From a7447fdb9d1362f57531e865c141c75f5b577d43 Mon Sep 17 00:00:00 2001
From: Anthony Li <38049831+doccstat@users.noreply.github.com>
Date: Tue, 9 Jan 2024 11:42:17 -0600
Subject: [PATCH] Adjust mean change cost function

---
 src/fastcpd_class_cost.cc                         | 2 +-
 tests/testthat/test-coverage.R                    | 4 ++--
 tests/testthat/test-examples-data-transcriptome.R | 4 ++--
 tests/testthat/test-examples-data-well_log.R      | 6 +++---
 vignettes/comparison-packages.Rmd                 | 2 +-
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/fastcpd_class_cost.cc b/src/fastcpd_class_cost.cc
index 70d36768..810f4a56 100644
--- a/src/fastcpd_class_cost.cc
+++ b/src/fastcpd_class_cost.cc
@@ -122,7 +122,7 @@ List Fastcpd::negative_log_likelihood_wo_theta(
           arma::trace(
             solve(mean_data_cov, residuals.t() * residuals)
           ) / data.n_rows
-      ),
+      ) + data.n_cols * log(data.n_rows),
       Named("residuals") = residuals
     );
   } else if (family == "variance") {
diff --git a/tests/testthat/test-coverage.R b/tests/testthat/test-coverage.R
index 30044d6a..28ef90cb 100644
--- a/tests/testthat/test-coverage.R
+++ b/tests/testthat/test-coverage.R
@@ -3,7 +3,7 @@ testthat::test_that(
     set.seed(1)
     data <- c(rnorm(300, 0, 100), rnorm(400, 100, 100), rnorm(300, 0, 100))
     result_mean <- fastcpd.mean(data)
-    testthat::expect_equal(result_mean@cp_set, c(294, 702))
+    testthat::expect_equal(result_mean@cp_set, c(300, 702))
   }
 )
 
@@ -102,6 +102,6 @@ testthat::test_that(
 testthat::test_that("beta x2", {
   testthat::expect_equal(
     fastcpd.mean(well_log, beta = log(length(well_log)))@cp_set,
-    c(566, 740, 1039, 1198, 1424, 1661, 1842, 2023, 2476, 2744, 3709, 3820)
+    c(572, 1039, 1424, 1661, 1842, 2023, 2476, 2744, 3709, 3820)
   )
 })
diff --git a/tests/testthat/test-examples-data-transcriptome.R b/tests/testthat/test-examples-data-transcriptome.R
index 0ebc2eb8..a361fd06 100644
--- a/tests/testthat/test-examples-data-transcriptome.R
+++ b/tests/testthat/test-examples-data-transcriptome.R
@@ -9,8 +9,8 @@ testthat::test_that(
     testthat::expect_equal(
       result@cp_set,
       c(
-        177, 264, 394, 534, 579, 656, 788, 811, 869, 934,
-        966, 1051, 1141, 1286, 1319, 1368, 1568, 1657,
+        177, 264, 401, 534, 579, 656, 788, 811, 869,
+        934, 966, 1051, 1141, 1286, 1319, 1386, 1657,
         1724, 1906, 1972, 1996, 2041, 2146, 2200
       )
     )
diff --git a/tests/testthat/test-examples-data-well_log.R b/tests/testthat/test-examples-data-well_log.R
index d765e1eb..75483592 100644
--- a/tests/testthat/test-examples-data-well_log.R
+++ b/tests/testthat/test-examples-data-well_log.R
@@ -4,9 +4,9 @@ testthat::test_that(
     testthat::expect_equal(
       result@cp_set,
       c(
-        10, 566, 704, 776, 1021, 1057, 1198, 1347, 1406, 1502,
-        1660, 1842, 2023, 2202, 2384, 2445, 2507, 2567, 2749,
-        2921, 3072, 3509, 3622, 3709, 3820, 3976
+        10, 572, 704, 830, 1021, 1057, 1198, 1347,
+        1406, 1502, 1660, 1842, 2023, 2385, 2445,
+        2507, 2567, 2749, 3709, 3820, 3976
       )
     )
   }
diff --git a/vignettes/comparison-packages.Rmd b/vignettes/comparison-packages.Rmd
index 55ae628c..7c466172 100644
--- a/vignettes/comparison-packages.Rmd
+++ b/vignettes/comparison-packages.Rmd
@@ -11,7 +11,7 @@ vignette: >
 
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
-  collapse = TRUE, comment = "#>", eval = TRUE, cache = TRUE,
+  collapse = TRUE, comment = "#>", eval = TRUE, cache = FALSE,
   warning = FALSE, fig.width = 8, fig.height = 5
 )
 ```