Add fct to make relative abunds matrices

Add function to transform abundances matrices to relative abundances matrices. It also works with sparse matrices. It has the corresponding tests.

NAMESPACE

@@ -6,6 +6,7 @@ export(distinctiveness_com)
 export(distinctiveness_stack)
 export(funrar)
 export(funrar_stack)
+export(make_relative)
 export(matrix_to_stack)
 export(restrictedness)
 export(restrictedness_stack)

R/make_relative.R

@@ -0,0 +1,31 @@
+#' Relative abundance matrix from absolute abundance matrix
+#'
+#' From an abundance matrix (numbers of individuals of a given species at a site)
+#' returns a relative abundance matrix (proportion of individuals of a given species
+#' at a given site). This function works also with sparse matrices.
+#'
+#' @param abund_matrix abundance matrix, with sites in rows and species in columns
+#'
+#' @export
+make_relative = function(abund_matrix) {
+
+  # Check input type using internal function
+  check_matrix(abund_matrix, "abundance")
+
+  # Compute relative abundances matrix
+  if (requireNamespace("Matrix", quietly = TRUE) &
+      is(abund_matrix, "sparseMatrix")) {
+
+    sites_abund = Matrix::rowSums(abund_matrix, na.rm = TRUE)
+
+    rel_abund_matrix = abund_matrix / sites_abund
+  } else {
+    # Compute total site abundances
+    sites_abund = rowSums(abund_matrix, na.rm = TRUE)
+
+    # Divide each individual abundace by total site abundance
+    rel_abund_matrix = sweep(abund_matrix, 1, sites_abund, "/")
+  }
+
+  return(rel_abund_matrix)
+}

tests/testthat/test-rel_abund.R

@@ -0,0 +1,37 @@
+# Test file for function to convert abundance matrix to relative abundances
+# matrix
+
+context("Abundances to Relative abundances Matrix")
+
+# Packages ---------------------------------------------------------------------
+library(Matrix)
+
+# Common objects ---------------------------------------------------------------
+
+# Abundance Matrix to test
+abs_abund_mat = matrix(c(1, 1, 1, NA,
+                         NA, rep(1, 3),
+                         NA, 1, 1, NA,
+                         NA, NA, 1, 1),
+                       ncol = 4)
+
+sparse_abs_abund = as(abs_abund_mat, "sparseMatrix")
+
+# Corresponding relative abundances matrix
+rel_abund_mat = matrix(c(1,  1/3, 1/4, NA,
+                         NA, 1/3, 1/4, 1/2,
+                         NA, 1/3, 1/4, NA,
+                         NA, NA,  1/4, 1/2),
+                       ncol = 4)
+
+sparse_rel_abund = as(rel_abund_mat, "sparseMatrix")
+
+# Tests ------------------------------------------------------------------------
+
+test_that("Can convert from absolute to relative abundances matrices", {
+  # On regular matrices
+  expect_equal(make_relative(abs_abund_mat), rel_abund_mat)
+
+  # On sparse matrices
+  expect_equal(make_relative(sparse_abs_abund), sparse_rel_abund)
+})