Fix most significant lints (#86)

* Use xor() where possible

* Mark fixed pattern detection as such

* Use anyNA() where possible

* Use %||% where possible

Author: Bisaloo

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,

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
@@ -71,11 +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)

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
 
@@ -145,7 +142,7 @@ 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'",

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)

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
+  }
+}

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)) +