Use algebraic eigenvalues, and get rid of useNames = NA warning

R/SFEMethod-multivariate.R

@@ -55,7 +55,7 @@ multispati_rsp <- function(x, listw, nfposi = 30L, nfnega = 30L, scale = TRUE) {
  if (scale) {
  # Note that dudi.pca divides by n instead of n-1 when scaling data
  n <- nrow(x)
- x <- sweep(x, 2, sqrt(colVars(x)*(n-1)/n), FUN = "/")
+ x <- sweep(x, 2, sqrt(matrixStats::colVars(x)*(n-1)/n), FUN = "/")
  }
  if (inherits(listw, "Matrix") || is.matrix(listw))
  W <- listw
@@ -65,9 +65,9 @@ multispati_rsp <- function(x, listw, nfposi = 30L, nfnega = 30L, scale = TRUE) {
  stop("listw must be either a listw object or an adjacency matrix.")
  covar <- t(x) %*% (W + t(W)) %*% x / (2*nrow(x))
  if (nfnega == 0L) {
- res <- eigs_sym(covar, k = nfposi, which = "LM")
+ res <- eigs_sym(covar, k = nfposi, which = "LA")
  } else if (nfposi == 0L) {
- res <- eigs_sym(covar, k = nfnega, which = "SM")
+ res <- eigs_sym(covar, k = nfnega, which = "SA")
  } else {
  nf <- max(nfposi, nfnega)
  res <- eigs_sym(covar, k = 2*nf, which = "BE")

tests/testthat/test-multivariate.R

@@ -30,6 +30,37 @@ test_that("Correct output structure of multispati_rsp", {
  expect_true(all(eigs[11:20] < 0))
 })
 
+test_that("Correct output structure of multispati_rsp, only positive", {
+ out <- multispati_rsp(t(mat), listw = g, nfposi = 10, nfnega = 0)
+ expect_equal(colnames(out), paste0("PC", 1:10))
+ expect_equal(rownames(out), colnames(sfe))
+ expect_true(is.numeric(out))
+ loadings <- attr(out, "rotation")
+ expect_equal(colnames(loadings), paste0("PC", 1:10))
+ expect_equal(rownames(loadings), rownames(mat))
+ expect_true(is.numeric(loadings))
+ eigs <- attr(out, "eig")
+ expect_equal(length(eigs), 10)
+ expect_true(is.numeric(eigs))
+ expect_true(all(eigs > 0))
+})
+
+test_that("Correct output structure of multispati_rsp, only negative", {
+ out <- multispati_rsp(t(mat), listw = g, nfposi = 0, nfnega = 10)
+ expect_equal(colnames(out), paste0("PC", 1:10))
+ expect_equal(rownames(out), colnames(sfe))
+ expect_true(is.numeric(out))
+ loadings <- attr(out, "rotation")
+ expect_equal(colnames(loadings), paste0("PC", 1:10))
+ expect_equal(rownames(loadings), rownames(mat))
+ expect_true(is.numeric(loadings))
+ eigs <- attr(out, "eig")
+ expect_equal(length(eigs), 10)
+ expect_true(is.numeric(eigs))
+ expect_true(all(diff(eigs) < 0))
+ expect_true(all(eigs < 0))
+})
+
 ref <- multispati_rsp(t(mat), listw = g, nfposi = 10, nfnega = 10)
 test_that("CalculateMultivariate for matrix", {
  out <- calculateMultivariate(mat, "multispati", listw = g,