Merge pull request #186 from imbs-hl/coverage

Increase coverage
imbs-hl · Apr 20, 2017 · e62ee27 · e62ee27
2 parents 8d8e2fa + 1a35c96
commit e62ee27
Show file tree

Hide file tree

Showing 27 changed files with 188 additions and 363 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,5 @@
 .Rcheck
 ranger.Rcheck/
 *.Rproj
+.project
+.cproject
diff --git a/R/timepoints.R b/R/timepoints.R
@@ -41,7 +41,7 @@ timepoints <- function(x, ...)  UseMethod("timepoints")
 ##' @author Marvin N. Wright
 ##' @export
 timepoints.ranger.prediction <- function(x, ...) {
-  if (class(x) != "ranger.predicton") {
+  if (class(x) != "ranger.prediction") {
     stop("Object ist no ranger.prediction object.")
   }
   if (x$treetype != "Survival") {

diff --git a/cpp_version/test/.cproject b/cpp_version/test/.cproject
diff --git a/cpp_version/test/.project b/cpp_version/test/.project
diff --git a/cpp_version/test/utility_test.cpp b/cpp_version/test/utility_test.cpp
@@ -962,7 +962,7 @@ TEST(maxstat, trt) {
       2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2 });
 
   const double expect_maxstat = 0.095071135385996;
-  const double expect_split = 1;
+  const double expect_split = 1.5;
 
   // Order
   std::vector<size_t> indices = order(x, false);
@@ -985,7 +985,7 @@ TEST(maxstat, celltype) {
   //  library(survival)
   //  library(maxstat)
   //  y <- Surv(veteran$time, veteran$status)
-  //  x <- veteran$trt
+  //  x <- veteran$celltype
   //  m <- maxstat(y, x, pmethod = "Lau92", smethod = "LogRank")
   //  dput(y[, 1], control = NULL)
   //  dput(y[, 2], control = NULL)
@@ -1012,7 +1012,7 @@ TEST(maxstat, celltype) {
       2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4 });
 
   const double expect_maxstat = 3.44263138354529;
-  const double expect_split = 1;
+  const double expect_split = 1.5;
 
   // Order
   std::vector<size_t> indices = order(x, false);
@@ -1035,7 +1035,7 @@ TEST(maxstat, karno) {
   //  library(survival)
   //  library(maxstat)
   //  y <- Surv(veteran$time, veteran$status)
-  //  x <- veteran$age
+  //  x <- veteran$karno
   //  m <- maxstat(y, x, pmethod = "Lau92", smethod = "LogRank")
   //  dput(y[, 1], control = NULL)
   //  dput(y[, 2], control = NULL)
@@ -1064,7 +1064,7 @@ TEST(maxstat, karno) {
       60, 80, 75, 60, 70, 80, 30 });
 
   const double expect_maxstat = 4.61806159115936;
-  const double expect_split = 40;
+  const double expect_split = 45;
 
   // Order
   std::vector<size_t> indices = order(x, false);
@@ -1087,7 +1087,7 @@ TEST(maxstat, diagtime) {
   //  library(survival)
   //  library(maxstat)
   //  y <- Surv(veteran$time, veteran$status)
-  //  x <- veteran$age
+  //  x <- veteran$diagtime
   //  m <- maxstat(y, x, pmethod = "Lau92", smethod = "LogRank")
   //  dput(y[, 1], control = NULL)
   //  dput(y[, 2], control = NULL)
@@ -1115,7 +1115,7 @@ TEST(maxstat, diagtime) {
       4, 15, 4, 12, 5, 11, 10, 1, 5, 18, 4, 3 });
 
   const double expect_maxstat = 0.800489478294775;
-  const double expect_split = 3;
+  const double expect_split = 3.5;
 
   // Order
   std::vector<size_t> indices = order(x, false);
@@ -1167,7 +1167,7 @@ TEST(maxstat, age) {
       49, 64, 65, 64, 67, 65, 37 });
 
   const double expect_maxstat = 1.7992993341166;
-  const double expect_split = 58;
+  const double expect_split = 58.5;
 
   // Order
   std::vector<size_t> indices = order(x, false);
@@ -1190,7 +1190,7 @@ TEST(maxstat, prior) {
   //  library(survival)
   //  library(maxstat)
   //  y <- Surv(veteran$time, veteran$status)
-  //  x <- veteran$age
+  //  x <- veteran$prior
   //  m <- maxstat(y, x, pmethod = "Lau92", smethod = "LogRank")
   //  dput(y[, 1], control = NULL)
   //  dput(y[, 2], control = NULL)
@@ -1218,7 +1218,7 @@ TEST(maxstat, prior) {
       10, 10, 0, 0, 10, 10, 0, 0, 10, 0, 0 });
 
   const double expect_maxstat = 0.7158562778385;
-  const double expect_split = 0;
+  const double expect_split = 5;
 
