Add rel to abs abund matrices conversion

Added function 'make_absolute()' to convert relative abundances matrix to absolute abundances matrix, corresponding tests and documentation. This function works with both regular and sparse matrices.

NAMESPACE

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

R/make_relative.R

@@ -6,6 +6,8 @@
 #'
 #' @param abund_matrix abundance matrix, with sites in rows and species in columns
 #'
+#' @seealso \code{\link[funrar]{make_absolute}} for the reverse operation
+#'
 #' @export
 make_relative = function(abund_matrix) {
 
@@ -29,3 +31,35 @@ make_relative = function(abund_matrix) {
 
   return(rel_abund_matrix)
 }
+
+#' Abundance matrix from relative abundances matrix
+#'
+#' Convert the input relative abundances matrix to an abundance matrix
+#'
+#' @param rel_abund_matrix a relative abundance matrix (proportion of individuals
+#'                         of a given species at a given site)
+#'
+#' @seealso \code{\link[funrar]{make_relative}} for the reverse operation
+#'
+#' @export
+make_absolute = function(rel_abund_matrix) {
+
+  # Compute absolute matrix
+  if (requireNamespace("Matrix", quietly = TRUE) &
+      is(rel_abund_matrix, "sparseMatrix")) {
+
+    sites_abund = Matrix::rowSums((rel_abund_matrix != 0) &
+                                    (!is.na(rel_abund_matrix)), na.rm = TRUE)
+
+    abs_matrix = rel_abund_matrix * sites_abund
+  } else {
+    # Compute total site abundances
+    sites_abund = rowSums((rel_abund_matrix != 0) &
+                            (!is.na(rel_abund_matrix)), na.rm = TRUE)
+
+    # Divide each individual abundace by total site abundance
+    abs_matrix = sweep(rel_abund_matrix, 1, sites_abund, "*")
+  }
+
+  return(abs_matrix)
+}

tests/testthat/test-rel_abund.R

@@ -1,7 +1,6 @@
 # Test file for function to convert abundance matrix to relative abundances
 # matrix
-
-context("Abundances to Relative abundances Matrix")
+context("Convert Absolute and Relative Abund Matrices")
 
 # Packages ---------------------------------------------------------------------
 library(Matrix)
@@ -35,3 +34,11 @@ test_that("Can convert from absolute to relative abundances matrices", {
   # On sparse matrices
   expect_equal(make_relative(sparse_abs_abund), sparse_rel_abund)
 })
+
+test_that("Convert relative abundances to absolute abundances matrices", {
+  # On regular matrices
+  expect_equal(make_absolute(rel_abund_mat), abs_abund_mat)
+
+  # On sparse matrices
+  expect_equal(make_absolute(sparse_rel_abund), sparse_abs_abund)
+})