check clean

.Rbuildignore

@@ -16,5 +16,5 @@
 CRAN-SUBMISSION
 cran-comments.md
 ^CRAN-SUBMISSION$
-^metadata\\.yml$
+metadata.yml
 featured.png

R/parse_forestable.R

@@ -14,12 +14,12 @@
     f <- emptyforest()
     if(is_tree) {
       f$treeData <- tree |>
-        dplyr::select(sp_name, sp_code, dbh, height, density_factor) |>
-        dplyr::rename(Species = sp_name,
-                      SpeciesCode = sp_code,
-                      DBH = dbh,
-                      Height = height,
-                      N = density_factor) |>
+        dplyr::select(.data$sp_name, .data$sp_code, .data$dbh, .data$height, .data$density_factor) |>
+        dplyr::rename(Species = .data$sp_name,
+                      SpeciesCode = .data$sp_code,
+                      DBH = .data$dbh,
+                      Height = .data$height,
+                      N = .data$density_factor) |>
         dplyr::mutate(DBH = as.numeric(DBH),
                       Height = as.numeric(Height)*100,
                       N = as.numeric(N)) |>
@@ -52,25 +52,25 @@
         dplyr::filter(DBH >= minimumTreeDBH)
       if(!keepSpeciesCodes) {
         f$treeData <- f$treeData |>
-          dplyr::select(-SpeciesCode)
+          dplyr::select(-.data$SpeciesCode)
       }
     }
     if(is_shrub) {
       shrub <- understory$shrub[[1]]
       f$shrubData <- shrub |>
-        dplyr::select(sp_name, sp_code, height, cover) |>
-        dplyr::rename(Species = sp_name,
-                      SpeciesCode = sp_code,
-                      Height = height,
-                      Cover = cover) |>
+        dplyr::select(.data$sp_name, .data$sp_code, .data$height, cover) |>
+        dplyr::rename(Species = .data$sp_name,
+                      SpeciesCode = .data$sp_code,
+                      Height = .data$height,
+                      Cover = .data$cover) |>
         dplyr::mutate(Height = as.numeric(Height),
                       Cover = as.numeric(Cover),
                       Z50 = as.numeric(NA),
                       Z95 = as.numeric(NA))
 
       if(!keepSpeciesCodes) {
         f$shrubData <- f$shrubData |>
-          dplyr::select(-SpeciesCode)
+          dplyr::select(-.data$SpeciesCode)
       }
 
     }

vignettes/PreparingInputs_I.Rmd

@@ -29,10 +29,14 @@ library(medfate)
 library(medfateland)
 library(ggplot2)
 library(tidyterra)
-library(forestables)
 ```
 
-The first section, **A**, shows how to create the spatial inputs from forest inventory data in tree lists, which will be the general case. The second section, **B**, shows the differences that occur when the starting point is a data structure issued from package **forestables**.
+
+The first section, **A**, shows how to create the spatial inputs from forest inventory data in tree lists, which will be the general case. The second section, **B**, shows the differences that occur when the starting point is a data structure issued from package **forestables**. For that part we need package **forestables** in our environment, because we will take an example data table from there. The package can be installed from GitHub:
+```{r}
+# remotes::install_github("emf-creaf/forestables")
+library(forestables)
+```
 
 ## A. General procedure
 
@@ -289,7 +293,7 @@ Here we will use only data from the last survey (IFN4):
 
 ```{r}
 ifn4_example <- ifn_output_example |>
-  filter(version == "ifn4")
+  dplyr::filter(version == "ifn4")
 ifn4_example
 ```