docs: improve the handling of possible errors with whitebox

DESCRIPTION

 Package: transfR
 Type: Package
 Title: Transfer of Hydrograph from Gauged to Ungauged Catchments
-Version: 1.0.6
-Date: 2023-01-20
+Version: 1.0.7
+Date: 2023-01-23
 Authors@R: c(
   person("Alban", "de Lavenne", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9448-3490"), email = "alban.delavenne@inrae.fr"),
   person("Christophe", "Cudennec", role = c("ths"), comment = c(ORCID = "0000-0002-1707-8926"), email = "christophe.cudennec@agrocampus-ouest.fr"),

vignettes/V03_inputs_preparation_whitebox.Rmd

@@ -40,7 +40,7 @@ The `elevatr` package allows retrieving grids (rasters) of elevation data worldw
 
 It is necessary to assign a geographic projection for the catchment delineation and hydraulic length maps with the `whitebox` package. We chose to use the Lambert93 projection, the official projection for maps of metropolitan France, for which the [EPSG code is 2154](https://epsg.io/2154).
 
-```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=TRUE, results='hide'}
+```{r, download_dem, echo=TRUE, message=FALSE, warning=FALSE, eval=TRUE, results='hide'}
 library(elevatr)
 library(rgdal) # Still often needed by elevatr
 library(progress) # Still often needed by elevatr
@@ -51,10 +51,7 @@ EPSG <- 2154
 # Define a bbox that will encompass the catchments of the study area
 blavet_bbox <- st_bbox(c(xmin = -3.3, xmax = -2.7, ymax = 48.11, ymin = 47.77), 
                            crs = st_crs(4326))
-```
-
 
-```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=FALSE, results='hide'}
 # Retrieve elevation data as raster
 dem_raw <- elevatr::get_elev_raster(st_as_sfc(blavet_bbox), z = 10) # ~76m resolution
 
@@ -69,19 +66,15 @@ dem_100m[dem_100m < 0] <- NA
 write_stars(dem_100m["warp"], file.path(wbt_wd,"dem_100m.tif"))
 ```
 
-
 ```{r, echo=FALSE, message=FALSE, warning=TRUE, eval=TRUE, results='hide'}
-# Similar to previous chunk but handles unavailable internet resources
-dem_raw <- try(elevatr::get_elev_raster(st_as_sfc(blavet_bbox), z = 10), silent = TRUE)
-if(!inherits(dem_raw, "try-error")){
-  dem_100m  <- st_warp(st_as_stars(dem_raw), cellsize = 100, crs = st_crs(EPSG))
-  names(dem_100m) <- "warp"
-  dem_100m[dem_100m < 0] <- NA
-  write_stars(dem_100m["warp"], file.path(wbt_wd,"dem_100m.tif"))
-  running <- TRUE
-}else{
-  warning("\nIssue when running elevatr::get_elev_raster(). \nThe vignette will not be fully built.")
+try_chunk <- try({
+<<download_dem>>
+}, silent = TRUE)
+if(inherits(try_chunk, "try-error")){
+  warning("\nIssue when downloading elevation data. \nThe vignette will not be fully built.")
   running <- FALSE
+}else{
+  running <- TRUE
 }
 ```
 
@@ -89,7 +82,7 @@ if(!inherits(dem_raw, "try-error")){
 
 The hydrological modelling distinguish the hillslope from the river network. Both will have very different transfer dynamics, and the `transfR` package aims to describe the transfer function of the river network only. Defining where this river network begins and the flow path it takes is a key, and non-trivial, issue for hydrogeomorphologists. The easiest way to draw a drainage network from a DEM is usually to define a minimum drainage area threshold at which the drainage network is assumed to start. However, defining this threshold can be difficult as it may vary spatially, especially with the geology of the region. It may therefore be better to use a known river network and force the flow paths to follow it. Here we will use the [French TOPAGE river network](https://bdtopage.eaufrance.fr/) as a reference (see the description of the `Blavet` dataset to download it from the Web Feature Service (WFS) "Sandre - Eau France"). We will implement a stream burning technique into the DEM using the function [`whitebox::wbt_burn_streams_at_roads()`](https://www.whiteboxgeo.com/manual/wbt_book/available_tools/hydrological_analysis.html#BurnStreamsAtRoads) and following @Lindsay2016a.
 
-```{r, echo=FALSE, message=FALSE, warning=TRUE, eval=running, results='hide'}
+```{r, install_whitebox, echo=FALSE, message=FALSE, warning=TRUE, eval=running, results='hide'}
 # If WhiteboxTools executable are not present, install it in the temporary directory
 library(whitebox)
 if(!wbt_init()){
@@ -112,20 +105,9 @@ if(!wbt_init()){
                 wd = wbt_wd,
                 verbose = TRUE)
   }
-# Try WhiteboxTools to detect any issue
-if(running){
-  wbt_test <- try(whitebox::wbt_fill_depressions(dem = "dem_100m.tif",
-                               output = "dem_fill.tif",
-                               wd = wbt_wd), silent = TRUE)
-  if(inherits(wbt_test, "try-error")){
-    warning("WhiteboxTools could not pass the test of the wbt_fill_depressions() function.")
-    running <- FALSE
-  }
-}
-
 ```
 
