From 98a5a40d85ee35d8f506d0cba54b7d9e9b10135d Mon Sep 17 00:00:00 2001
From: ArslanBatyrov <batyrovarslan7@gmail.com>
Date: Fri, 27 Mar 2026 08:40:47 +0000
Subject: [PATCH 1/5] Add plot.envcpt argument validation tests

---
 tests/testthat/test-plot-extra.R | 41 ++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
 create mode 100644 tests/testthat/test-plot-extra.R

diff --git a/tests/testthat/test-plot-extra.R b/tests/testthat/test-plot-extra.R
new file mode 100644
index 0000000..f298342
--- /dev/null
+++ b/tests/testthat/test-plot-extra.R
@@ -0,0 +1,41 @@
+library(testthat)
+library(EnvCpt)
+
+test_that("plot.envcpt errors when x is not envcpt", {
+  expect_error(
+    EnvCpt:::plot.envcpt(list()),
+    "x must be an object with class envcpt"
+  )
+})
+
+if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+  set.seed(99)
+  x <- c(rnorm(40, 0, 1), rnorm(40, 3, 1))
+  out <- envcpt(x)
+  
+  test_that("plot.envcpt accepts colours alias but warns", {
+    expect_warning(plot(out, type = "aic", colours = rep("black", 12)))
+  })
+  
+  test_that("plot.envcpt errors when colors vector is too short", {
+    expect_error(
+      plot(out, type = "aic", colors = rep("black", 3)),
+      "colors must be a vector of length 12"
+    )
+  })
+  
+  test_that("plot.envcpt errors when a color is invalid", {
+    bad_cols <- c(rep("black", 11), "not_a_colour")
+    expect_error(
+      plot(out, type = "aic", colors = bad_cols),
+      "Atleast one of your colours is not resolvable by col2rgb."
+    )
+  })
+  
+  test_that("plot.envcpt errors on unsupported plot type", {
+    expect_error(
+      plot(out, type = "weird"),
+      "type supplied can only be 'aic', 'bic' or 'fit'"
+    )
+  })
+}
\ No newline at end of file

From 536d43d824caef5a6dfe3f1b2071b31645bbcca0 Mon Sep 17 00:00:00 2001
From: ArslanBatyrov <batyrovarslan7@gmail.com>
Date: Fri, 27 Mar 2026 09:10:06 +0000
Subject: [PATCH 2/5] Add diagnostics coverage tests for AIC and AICweights

---
 tests/testthat/test-diagnostics-extra.R | 30 +++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 tests/testthat/test-diagnostics-extra.R

diff --git a/tests/testthat/test-diagnostics-extra.R b/tests/testthat/test-diagnostics-extra.R
new file mode 100644
index 0000000..080acff
--- /dev/null
+++ b/tests/testthat/test-diagnostics-extra.R
@@ -0,0 +1,30 @@
+library(testthat)
+library(EnvCpt)
+
+fake_envcpt <- list(
+  summary = matrix(
+    c(10, 20,
+      1,  2),
+    nrow = 2,
+    byrow = TRUE
+  )
+)
+class(fake_envcpt) <- "envcpt"
+
+test_that("AIC.envcpt respects custom penalty k", {
+  out <- AIC(fake_envcpt, k = 3)
+  expect_equal(out, c(13, 26))
+})
+
+test_that("AICweights.default returns fallback message", {
+  out <- AICweights(1:5)
+  expect_equal(out, "No default method created for S3 class AICweights.")
+})
+
+test_that("AICweights.envcpt returns normalized weights", {
+  w <- AICweights(fake_envcpt)
+  aic <- AIC(fake_envcpt)
+  expected <- exp(-0.5 * (aic - min(aic)))
+  expected <- expected / sum(expected)
+  expect_equal(w, expected)
+})
\ No newline at end of file

From 0011472cd56c74b10275a32e5e97477d72d91d9c Mon Sep 17 00:00:00 2001
From: ArslanBatyrov <batyrovarslan7@gmail.com>
Date: Fri, 27 Mar 2026 09:24:21 +0000
Subject: [PATCH 3/5] Normalize newline in plot test file

