Fix no site names (fixes #76)

R/fd_fdis.R

@@ -16,6 +16,9 @@
 #' * `site` the names of the sites as the row names of the input `sp_com`,
 #' * `FDis` the values of functional dispersion at each site.
 #'
+#' ```{r child = "man/rmdchunks/no_row_names.Rmd"}
+#' ```
+#'
 #' NB: when a site contains no species FDis is equal to 0.
 #'
 #' @references
@@ -62,6 +65,12 @@ fd_fdis <- function(traits, sp_com) {
 
   }
 
+  if (is.null(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)
   site_abundances[site_abundances == 0] <- 1  # Account for site with no species

R/fd_fdiv.R

@@ -17,6 +17,9 @@
 #' * `site` the names of the sites as the row names of the input `sp_com`,
 #' * `FDiv` the values of functional divergence at each site.
 #'
+#' ```{r child = "man/rmdchunks/no_row_names.Rmd"}
+#' ```
+#'
 #' NB: when a site contains no species FDiv is equal to 0. If for a site
 #' there are less traits than species, then FDiv is equal to `NaN`.
 #'
@@ -61,6 +64,12 @@ fd_fdiv <- function(traits, sp_com) {
 
   }
 
+  if (is.null(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)
   site_abundances[site_abundances == 0] <- 1  # Account for site with no species

R/fd_feve.R

@@ -17,6 +17,9 @@
 #' row names,
 #' * `FEve` numeric column that contains FEve values corresponding to each site.
 #'
+#' ```{r child = "man/rmdchunks/no_row_names.Rmd"}
+#' ```
+#'
 #' NB: By definition FEve is equal to `NA` when the number of species per site
 #' is strictly lower than 3.
 #'
@@ -68,6 +71,12 @@ 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)))
+
+  }
+
   # Standardize abundance per site
   site_abundances <- rowSums(sp_com, na.rm = TRUE)
   site_abundances[site_abundances == 0] <- 1  # Account for site with no species

R/fd_fric.R

@@ -44,6 +44,9 @@
 #' * `site` the names of the sites as the row names of the input `sp_com`,
 #' * `FRic` the values of functional richness at each site.
 #'
+#' ```{r child = "man/rmdchunks/no_row_names.Rmd"}
+#' ```
+#'
 #' NB: FRic is equal to `NA` when there are strictly less species in a site
 #' than the number of provided traits. Note that only species with strictly
 #' different trait combinations are considered unique, species that share the
@@ -94,6 +97,12 @@ fd_fric <- function(traits, sp_com, stand = FALSE) {
 
   }
 
+  if (is.null(rownames(sp_com))) {
+
+    rownames(sp_com) <- paste0("s", seq_len(nrow(sp_com)))
+
+  }
+
   max_range <- 1
 
   if (stand) {

R/fd_fric_intersect.R

@@ -19,6 +19,9 @@
 #' * `FRic_intersect` the volume of the convex hulls intersection of each
 #' pair of site.
 #'
+#' ```{r child = "man/rmdchunks/no_row_names.Rmd"}
+#' ```
+#'
 #' NB: FRic_intersect is equal to `NA` when there are strictly less species in
 #' one of the sites than the number of provided traits. Note that only species
 #' with strictly different trait combinations are considered unique, species
@@ -73,6 +76,12 @@ fd_fric_intersect <- function(traits, sp_com, stand = FALSE) {
 
   }
 
+  if (is.null(rownames(sp_com))) {
+
+    rownames(sp_com) <- paste0("s", seq_len(nrow(sp_com)))
+
+  }
+
   max_range <- 1
 
   if (stand) {

R/fd_raoq.R

@@ -17,6 +17,9 @@
 #' * `site` the names of the sites as the row names of the input `sp_com`,
 #' * `Q` the values of Rao's quadratic entropy at each site.
 #'
+#' ```{r child = "man/rmdchunks/no_row_names.Rmd"}
+#' ```
+#'
 #' NB: Rao's quadratic entropy is 0 when there are no species in the site.
 #'
 #' @references
@@ -76,6 +79,12 @@ 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)))
+
+  }
+
   # Standardize abundance per site
   site_abundances <- rowSums(sp_com, na.rm = TRUE)
   site_abundances[site_abundances == 0] <- 1  # Account for site with no species

man/rmdchunks/no_row_names.Rmd

@@ -0,0 +1,2 @@
+If the `sp_com` argument is not provided or if `sp_com` doesn't have rownames,
+arbitrary rownames `s1`, `s2`, `s3`, etc. will be used.

tests/testthat/test-fdis.R

@@ -94,6 +94,22 @@ test_that("Functional Dispersion works on data.frame as well as matrix", {
   )
 })
 
