Refactor code

src/fastcpd_class_private.cc → src/fastcpd_class.cc

@@ -1,4 +1,4 @@
-#include "fastcpd_classes.h"
+#include "fastcpd_class.h"
 #include "fastcpd_constants.h"
 #include "RProgress.h"
 

src/fastcpd_classes.h → src/fastcpd_class.h

@@ -1,120 +1,17 @@
-#ifndef FASTCPD_CLASSES_H_
-#define FASTCPD_CLASSES_H_
+#ifndef FASTCPD_CLASS_H_
+#define FASTCPD_CLASS_H_
 
 #include <memory>
 
+#include "fastcpd_test.h"
 #include "fastcpd_types.h"
+#include "fastcpd_wrapper.h"
 #include "RcppClock.h"
 #include "RProgress.h"
 
-namespace fastcpd::classes {
-
-struct ColMat {
-  mat data;
-
-  operator colvec() const;
-  operator mat() const;
-  operator rowvec() const;
-};
-
-struct CostResult {
-  ColMat par;
-  ColMat residuals;
-  double value;
-};
-
-struct CostFunction {
-  const Function cost;
-  const mat& data;
-
-  CostFunction(const Function& cost, const mat& data);
-  CostResult operator() (
-      const unsigned int segment_start,
-      const unsigned int segment_end,
-      const Nullable<colvec>& theta,
-      const double lambda,  // UNUSED
-      const bool cv,  // UNUSED
-      const Nullable<colvec>& start  // UNUSED
-  ) const;
-};
-
-struct CostGradient {
-  const Function cost_gradient;
-  const mat& data;
-
-  CostGradient(const Function& cost_gradient, const mat& data);
-  const colvec operator() (
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    const colvec& theta
-  ) const;
-};
-
-struct CostHessian {
-  const Function cost_hessian;
-  const mat& data;
-
-  CostHessian(const Function& cost_hessian, const mat& data);
-  const mat operator() (
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    const colvec& theta
-  ) const;
-};
-
-class FastcpdTest {
- public:
-  static colvec get_gradient_arma(
-    const mat& data,
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    const colvec& theta
-  );
-
-  static mat get_hessian_arma(
-    const mat& data,
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    const colvec& theta
-  );
+using ::fastcpd::test::FastcpdTest;
 
-  static mat get_hessian_binomial(
-    const mat& data,
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    const colvec& theta
-  );
-
-  static mat get_hessian_poisson(
-    const mat& data,
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    const colvec& theta
-  );
-
-  static double get_nll_wo_cv(
-    const mat& data,
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    colvec theta,
-    double lambda
-  );
-
-  static CostResult get_nll_wo_theta(
-    const mat& data,
-    const unsigned int segment_start,
-    const unsigned int segment_end,
-    double lambda,
-    bool cv,
-    Nullable<colvec> start
-  );
-
-  static mat update_theta_sum(
-    const unsigned int col,
-    colvec old_theta_sum,
-    colvec new_theta_sum
-  );
-};
+namespace fastcpd::classes {
 
 class Fastcpd {
  public:
@@ -605,4 +502,4 @@ class Fastcpd {
 
 }  // namespace fastcpd::classes
 
-#endif  // FASTCPD_CLASSES_H_
+#endif  // FASTCPD_CLASS_H_

src/fastcpd_class_nll.cc

@@ -1,4 +1,4 @@
-#include "fastcpd_classes.h"
+#include "fastcpd_class.h"
 
 namespace fastcpd::classes {
 

src/fastcpd_impl.cc

@@ -1,4 +1,4 @@
-#include "fastcpd_classes.h"
+#include "fastcpd_class.h"
 #include "fastcpd_impl.h"
 
 List fastcpd_impl(

src/fastcpd_class_test.cc → src/fastcpd_test.cc

@@ -1,6 +1,9 @@
-#include "fastcpd_classes.h"
+#include "fastcpd_class.h"
+#include "fastcpd_test.h"
 
-namespace fastcpd::classes {
+using ::fastcpd::classes::Fastcpd;
+
+namespace fastcpd::test {
 
 colvec FastcpdTest::get_gradient_arma(
   const mat& data,
@@ -267,4 +270,4 @@ mat FastcpdTest::update_theta_sum(
   return fastcpd_class.theta_sum;
 }
 
