Fix some recent lints

.github/workflows/touchstone-comment.yaml

@@ -10,6 +10,11 @@ on:
     types:
       - completed
 
+permissions:
+  contents: read
+  statuses: write
+  pull-requests: write
+
 jobs:
   upload:
     runs-on: ubuntu-latest

.github/workflows/touchstone-receive.yaml

@@ -7,15 +7,18 @@ concurrency:
 on: 
   pull_request:
 
+permissions:
+  contents: read
+
 jobs:
   prepare:
     runs-on: ubuntu-latest 
     if:
       true &&
       (
-        github.event.comment.author_association == 'OWNER' ||
-        github.event.comment.author_association == 'MEMBER' ||
-        github.event.comment.author_association == 'COLLABORATOR' 
+        github.event.pull_request.author_association == 'OWNER' ||
+        github.event.pull_request.author_association == 'MEMBER' ||
+        github.event.pull_request.author_association == 'COLLABORATOR' 
       )
     outputs:
       config: ${{ steps.read_touchstone_config.outputs.config }}

R/dev_utils.R

@@ -1,5 +1,5 @@
 release_bullets <- function() {
  c(
-   'Re-render vignettes'
+   "Re-render vignettes"
  )
 }

R/fd_fric.R

@@ -83,7 +83,7 @@ fd_fric <- function(traits, sp_com, stand = FALSE) {
   if (ncol(traits) > 16) {
     stop("Due to computational limits FRic can only be computed with n <= 16 ",
          "traits\nConsider dimension reduction techniques if you have more ",
-         "than 16 traits")
+         "than 16 traits", call. = FALSE)
   }
 
   traits <- remove_species_without_trait(traits)
@@ -128,7 +128,8 @@ fd_fric <- function(traits, sp_com, stand = FALSE) {
 
   if (any(is.na(fric_site))) {
     warning(
-      "Some sites had less species than traits so returned FRic is 'NA'"
+      "Some sites had less species than traits so returned FRic is 'NA'",
+      call. = FALSE
     )
   }
 

R/fd_fric_intersect.R

@@ -56,7 +56,7 @@ fd_fric_intersect <- function(traits, sp_com, stand = FALSE) {
   if (ncol(traits) > 16) {
     stop("Due to computational limits FRic intersect can only be computed ",
          "with n <= 16 traits\nConsider dimension reduction techniques ",
-         "if you have more than 16 traits")
+         "if you have more than 16 traits", call. = FALSE)
   }
 
   traits <- remove_species_without_trait(traits)
@@ -136,7 +136,8 @@ fd_fric_intersect <- function(traits, sp_com, stand = FALSE) {
   if (any(is.na(fric_intersect))) {
     warning(
       "Some sites had less species than traits so returned FRic_intersect ",
-      "is 'NA'"
+      "is 'NA'",
+      call. = FALSE
     )
   }
 

data-raw/DATASET.R

@@ -9,12 +9,14 @@ csv_files <- rdryad::dryad_download("10.5061/dryad.c0n737b")[[1]] %>%
 
 # Trait matrices ---------------------------------------------------------------
 
-traits_plants <- read.csv(grep("Traits_plants", csv_files, value = TRUE)) %>%
+traits_plants <- grep("Traits_plants", csv_files, value = TRUE, fixed = TRUE) %>%
+  read.csv() %>%
   select(Species, where(is.numeric)) %>%
   column_to_rownames("Species") %>%
   as.matrix()
 
-traits_birds <- read.csv(grep("Traits_birds", csv_files, value = TRUE)) %>%
+traits_birds <- grep("Traits_birds", csv_files, value = TRUE, fixed = TRUE) %>%
+  read.csv() %>%
   select(Species, where(is.numeric)) %>%
   column_to_rownames("Species") %>%
   as.matrix()
@@ -23,7 +25,8 @@ traits_birds <- read.csv(grep("Traits_birds", csv_files, value = TRUE)) %>%
 # Site-species matrices --------------------------------------------------------
 
 # Birds site-species matrix
-elev_birds <- read.csv(grep("Elevation_birds", csv_files, value = TRUE))
+elev_birds <- grep("Elevation_birds", csv_files, value = TRUE, fixed = TRUE) %>%
+  read.csv()
 
 elevations <- union(elev_birds$Min..elevation..m.a.s.l..,
                     elev_birds$Max..elevation..m.a.s.l..) %>%
@@ -48,7 +51,8 @@ site_sp_birds <- elev_birds %>%
 
 
 # Plants site-species matrix
-elev_plants <- read.csv(grep("Elevation_plants", csv_files, value = TRUE))
+elev_plants <- grep("Elevation_plants", csv_files, value = TRUE, fixed = TRUE) %>%
+  read.csv()
 
 plant_elev <- union(elev_plants$Min..elevation..m.a.s.l..,
                     elev_plants$Max..elevation..m.a.s.l..) %>%