Updates

DESCRIPTION

@@ -26,7 +26,11 @@ Roxygen: list(markdown = TRUE)
 URL: https://christiangoueguel.github.io/ConfidenceEllipse/
 Suggests: 
     knitr,
-    rmarkdown
+    rmarkdown,
+    spelling,
+    testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Depends: 
     R (>= 2.10)
+Language: en-US
+Config/testthat/edition: 3

R/confidence_ellipse.R

@@ -8,9 +8,7 @@
 #' @param conf_level The confidence level for the ellipse (0.95 by default).
 #' @return A data frame of the coordinates points of the ellipse.
 #' @export confidence_ellipse
-
 confidence_ellipse <- function(.data, x, y, .group_by = NULL, conf_level = 0.95) {
-
   if (missing(.data)) {
     stop("Missing 'data' argument.")
   }
@@ -20,24 +18,23 @@ confidence_ellipse <- function(.data, x, y, .group_by = NULL, conf_level = 0.95)
   if (!is.numeric(conf_level)) {
     stop("'conf_level' must be numeric.")
   }
-  if (conf_level < 0 && conf_level > 1) {
+  if (conf_level < 0 || conf_level > 1) {
     stop("'conf_level' must be between 0 and 1.")
   }
-
   transform_data <- function(.x, conf_level) {
     mean_vec <- colMeans(.x)
-    cov_mat <- stats::cov(.x)
-    if (any(is.na(cov_mat))) {
-      stop("warning: the covariance matrix is singular")
+    cov_matrix <- stats::cov(.x)
+    if (any(is.na(cov_matrix))) {
+      stop("Covariance matrix contains NA values.")
     }
     else {
-      eig <- eigen(cov_mat)
+      eig <- eigen(cov_matrix)
       theta <- (2 * pi * seq(0, 360, 1)) / 360
       X <- sqrt(eig$values[1] * stats::qchisq(conf_level, 2)) * cos(theta)
       Y <- sqrt(eig$values[2] * stats::qchisq(conf_level, 2)) * sin(theta)
       R <- cbind(X, Y) %*% t(eig$vectors)
-      res <- R + matrix(rep(t(mean_vec), 361), ncol = ncol(t(mean_vec)), byrow = TRUE)
-      return(res)
+      result <- R + matrix(rep(t(mean_vec), 361), ncol = ncol(t(mean_vec)), byrow = TRUE)
+      return(result)
     }
   }
   if (rlang::quo_is_null(rlang::enquo(.group_by))) {

R/confidence_ellipsoid.R

@@ -8,9 +8,7 @@
 #' @param conf_level The confidence level for the ellipse (0.95 by default).
 #' @return A data frame of the coordinates points of the ellipse.
 #' @export confidence_ellipsoid
-
 confidence_ellipsoid <- function(.data, x, y, z, .group_by = NULL, conf_level = 0.95) {
-
   if (missing(.data)) {
     stop("Missing 'data' argument.")
   }
@@ -23,23 +21,23 @@ confidence_ellipsoid <- function(.data, x, y, z, .group_by = NULL, conf_level =
   if (conf_level < 0 || conf_level > 1) {
     stop("'conf_level' must be between 0 and 1.")
   }
-
   transform_data <- function(.x, conf_level) {
     mean_vec <- colMeans(.x)
-    cov_mat <- stats::cov(.x)
-    if (any(is.na(cov_mat))) {
-      stop("Warning: The covariance matrix is singular.")
-    } else {
-      eig <- eigen(cov_mat)
+    cov_matrix <- stats::cov(.x)
+    if (any(is.na(cov_matrix))) {
+      stop("Covariance matrix contains NA values.")
+    }
+    else {
+      eig <- eigen(cov_matrix)
       theta <- seq(0, 2 * pi, length.out = 50)
       phi <- seq(0, pi, length.out = 50)
       grid <- expand.grid(Theta = theta, Phi = phi)
       X <- sqrt(eig$values[1] * stats::qchisq(conf_level, 3)) * sin(grid$Phi) * cos(grid$Theta)
       Y <- sqrt(eig$values[2] * stats::qchisq(conf_level, 3)) * sin(grid$Phi) * sin(grid$Theta)
       Z <- sqrt(eig$values[3] * stats::qchisq(conf_level, 3)) * cos(grid$Phi)
       R <- cbind(X, Y, Z) %*% t(eig$vectors)
-      res <- R + matrix(rep(mean_vec, nrow(R)), ncol = length(mean_vec), byrow = TRUE)
-      return(res)
+      result <- R + matrix(rep(mean_vec, nrow(R)), ncol = length(mean_vec), byrow = TRUE)
+      return(result)
     }
   }
   if (rlang::quo_is_null(rlang::enquo(.group_by))) {

inst/WORDLIST

@@ -0,0 +1,14 @@
+Acta
+CMD
+De
+Janssen
+Lifecycle
+Microchim
+Raedt
+Schalm
+Trivariate
+Veeckman
+magrittr
+th
+tibble
+trivariate

