Question 2

DESCRIPTION

@@ -9,8 +9,13 @@ Description: One paragraph description of what the package does as
        one or more full sentences.
 License: GPL (>= 2)
 Imports: 
-    Rcpp
+    Rcpp,
+    graphics,
+    dplyr
 LinkingTo: Rcpp
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

NAMESPACE

@@ -1,5 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
+export(myplot)
 export(rcpp_hello_world)
+import(dplyr)
+import(graphics)
 importFrom(Rcpp,evalCpp)
 useDynLib(egpkg, .registration = TRUE)

R/add_plot.R

@@ -0,0 +1,32 @@
+#' Add myplot function
+#' @param x A numeric vector.
+#' @param y A numeric vector.
+#' @return A plot of x and y.
+#' @examples
+# Here is an example
+#' set.seed(312)
+#' x <- rnorm(100)
+#' y <- rnorm(100)
+#' myplot(x, y)
+#' @import graphics
+#' @import dplyr
+#' @export
+# Here is the function
+myplot <- function(x, y) {
+
+  if (!is.numeric(x) | !is.numeric(y)) {
+    stop("x and y must be numeric")
+  }
+
+  plot(x, y, col = "blue", pch = 19, cex = 2)
+
+  invisible(
+    list(
+      x = x,
+      y = y
+    )
+  )
+
+}
+
+

egpkg.Rproj.Rcheck/00check.log

@@ -0,0 +1,8 @@
+* using log directory ‘/Users/u6046094/Desktop/Fall 24/PHS 7045 R Programming/Labs/R_package/egpkg-lab07/egpkg.Rproj.Rcheck’
+* using R version 4.4.1 (2024-06-14)
+* using platform: aarch64-apple-darwin20
+* R was compiled by
+    Apple clang version 14.0.0 (clang-1400.0.29.202)
+    GNU Fortran (GCC) 12.2.0
+* running under: macOS Sonoma 14.6.1
+* using session charset: UTF-8

src/ps_match.cpp

@@ -0,0 +1,183 @@
+#include <Rcpp.h>
+
+using namespace Rcpp;
+
+// [[Rcpp::export]]
+List ps_match1(const NumericVector & x) {
+
+  int n = static_cast<int>(x.size());
+
+  IntegerVector indices(n);
+  NumericVector values(n);
+
+  for (int i = 0; i < n; ++i) {
+
+    // Maximum value
+    double cur_best = std::numeric_limits< double >::max();
+    int cur_i = 0;
+
+    for (int j = 0; j < n; ++j) {
+
+      // We can't compare to oneself
+      if (i == j)
+        continue;
+
+      // If it is lower, then update
+      if (std::abs(x[i] - x[j]) < cur_best) {
+
+        cur_best = std::abs(x[i] - x[j]);
+        cur_i    = j;
+
+      }
+
+    }
+
+    // In the end, we register the result
+    indices[i] = cur_i;
+    values[i]  = x[cur_i];
+
+  }
+
+  return List::create(
+    _["match_id"] = indices + 1, // We add one to match R's indices
+    _["match_x"]  = values
+  );
+
+}
+
+// [[Rcpp::export]]
+List ps_match2(const NumericVector & x) {
+
+  int n = static_cast<int>(x.size());
+
+  IntegerVector indices(n);
+  NumericVector values(n);
+
+  for (int i = 0; i < n; ++i) {
+
+    // Instead of allocating new memory, we can point by reference
+    // (saves operations)
+    double & cur_best = values[i];
+    int    & cur_i    = indices[i];
+
+    cur_best = std::numeric_limits< double >::max();
+
+    cur_i = 0;
+
+    for (int j = 0; j < n; ++j) {
+
+      // We can't compare to oneself
+      if (i == j)
+        continue;
+
+      // If it is lower, then update
+      if (std::abs(x[i] - x[j]) < cur_best) {
+
+        cur_best = std::abs(x[i] - x[j]);
+        cur_i    = j;
+
+      }
+
+    }
+
+  }
+
+  for (int i = 0; i < n; ++i)
+    values[i] = x[indices[i]];
+
+  return List::create(
+    _["match_id"] = indices + 1, // We add one to match R's indices
+    _["match_x"]  = values
+  );
+
+}
+
+// [[Rcpp::export]]
+List ps_match3(const NumericVector & x) {
+
+  int n = static_cast<int>(x.size());
+
+  IntegerVector indices(n);
+  NumericVector values(n);
+  values.fill(std::numeric_limits< double >::max());
+
+  for (int i = 0; i < n; ++i) {
+
+    // Instead of allocating new memory, we can point by reference
+    // (saves operations)
+    double & cur_best = values[i];
+    auto & cur_i    = indices[i];
+
+    for (int j = 0; j < i; ++j) {
+
+      // If it is lower, then update
+      double d = std::abs(x[i] - x[j]);
+      if (d < cur_best) {
+
+        cur_best = d;
+        cur_i    = j;
+
+      }
+
+      if (d < values[j]) {
+
+        values[j] = d;
+        indices[j] = i;
+
+      }
+
+    }
+
+  }
+
+  for (int i = 0; i < n; ++i)
+    values[i] = x[indices[i]];
+
+  return List::create(
+    _["match_id"] = indices + 1, // We add one to match R's indices
+    _["match_x"]  = values
+  );
+
+}
+
+
+/***R
+set.seed(1231)
+x <- cbind(runif(5))
+
+ps_matchR <- function(x) {
+
+  match_expected <- dist(x) |> as.matrix()
+  diag(match_expected) <- .Machine$integer.max
+  indices <- apply(match_expected, 1, which.min)
+
+  list(
+    match_id = as.integer(unname(indices)),
+    match_x  = x[indices]
+  )
+
+}
+
+resR <- ps_matchR(x)
+res1 <- ps_match1(x)
+res2 <- ps_match2(x)
+res3 <- ps_match3(x)
+
+cbind(
+  X     = x,
+  R     = resR$match_id,
+  Rcpp1 = res$match_id,
+  Rcpp2 = res2$match_id,
+  Rcpp3 = res3$match_id
+) |> head()
+
+# Benchmarking
+x <- cbind(runif(10000))
+bench::mark(
+  resR = ps_matchR(x)$match_x,
+  res1 = ps_match1(x)$match_x,
+  res2 = ps_match2(x)$match_x,
+  res3 = ps_match3(x)$match_x,
+  relative = TRUE
+)
+*/

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(egpkg)
+
+test_check("egpkg")

tests/testthat/test_add_plot.R

@@ -0,0 +1,9 @@
+# test add_plot function
+# when input is not numeric
+
+library(testthat)
+library(egpkg)
+
+test_that("add_plot function", {
+  expect_error(myplot("a", "b"), "x and y must be numeric")
+})