-}  // namespace fastcpd::classes
+}  // namespace fastcpd::test

src/fastcpd_test.h

@@ -0,0 +1,67 @@
+#ifndef FASTCPD_TEST_H_
+#define FASTCPD_TEST_H_
+
+#include "fastcpd_types.h"
+#include "fastcpd_wrapper.h"
+
+using ::fastcpd::classes::CostResult;
+
+namespace fastcpd::test {
+
+class FastcpdTest {
+ public:
+  static colvec get_gradient_arma(
+    const mat& data,
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    const colvec& theta
+  );
+
+  static mat get_hessian_arma(
+    const mat& data,
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    const colvec& theta
+  );
+
+  static mat get_hessian_binomial(
+    const mat& data,
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    const colvec& theta
+  );
+
+  static mat get_hessian_poisson(
+    const mat& data,
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    const colvec& theta
+  );
+
+  static double get_nll_wo_cv(
+    const mat& data,
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    colvec theta,
+    double lambda
+  );
+
+  static CostResult get_nll_wo_theta(
+    const mat& data,
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    double lambda,
+    bool cv,
+    Nullable<colvec> start
+  );
+
+  static mat update_theta_sum(
+    const unsigned int col,
+    colvec old_theta_sum,
+    colvec new_theta_sum
+  );
+};
+
+}  // namespace fastcpd::test
+
+#endif  // FASTCPD_TEST_H_

src/fastcpd_class_cost.cc → src/fastcpd_wrapper.cc

@@ -1,4 +1,4 @@
-#include "fastcpd_classes.h"
+#include "fastcpd_wrapper.h"
 
 namespace fastcpd::classes {
 

src/fastcpd_wrapper.h

@@ -0,0 +1,63 @@
+#ifndef FASTCPD_WRAPPER_H_
+#define FASTCPD_WRAPPER_H_
+
+#include "fastcpd_types.h"
+
+namespace fastcpd::classes {
+
+struct ColMat {
+  mat data;
+
+  operator colvec() const;
+  operator mat() const;
+  operator rowvec() const;
+};
+
+struct CostResult {
+  ColMat par;
+  ColMat residuals;
+  double value;
+};
+
+struct CostFunction {
+  const Function cost;
+  const mat& data;
+
+  CostFunction(const Function& cost, const mat& data);
+  CostResult operator() (
+      const unsigned int segment_start,
+      const unsigned int segment_end,
+      const Nullable<colvec>& theta,
+      const double lambda,  // UNUSED
+      const bool cv,  // UNUSED
+      const Nullable<colvec>& start  // UNUSED
+  ) const;
+};
+
+struct CostGradient {
+  const Function cost_gradient;
+  const mat& data;
+
+  CostGradient(const Function& cost_gradient, const mat& data);
+  const colvec operator() (
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    const colvec& theta
+  ) const;
+};
+
+struct CostHessian {
+  const Function cost_hessian;
+  const mat& data;
+
+  CostHessian(const Function& cost_hessian, const mat& data);
+  const mat operator() (
+    const unsigned int segment_start,
+    const unsigned int segment_end,
+    const colvec& theta
+  ) const;
+};
+
+}  // namespace fastcpd::classes
+
+#endif  // FASTCPD_WRAPPER_H_

src/test-functions.cc → src/test-fastcpd.cc

@@ -1,13 +1,13 @@
-#include "fastcpd_classes.h"
+#include "fastcpd_test.h"
 #include "fastcpd_test_constants.h"
 #include "testthat.h"
 
-using ::fastcpd::classes::FastcpdTest;
+using ::fastcpd::classes::CostResult;
+using ::fastcpd::test::FastcpdTest;
 
 context("get_nll_wo_theta Unit Test") {
   test_that("arma(3, 2) is correct for 200 data points") {
-    const fastcpd::classes::CostResult cost_result =
-    FastcpdTest::get_nll_wo_theta(
+    const CostResult cost_result = FastcpdTest::get_nll_wo_theta(
       colvec(kARMA32.data(), kARMA32.size()), 0, 199, 0, false, R_NilValue
     );
     const colvec par = cost_result.par;
@@ -91,6 +91,8 @@ context("update_theta_sum Unit Test") {
     expect_true(theta_sum.n_cols == 1);
     colvec theta_sum_col = theta_sum.col(0);
     colvec expected_theta_sum = {5, 7, 9};
-    expect_true(approx_equal(theta_sum_col, expected_theta_sum, "absdiff", 1e-6));
+    expect_true(
+      approx_equal(theta_sum_col, expected_theta_sum, "absdiff", 1e-6)
+    );
   }
 }