update tests, checks version bump

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rEDM
 Type: Package
 Title: Applications of Empirical Dynamic Modeling from Time Series
-Version: 0.7.4
+Version: 0.7.5
 Authors@R: c(person("Hao", "Ye", role = c("aut", "cre"), 
                     email = "[email protected]", 
                     comment = c(ORCID = "0000-0002-8630-1458")), 

R/block_GP.R

@@ -235,8 +235,14 @@ block_gp <- function(block, lib = c(1, NROW(block)), pred = lib,
                              x_pred = x_pred, ...)
 
         # compute stats for mean predictions
-        stats <- compute_stats(y_pred, out_gp$mean_pred)
-
+        if (silent)
+        {
+            suppressWarnings(stats <- compute_stats(y_pred, out_gp$mean_pred)
+            )
+        } else {
+            stats <- compute_stats(y_pred, out_gp$mean_pred)
+        }
+
         # prepare output (default is param settings and stats)
         out_df <- data.frame(embedding = paste(embedding, sep = "", 
                                                collapse = ", "), 
@@ -473,6 +479,12 @@ compute_gp <- function(x_lib, y_lib,
     K_lib_lib <- eta_scaled * exp(-phi ^ 2 * squared_dist_lib_lib)
     Sigma <- K_lib_lib + v_e_scaled * diag(NROW(x_lib))
 
+    # error checking on Sigma
+    if (any(!is.finite(Sigma)) || !all(Sigma > 0))
+    {
+        stop("Distance matrix is not positive-definite; Is the input data degenerate?")
+    }
+
     # cholesky algorithm from Rasmussen & Williams (2006, algorithm 2.1)
     R <- chol(Sigma)
     alpha <- backsolve(R, forwardsolve(t(R), y_lib - mean_y))

tests/testthat/test_10_tde_gp.R

@@ -55,3 +55,17 @@ test_that("tde_gp works on time series", {
     attributes(output) <- attributes(output)[sort(names(attributes(output)))]
     expect_equal(digest::digest(output), "5c59eef4c687a6bd589f72a64d35c5f8")
 })
+
+
+test_that("Error checking works", {
+    ts_1 <- rep.int(0, 30)
+    ts_2 <- sample(c(0, 1), 30, replace = TRUE)
+    ts_3 <- rep.int(1, 30)
+
+    expect_error(out_1 <- tde_gp(ts_1, E = 1:3), 
+                 "Distance matrix is not positive-definite; Is the input data degenerate?")
+    expect_error(out_2 <- tde_gp(ts_2, E = 1:3), 
+                 NA)
+    expect_error(out_3 <- tde_gp(ts_3, E = 1:3), 
+                 "Distance matrix is not positive-definite; Is the input data degenerate?")
+})