---
 tests/testthat/test-plot-extra.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-plot-extra.R b/tests/testthat/test-plot-extra.R
index f298342..e0b70fc 100644
--- a/tests/testthat/test-plot-extra.R
+++ b/tests/testthat/test-plot-extra.R
@@ -38,4 +38,4 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
       "type supplied can only be 'aic', 'bic' or 'fit'"
     )
   })
-}
\ No newline at end of file
+}

From c87ff17f44ef16c1cf1aae710cd5635a3de173a6 Mon Sep 17 00:00:00 2001
From: ArslanBatyrov <batyrovarslan7@gmail.com>
Date: Fri, 27 Mar 2026 10:16:16 +0000
Subject: [PATCH 4/5] Add comments to new coverage tests

---
 tests/testthat/test-diagnostics-extra.R | 6 ++++++
 tests/testthat/test-plot-extra.R        | 4 +++-
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-diagnostics-extra.R b/tests/testthat/test-diagnostics-extra.R
index 080acff..12fff4c 100644
--- a/tests/testthat/test-diagnostics-extra.R
+++ b/tests/testthat/test-diagnostics-extra.R
@@ -1,6 +1,9 @@
+# Additional coverage tests for AIC / AICweights diagnostics methods
+# Additional coverage tests for AIC / AICweights diagnostics methods
 library(testthat)
 library(EnvCpt)
 
+# Minimal envcpt-like object for exercising diagnostics methods directly
 fake_envcpt <- list(
   summary = matrix(
     c(10, 20,
@@ -11,16 +14,19 @@ fake_envcpt <- list(
 )
 class(fake_envcpt) <- "envcpt"
 
+# AIC.envcpt should respect a user-supplied penalty value
 test_that("AIC.envcpt respects custom penalty k", {
   out <- AIC(fake_envcpt, k = 3)
   expect_equal(out, c(13, 26))
 })
 
+# The default AICweights method should return the documented fallback message
 test_that("AICweights.default returns fallback message", {
   out <- AICweights(1:5)
   expect_equal(out, "No default method created for S3 class AICweights.")
 })
 
+# AICweights.envcpt should return normalized weights derived from AIC values
 test_that("AICweights.envcpt returns normalized weights", {
   w <- AICweights(fake_envcpt)
   aic <- AIC(fake_envcpt)
diff --git a/tests/testthat/test-plot-extra.R b/tests/testthat/test-plot-extra.R
index e0b70fc..227f2b4 100644
--- a/tests/testthat/test-plot-extra.R
+++ b/tests/testthat/test-plot-extra.R
@@ -1,3 +1,4 @@
+# Additional coverage tests for plot.envcpt argument handling
 library(testthat)
 library(EnvCpt)
 
@@ -8,11 +9,12 @@ test_that("plot.envcpt errors when x is not envcpt", {
   )
 })
 
+# These plotting branches are run locally / outside CRAN
 if (identical(Sys.getenv("NOT_CRAN"), "true")) {
   set.seed(99)
   x <- c(rnorm(40, 0, 1), rnorm(40, 3, 1))
   out <- envcpt(x)
-  
+# The function accepts the British spelling "colours", although it currently warns
   test_that("plot.envcpt accepts colours alias but warns", {
     expect_warning(plot(out, type = "aic", colours = rep("black", 12)))
   })

From b7d06449195b8d97e215ffed20aa5274ee9e7d9e Mon Sep 17 00:00:00 2001
From: ArslanBatyrov <batyrovarslan7@gmail.com>
Date: Fri, 27 Mar 2026 10:31:53 +0000
Subject: [PATCH 5/5] Remove duplicates in diagnostics

---
 tests/testthat/test-diagnostics-extra.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/testthat/test-diagnostics-extra.R b/tests/testthat/test-diagnostics-extra.R
index 12fff4c..66e86f1 100644
--- a/tests/testthat/test-diagnostics-extra.R
+++ b/tests/testthat/test-diagnostics-extra.R
@@ -1,5 +1,4 @@
 # Additional coverage tests for AIC / AICweights diagnostics methods
-# Additional coverage tests for AIC / AICweights diagnostics methods
 library(testthat)
 library(EnvCpt)