(points = points_sf, polygon = polygon_sf))
+    return(
+        structure(
+            list(points = points_sf, polygon = polygon_sf),
+            class = "sav_data"
+        )
+    )
 }
 
 

R/preview_grid.R

@@ -0,0 +1,18 @@
+#' Preview grid
+#'
+#' @param x an object of class `sav_data`.
+#'
+#' @export
+#'
+preview_grid <- function(x) {
+    UseMethod("preview_grid")
+}
+
+#' @describeIn preview_grid  Preview spatail grid.
+#'
+#' @export
+#'
+preview_grid.sav_data <- function(x) {
+    plot(x$polygon |> sf::st_geometry(), border = 1)
+    plot(x$points |> sf::st_geometry(), col = "grey50", pch = 19, add = TRUE)
+}

man/data_input.Rd

@@ -80,7 +80,7 @@ erie_lake |>
   plot(col = 1)
 ```
 
-The file can then be exported in various format, for instance in [GeoPackage](https://www.geopackage.org/):
+Using `sf` capacities, the file can then be exported in various format, for instance in [GeoPackage](https://www.geopackage.org/):
 
 ```R
 erie_lake |> sf::st_write(erie_lake, "lake_erie.gpkg")
@@ -91,22 +91,35 @@ we will use the package [`stars`](https://r-spatial.github.io/stars/) that works
 
 
 
-
 ## Reading file 
 
 Now we consider a zone near Buffalo in the Lake Erie. Note that all 
-the data required data are included on in the package SAVM.  
+the data required are included on in the package SAVM. We first load the geopackage of Lake Erie. 
 
-```{r reading}
+```{r reading1}
 # Lake Erie boundaries polygon (reading from SAVM internal files)
 le_bound <- system.file("example", "lake_erie.gpkg", package = "SAVM") |>
   sf::st_read() |>
   sf::st_transform(crs = 3857)
+```
 
+We then load the shapefile of the area of interest that is stored as a GeoJSON file. Note that for the area (or points) of interest, we use `read_sav()` that returns an object of class `sav_data`. 
+
+```{r reading2}
 # Lake Erie study zone: read
 study_zone <- system.file("example", "study_zone.geojson", package = "SAVM") |>
   read_sav(spacing = 2000)
+```
+
+Note that the corresponfing grid can be visualized using the `preview_grid()` function. 
+
+```{r preview_grid}
+preview_grid(study_zone)
+```
+
+We now load the depth data.
 
+```{r reading3}
 # Depth (reading with stars)
 study_depth <- stars::read_stars(system.file("example", "le_bathy.tiff", package = "SAVM"))
 ```
@@ -118,7 +131,7 @@ study_depth <- stars::read_stars(system.file("example", "le_bathy.tiff", package
 
 ### Compute fetch 
 
-To compute wind fetch (in kilometers, we called `compute_fetch()`), by default, the maximum distance is set to 15 km (see argument `max_dist`) and the default number of radial transect by quadrant is 9 (see argument `n_quad_seg`).
+To compute wind fetch (in kilometers), we called `compute_fetch()`. By default, the maximum distance is set to 15 km (see argument `max_dist`) and the default number of bearings is 16 (see argument `n_bearings`).
 
 ```{r fetch}
 fetch <- compute_fetch(study_zone$points, le_bound)