+test_that("Functional Dispersion works when sites have no names", {
+
+  site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
+  rownames(site_sp_no_names) <- NULL
+
+  fdis <- expect_silent(fd_fdis(traits_birds, site_sp_no_names))
+
+  expect_s3_class(fdis, "data.frame")
+  expect_identical(dim(fdis), c(1L, 2L))
+  expect_named(fdis, c("site", "FDis"))
+
+  expect_equal(fdis$FDis, 151.3885, tolerance = 1e-7)
+  expect_equal(fdis[1, "site"], "s1")
+
+})
+
 # Tests for invalid inputs -----------------------------------------------------
 
 test_that("Functional Dispersion fails gracefully", {

tests/testthat/test-fdiv.R

@@ -106,6 +106,22 @@ test_that("Functional Divergence works on data.frame as well as matrix", {
   )
 })
 
+test_that("Functional Divergence works when sites have no names", {
+
+  site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
+  rownames(site_sp_no_names) <- NULL
+
+  fdiv <- expect_silent(fd_fdiv(traits_birds, site_sp_no_names))
+
+  expect_s3_class(fdiv, "data.frame")
+  expect_identical(dim(fdiv), c(1L, 2L))
+  expect_named(fdiv, c("site", "FDiv"))
+
+  expect_equal(fdiv$FDiv, 0.6847251, tolerance = 1e-7)
+  expect_equal(fdiv[1, "site"], "s1")
+
+})
+
 # Tests for invalid inputs -----------------------------------------------------
 
 test_that("Functional Divergence fails gracefully", {

tests/testthat/test-feve.R

@@ -143,6 +143,23 @@ test_that("Functional Evenness works on data.frame as well as matrix", {
   )
 })
 
+test_that("Functional Evenness works when sites have no names", {
+
+  site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
+  rownames(site_sp_no_names) <- NULL
+
+  feve <- expect_silent(fd_feve(traits_birds, site_sp_no_names))
+
+  expect_s3_class(feve, "data.frame")
+  expect_identical(dim(feve), c(1L, 2L))
+  expect_named(feve, c("site", "FEve"))
+
+  expect_equal(feve$FEve, 0.3841202, tolerance = 1e-7)
+  expect_equal(feve[1, "site"], "s1")
+
+})
+
+
 # Tests for invalid inputs -----------------------------------------------------
 
 test_that("Functional Evenness fails gracefully", {

tests/testthat/test-fric.R

@@ -160,6 +160,22 @@ test_that("Functional Richness works on data.frame as well as matrix", {
   )
 })
 
+test_that("Functional Richness works when sites have no names", {
+
+  site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
+  rownames(site_sp_no_names) <- NULL
+
+  fric <- expect_silent(fd_fric(traits_birds, site_sp_no_names))
+
+  expect_s3_class(fric, "data.frame")
+  expect_identical(dim(fric), c(1L, 2L))
+  expect_named(fric, c("site", "FRic"))
+
+  expect_equal(fric$FRic, 171543.730, tolerance = 1e-7)
+  expect_equal(fric[1, "site"], "s1")
+
+})
+
 
 # Tests for invalid inputs -----------------------------------------------------
 

tests/testthat/test-fric_intersect.R

@@ -187,6 +187,23 @@ test_that("Functional Richness Inters. works on data.frame as well as matrix", {
   )
 })
 
+test_that("Functional Richness Intersection works when sites have no names", {
+
+  site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
+  rownames(site_sp_no_names) <- NULL
+
+  fric_int <- expect_silent(fd_fric_intersect(traits_birds, site_sp_no_names))
+
+  expect_s3_class(fric_int, "data.frame")
+  expect_identical(dim(fric_int), c(1L, 3L))
+  expect_named(fric_int, c("first_site", "second_site", "FRic_intersect"))
+
+  expect_equal(fric_int$FRic_intersect, 171543.73, tolerance = 1e-7)
+  expect_equal(fric_int[1, "first_site"], "s1")
+  expect_equal(fric_int[1, "second_site"], "s1")
+
+})
+
 # Tests for invalid inputs -----------------------------------------------------
 
 test_that("Functional Richness Intersection fails gracefully", {

tests/testthat/test-raoq.R

@@ -122,6 +122,22 @@ test_that("Rao's Quadratic Entropy works on data.frame as well as matrix", {
   )
 })
 
+test_that("Rao's Quadratric Entropy works when sites have no names", {
+
+  site_sp_no_names <- site_sp_birds[1,, drop = FALSE]
+  rownames(site_sp_no_names) <- NULL
+
+  raoq <- expect_silent(fd_raoq(traits_birds, site_sp_no_names))
+
+  expect_s3_class(raoq, "data.frame")
+  expect_identical(dim(raoq), c(1L, 2L))
+  expect_named(raoq, c("site", "Q"))
+
+  expect_equal(raoq$Q, 194.78095, tolerance = 1e-7)
+  expect_equal(raoq[1, "site"], "s1")
+
+})
+
 
 # Tests for invalid inputs -----------------------------------------------------