fix rds matrix conversion and compiling warning

Author: rvalavi

R/benchmark.R

@@ -130,15 +130,19 @@ benchmark <- function(
         }
     }
 
-    # interpolate reference density
-    if (interpolate) {
-        ref_density <- terra::as.matrix(
-            terra::disagg(terra::rast(ref_density), fact = 2, method = "bilinear"),
-            wide = TRUE
-        )
-        # update the binwidth and offset
-        bin_width <- bin_width / 2
-        offset <- offset * 2
+    # interpolate reference density
+    if (interpolate) {
+        ref_density <- terra::as.matrix(
+            terra::disagg(
+                terra::rast(.check_mat(unclass(ref_density), name = "ref_density")),
+                fact = 2,
+                method = "bilinear"
+            ),
+            wide = TRUE
+        )
+        # update the binwidth and offset
+        bin_width <- bin_width / 2
+        offset <- offset * 2
     }
     # get the bin number after interpolation
     bin_num <- min(dim(ref_density))

R/ref_density.R

@@ -200,6 +200,6 @@ plot.reference_density <- function(x, ...) {
         message("For aesthetic, the normalised reference density plot is reversed and transposed.")
     }
     terra::plot(
-        terra::rast(x), col = palettes(150, "ref_density"), ...
+        terra::rast(.check_mat(unclass(x), name = "x")), col = palettes(150, "ref_density"), ...
     )
 }

src/Benchmark.cpp

@@ -1,5 +1,9 @@
 // [[Rcpp::plugins(openmp)]]
 // [[Rcpp::plugins("cpp11")]]
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wignored-attributes"
+#endif
 #include <Rcpp.h>
 #include <cmath>
 #include <vector>
@@ -241,3 +245,7 @@ Rcpp::NumericMatrix bench_cpp(
 
     return out_mat;
 }
+
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic pop
+#endif

src/Matrix.h

@@ -1,7 +1,8 @@
 #ifndef MATRIX_T
 #define MATRIX_T
 
-#include "RcppEigenQuiet.h"
+#include <Rcpp.h>
+#include <RcppEigen.h>
 
 // Generic row-major matrix type
 template <typename T>

src/Radial.cpp

@@ -1,5 +1,9 @@
 // [[Rcpp::plugins(openmp)]]
 // [[Rcpp::plugins("cpp11")]]
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wignored-attributes"
+#endif
 #include <Rcpp.h>
 #include <vector>
 #include <cmath>
@@ -120,5 +124,9 @@ Rcpp::IntegerVector radial_count_cpp(
         out[i] = count;
     }
 
-    return Rcpp::wrap(out);
-}
+    return Rcpp::wrap(out);
+}
+
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic pop
+#endif

src/RcppEigenQuiet.h

@@ -1,5 +1,9 @@
 // [[Rcpp::plugins(openmp)]]
 // [[Rcpp::plugins("cpp11")]]
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wignored-attributes"
+#endif
 #include <Rcpp.h>
 #include <cmath>
 #include <vector>
@@ -151,3 +155,7 @@ Rcpp::IntegerMatrix ref_density_cpp(
 
     return matrix;
 }
+
+#if defined(__GNUC__) || defined(__clang__)
+#pragma GCC diagnostic pop
+#endif

src/Reference.cpp

@@ -43,3 +43,49 @@ test_that("benchmark uses reference density attributes when they are not supplie
   expect_equal(dim(out), c(2, 1))
   expect_true(all(is.finite(out[, 1])))
 })
+
+test_that("benchmark interpolates reference_density objects", {
+  skip_if_not_installed("terra")
+
+  samples <- matrix(
+    c(
+      0, 0, 0.2, 0.3, 0.2, 0.3,
+      1, 1, 0.4, 0.5, 0.4, 0.5,
+      2, 2, 0.6, 0.7, 0.6, 0.7,
+      3, 3, 0.8, 0.9, 0.8, 0.9
+    ),
+    ncol = 6,
+    byrow = TRUE
+  )
+
+  ref <- ref_density(
+    data = samples,
+    radius_km = 1000,
+    bin_width = 0.1,
+    bin_num = 10,
+    num_threads = 1L
+  )
+  ref_norm <- normalise(
+    x = ref,
+    trim_size = 6,
+    offset = 1
+  )
+
+  expect_no_error(
+    out <- benchmark(
+      data = samples[1:2, , drop = FALSE],
+      samples = samples,
+      ref_density = ref_norm,
+      radius_km = 1000,
+      k_pred = 2,
+      k_obs = 1,
+      bin_width = NULL,
+      offset = NULL,
+      interpolate = TRUE,
+      num_threads = 1L
+    )
+  )
+
+  expect_equal(dim(out), c(2, 1))
+  expect_true(all(is.finite(out[, 1])))
+})

tests/testthat/test-benchmark-wrapper.R

@@ -47,3 +47,17 @@ test_that("normalise handles reference_density objects and normalises rows", {
   expect_equal(rowSums(out), rep(1, 4), tolerance = 1e-8)
   expect_true(file.exists(paste0(outfile, ".txt")))
 })
+
+test_that("plot.reference_density handles custom class objects", {
+  skip_if_not_installed("terra")
+
+  x <- matrix(seq_len(36), nrow = 6)
+  class(x) <- c("reference_density", "matrix", "array")
+  attr(x, "bin.width") <- 0.5
+
+  plot_file <- tempfile(fileext = ".pdf")
+  grDevices::pdf(plot_file)
+  on.exit(grDevices::dev.off(), add = TRUE)
+
+  expect_no_error(plot(x))
+})