From 8045645569483b02bee0ef8fe736275c8484f916 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Thu, 10 Jul 2025 10:11:01 +0200
Subject: [PATCH 1/4] Use xor() where possible

---
 R/fd_feve.R | 3 +--
 R/fd_raoq.R | 9 ++-------
 2 files changed, 3 insertions(+), 9 deletions(-)

diff --git a/R/fd_feve.R b/R/fd_feve.R
index aadcc3ce..855273d7 100644
--- a/R/fd_feve.R
+++ b/R/fd_feve.R
@@ -34,8 +34,7 @@
 #' @export
 fd_feve <- function(traits = NULL, sp_com, dist_matrix = NULL) {
 
-  if ((!is.null(traits) && !is.null(dist_matrix)) ||
-      (is.null(traits) && is.null(dist_matrix))) {
+  if (!xor(is.null(traits), is.null(dist_matrix))) {
     stop(
       "Please provide either a trait dataset or a dissimilarity matrix",
       call. = FALSE
diff --git a/R/fd_raoq.R b/R/fd_raoq.R
index e77f1533..22d9f595 100644
--- a/R/fd_raoq.R
+++ b/R/fd_raoq.R
@@ -34,8 +34,7 @@
 #' @export
 fd_raoq <- function(traits = NULL, sp_com, dist_matrix = NULL) {
 
-  if ((!is.null(traits) && !is.null(dist_matrix)) ||
-      (is.null(traits) && is.null(dist_matrix))) {
+  if (!xor(is.null(traits), is.null(dist_matrix))) {
     stop(
       "Please provide either a trait dataset or a dissimilarity matrix",
       call. = FALSE
@@ -79,11 +78,7 @@ fd_raoq <- function(traits = NULL, sp_com, dist_matrix = NULL) {
 
   }
 
-  if (is.null(rownames(sp_com))) {
-
-    rownames(sp_com) <- paste0("s", seq_len(nrow(sp_com)))
-
-  }
+  rownames(sp_com) <- rownames(sp_com) %||% paste0("s", seq_len(nrow(sp_com)))
 
   # Standardize abundance per site
   site_abundances <- rowSums(sp_com, na.rm = TRUE)

From 7db98f101904376f2d46a539b2a7ce046811993a Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Thu, 10 Jul 2025 10:11:35 +0200
Subject: [PATCH 2/4] Mark fixed pattern detection as such

---
 vignettes/_fundiversity_2-performance.Rmd | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/vignettes/_fundiversity_2-performance.Rmd b/vignettes/_fundiversity_2-performance.Rmd
index 006750cb..a5614376 100644
--- a/vignettes/_fundiversity_2-performance.Rmd
+++ b/vignettes/_fundiversity_2-performance.Rmd
@@ -386,8 +386,7 @@ all_bench_sites <- list(fric = bench_sites_fric,
                         raoq = bench_sites_raoq,
                         feve = bench_sites_feve) %>%
   bind_rows(.id = "fd_index") %>%
-  mutate(n_sites = gsub("sites", "", expr) %>%
-           as.numeric())
+  mutate(n_sites = as.numeric(gsub("sites", "", expr, fixed = TRUE)))
 
 all_bench_sites %>%
   ggplot(aes(n_sites, time * 1e-9, color = fd_index)) +

From 06d6ac8e354ed4a1b664fa388172d4d49d3b7f8a Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Thu, 10 Jul 2025 10:12:35 +0200
Subject: [PATCH 3/4] Use anyNA() where possible

---
 DESCRIPTION           | 6 +++---
 R/fd_fric_intersect.R | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5f9bc8e1..65acaa9c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: fundiversity
 Title: Easy Computation of Functional Diversity Indices
 Version: 1.1.1
-Authors@R: 
+Authors@R:
     c(
       person("Matthias", "Grenié",
         email = "matthias.grenie@gmail.com",
@@ -24,8 +24,8 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Depends: 
-    R (>= 2.10)
+Depends:
+    R (>= 3.2.0)
 Imports:
     future.apply,
     geometry,
diff --git a/R/fd_fric_intersect.R b/R/fd_fric_intersect.R
index dc8cb46a..e5dc11c7 100644
--- a/R/fd_fric_intersect.R
+++ b/R/fd_fric_intersect.R
@@ -145,7 +145,7 @@ fd_fric_intersect <- function(traits, sp_com, stand = FALSE) {
     }
   }, future.globals = FALSE)
 
-  if (any(is.na(fric_intersect))) {
+  if (anyNA(fric_intersect)) {
     warning(
       "Some sites had less species than traits so returned FRic_intersect ",
       "is 'NA'",

From 51fb1a1188a1bea5e9f8d6f578216f3c5ecca3d8 Mon Sep 17 00:00:00 2001
From: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: Thu, 10 Jul 2025 11:06:30 +0200
Subject: [PATCH 4/4] Use %||% where possible

---
 R/fd_feve.R           | 6 +-----
 R/fd_fric_intersect.R | 5 +----
 R/utils.R             | 9 +++++++++
 3 files changed, 11 insertions(+), 9 deletions(-)
 create mode 100644 R/utils.R

diff --git a/R/fd_feve.R b/R/fd_feve.R
index 855273d7..a448e8a5 100644
--- a/R/fd_feve.R
+++ b/R/fd_feve.R
@@ -70,11 +70,7 @@ fd_feve <- function(traits = NULL, sp_com, dist_matrix = NULL) {
     )
   }
 
-  if (is.null(rownames(sp_com))) {
-
-    rownames(sp_com) <- paste0("s", seq_len(nrow(sp_com)))
-
-  }
+  rownames(sp_com) <- rownames(sp_com) %||% paste0("s", seq_len(nrow(sp_com)))
 
   # Standardize abundance per site
   site_abundances <- rowSums(sp_com, na.rm = TRUE)
diff --git a/R/fd_fric_intersect.R b/R/fd_fric_intersect.R
index e5dc11c7..793aba3a 100644
--- a/R/fd_fric_intersect.R
+++ b/R/fd_fric_intersect.R
@@ -88,11 +88,8 @@ fd_fric_intersect <- function(traits, sp_com, stand = FALSE) {
 
   }
 
-  if (is.null(rownames(sp_com))) {
+  rownames(sp_com) <- rownames(sp_com) %||% paste0("s", seq_len(nrow(sp_com)))
 
-    rownames(sp_com) <- paste0("s", seq_len(nrow(sp_com)))
-
-  }
 
   max_range <- 1
 
diff --git a/R/utils.R b/R/utils.R
new file mode 100644
index 00000000..0ec70aa2
--- /dev/null
+++ b/R/utils.R
@@ -0,0 +1,9 @@
+# This can be deleted in favour of base R version if we ever start depending
+# on R (>= 4.4.0)
+`%||%` <- function(x, y) {
+  if (is.null(x)) {
+    y
+  } else {
+    x
+  }
+}
\ No newline at end of file