-```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
+```{r, burn_stream, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
 library(transfR)
 library(whitebox)
 
@@ -154,6 +136,15 @@ whitebox::wbt_burn_streams_at_roads(dem = "dem_100m.tif",
                         output = "dem_100m_burn.tif", 
                         wd = wbt_wd)
 ```
+```{r, echo=FALSE, message=FALSE, warning=TRUE, eval=running, results='hide'}
+try_chunk <- try({
+<<burn_stream>>
+}, silent = TRUE)
+if(inherits(try_chunk, "try-error")){
+  warning("\nIssue when burning the river network on the DEM. \nThe vignette will not be fully built.")
+  running <- FALSE
+}
+```
 
 ## 3. Delineate catchments from their outlets coordinates
 
@@ -167,7 +158,7 @@ The `whitebox` package provides all the tools to perform a usual catchment delin
 * [Delimit the catchments](https://www.whiteboxgeo.com/manual/wbt_book/available_tools/hydrological_analysis.html#Watershed).
 
 
-```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
+```{r, extract_stream, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
 # Remove the depressions on the DEM
 whitebox::wbt_fill_depressions(dem = "dem_100m_burn.tif",
                                output = "dem_fill.tif",
@@ -197,9 +188,19 @@ whitebox::wbt_remove_short_streams(d8_pntr = "d8.tif",
                                    wd = wbt_wd)
 ```
 
+```{r, echo=FALSE, message=FALSE, warning=TRUE, eval=running, results='hide'}
+try_chunk <- try({
+<<extract_stream>>
+}, silent = TRUE)
+if(inherits(try_chunk, "try-error")){
+  warning("\nIssue when extracting the river network from the DEM. \nThe vignette will not be fully built.")
+  running <- FALSE
+}
+```
+
 Coordinates of the outlets are retrieved from [hydro.eaufrance.fr](https://www.hydro.eaufrance.fr/) and snapped to the pixel of the river network that is consistent with the previously defined flow directions.
 
-```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
+```{r, delineate_catchments, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
 # Localize the outlets of the studied catchments (with manual adjustments to help snapping)
 outlets_coordinates <- data.frame(id = names(Blavet$hl),
                              X = c(254010.612,255940-100,255903,237201,273672,265550),
@@ -233,6 +234,16 @@ for(id in outlets_snapped$id){
 }
 ```
 
+```{r, echo=FALSE, message=FALSE, warning=TRUE, eval=running, results='hide'}
+try_chunk <- try({
+<<delineate_catchments>>
+}, silent = TRUE)
+if(inherits(try_chunk, "try-error")){
+  warning("\nIssue when delineating catchments. \nThe vignette will not be fully built.")
+  running <- FALSE
+}
+```
+
 Resulting catchments delineation can be plotted and checked.
 
 ```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=running}
@@ -263,7 +274,7 @@ The `whitebox` package does not provide a function to compute hydraulic length d
 Flow path lengths are computed once for all the study area. For each catchment, this raster is then trimmed (i.e. removing NA values outside the bounding box of the catchment) and the values of flow path lengths are corrected such as the minimum flow path length is equal to half a pixel width/height. The hydraulic lengths are finally gathered in a list as expected by the `as_transfr()` function.
 
 
-```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
+```{r, hydraulic_length, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide'}
 # Compute hydraulic length
 whitebox::wbt_downslope_flowpath_length(d8_pntr = "d8.tif",
                                         output = "fpl.tif",
@@ -288,6 +299,17 @@ for(id in catchments$id){
 
 ```
 
+
+```{r, echo=FALSE, message=FALSE, warning=TRUE, eval=running, results='hide'}
+try_chunk <- try({
+<<hydraulic_length>>
+}, silent = TRUE)
+if(inherits(try_chunk, "try-error")){
+  warning("\nIssue when computing hydraulic length. \nThe vignette will not be fully built.")
+  running <- FALSE
+}
+```
+
 Resulting maps of hydraulic length can be plotted and checked.
 
 ```{r, echo=TRUE, message=FALSE, warning=FALSE, eval=running, results='hide', fig.width=7, fig.height=4}