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = 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(ConfidenceEllipse)
+
+test_check("ConfidenceEllipse")

tests/testthat/test-confidence_ellipse.R

@@ -0,0 +1,57 @@
+library(tibble)
+data("glass", package = "ConfidenceEllipse")
+# Test cases covered:
+# confidence_ellipse function stops when no data is provided.
+# confidence_ellipse function stops when input data is not a data frame or tibble.
+# confidence_ellipse function stops when the conf_level is not numeric.
+# confidence_ellipse function stops when the conf_level is not between 0 and 1.
+# confidence_ellipse function returns a tibble.
+# confidence_ellipse function works correctly with a simple example.
+# confidence_ellipse function works correctly with a grouping factor.
+# confidence_ellipse function stops when the covariance matrix contains NA's.
+test_that("function stops with no data", {
+  expect_error(confidence_ellipse(), "Missing 'data' argument.")
+})
+test_that("function stops with non df or tbl input", {
+  expect_error(confidence_ellipse(.data = 123), "Input 'data' must be a data frame or tibble.")
+})
+test_that("function stops with non-numeric conf_level", {
+  expect_error(
+    confidence_ellipse(
+      .data = glass,
+      x = BaO,
+      y = PbO,
+      conf_level = "high"),
+    "'conf_level' must be numeric.")
+})
+test_that("function stops with invalid conf_level", {
+  expect_error(
+    confidence_ellipsoid(
+      .data = glass,
+      x = BaO,
+      y = PbO,
+      conf_level = 37),
+    "'conf_level' must be between 0 and 1.")
+})
+test_that("function returns a data frame or tibble", {
+  result <- confidence_ellipse(glass, BaO, PbO)
+  expect_true(is_tibble(result))
+})
+test_that("function works with simple example", {
+  df <- data.frame(x = 1:10, y = 11:20)
+  result <- confidence_ellipse(df, x, y)
+  expect_true(is_tibble(result))
+})
+test_that("function works with grouping factor", {
+  result <- confidence_ellipse(
+    .data = glass,
+    x = BaO,
+    y = PbO,
+    .group_by = glassType)
+  expect_true(is_tibble(result))
+})
+test_that("function stops with NA's in covariance matrix", {
+  df <- data.frame(x = 1:10, y = c(11, 2, 4, NA, 6, 3, 1, NA, NA, 10))
+  expect_error(confidence_ellipse(df, x, y), "Covariance matrix contains NA values.")
+})
+

tests/testthat/test-confidence_ellipsoid.R

@@ -0,0 +1,63 @@
+library(tibble)
+# Test cases covered:
+# confidence_ellipsoid function stops when no data is provided.
+# confidence_ellipsoid function stops when input data is not a data frame or tibble.
+# confidence_ellipsoid function stops when the conf_level is not numeric.
+# confidence_ellipsoid function stops when the conf_level is not between 0 and 1.
+# confidence_ellipsoid function returns a tibble.
+# confidence_ellipsoid function works correctly with a simple example.
+# confidence_ellipsoid function works correctly with a grouping factor.
+# confidence_ellipsoid function stops when the covariance matrix contains NA's.
+test_that("function stops with no data", {
+  expect_error(confidence_ellipsoid(), "Missing 'data' argument.")
+})
+test_that("function stops with non df or tbl input", {
+  expect_error(confidence_ellipsoid(.data = 123), "Input 'data' must be a data frame or tibble.")
+})
+test_that("function stops with non-numeric conf_level", {
+  expect_error(
+    confidence_ellipsoid(
+      .data = glass,
+      x = BaO,
+      y = PbO,
+      z = Na2O,
+      conf_level = "high"),
+    "'conf_level' must be numeric.")
+})
+test_that("function stops with invalid conf_level", {
+  expect_error(
+    confidence_ellipsoid(
+      .data = glass,
+      x = BaO,
+      y = PbO,
+      z = Na2O,
+      conf_level = 37),
+    "'conf_level' must be between 0 and 1.")
+})
+test_that("function returns a data frame or tibble", {
+  result <- confidence_ellipsoid(glass, BaO, PbO, Na2O)
+  expect_true(is_tibble(result))
+})
+test_that("function works with simple example", {
+  df <- data.frame(x = 1:10, y = 11:20, z = 11:20)
+  result <- confidence_ellipsoid(df, x, y, z)
+  expect_true(is_tibble(result))
+})
+test_that("function works with grouping factor", {
+  result <- confidence_ellipsoid(
+    .data = glass,
+    x = BaO,
+    y = PbO,
+    z = Na2O,
+    .group_by = glassType)
+  expect_true(is_tibble(result))
+})
+test_that("function stops with NA's in covariance matrix", {
+  df <- data.frame(
+    x = 1:10,
+    y = c(11, 2, 4, NA, 6, 3, 1, NA, NA, 10),
+    z = 11:20)
+  expect_error(confidence_ellipsoid(df, x, y, z), "Covariance matrix contains NA values.")
+})
+
+