   // Order
   std::vector<size_t> indices = order(x, false);
@@ -1274,7 +1274,7 @@ TEST(maxstat, regression) {
     3.4, 3 });
 
   const double expect_maxstat = 3.73535181856697;
-  const double expect_split = 3.3;
+  const double expect_split = 3.35;
 
   // Order x
   std::vector<size_t> indices = order(x, false);

diff --git a/src/Data.cpp b/src/Data.cpp
@@ -60,6 +60,7 @@ void Data::addSparseData(unsigned char* sparse_data, size_t num_cols_sparse) {
   this->sparse_data = sparse_data;
 }
 
+// #nocov start
 bool Data::loadFromFile(std::string filename) {
 
   bool result;
@@ -166,6 +167,7 @@ bool Data::loadFromFileOther(std::ifstream& input_file, std::string header_line,
   num_rows = row;
   return error;
 }
+// #nocov end
 
 void Data::getAllValues(std::vector<double>& all_values, std::vector<size_t>& sampleIDs, size_t varID) {
 

diff --git a/src/DataChar.cpp b/src/DataChar.cpp
@@ -26,6 +26,9 @@ Ratzeburger Allee 160
 [email protected]
 #-------------------------------------------------------------------------------*/
 
+// Ignore in coverage report (not used in R package)
+// #nocov start
+
 #include <limits.h>
 #include <math.h>
 #include <iostream>
@@ -66,3 +69,5 @@ DataChar::~DataChar() {
     delete[] data;
   }
 }
+
+// #nocov end
diff --git a/src/DataChar.h b/src/DataChar.h
@@ -26,6 +26,9 @@ Ratzeburger Allee 160
 [email protected]
 #-------------------------------------------------------------------------------*/
 
+// Ignore in coverage report (not used in R package)
+// #nocov start
+
 #ifndef DATACHAR_H_
 #define DATACHAR_H_
 
@@ -71,3 +74,4 @@ class DataChar: public Data {
 };
 
 #endif /* DATACHAR_H_ */
+// #nocov end
diff --git a/src/DataFloat.cpp b/src/DataFloat.cpp
@@ -26,6 +26,9 @@ Ratzeburger Allee 160
 [email protected]
 #-------------------------------------------------------------------------------*/
 
+// Ignore in coverage report (not used in R package)
+// #nocov start
+
 #include <iostream>
 #include <vector>
 
@@ -55,3 +58,5 @@ DataFloat::~DataFloat() {
   }
 }
 
+// #nocov end
+
diff --git a/src/DataFloat.h b/src/DataFloat.h
@@ -26,6 +26,9 @@ Ratzeburger Allee 160
 [email protected]
 #-------------------------------------------------------------------------------*/
 
+// Ignore in coverage report (not used in R package)
+// #nocov start
+
 #ifndef DATAFLOAT_H_
 #define DATAFLOAT_H_
 
@@ -63,3 +66,5 @@ class DataFloat: public Data {
 };
 
 #endif /* DATAFLOAT_H_ */
+// #nocov end
+
diff --git a/src/Forest.cpp b/src/Forest.cpp
@@ -58,6 +58,7 @@ Forest::~Forest() {
   }
 }
 
+// #nocov start
 void Forest::initCpp(std::string dependent_variable_name, MemoryMode memory_mode, std::string input_file, uint mtry,
     std::string output_prefix, uint num_trees, std::ostream* verbose_out, uint seed, uint num_threads,
     std::string load_forest_filename, ImportanceMode importance_mode, uint min_node_size,
@@ -149,6 +150,7 @@ void Forest::initCpp(std::string dependent_variable_name, MemoryMode memory_mode
     }
   }
 }
+// #nocov end
 
 void Forest::initR(std::string dependent_variable_name, Data* input_data, uint mtry, uint num_trees,
     std::ostream* verbose_out, uint seed, uint num_threads, ImportanceMode importance_mode, uint min_node_size,
@@ -306,6 +308,7 @@ void Forest::run(bool verbose) {
   }
 }
 
+// #nocov start
 void Forest::writeOutput() {
 
   *verbose_out << std::endl;
@@ -399,6 +402,7 @@ void Forest::saveToFile() {
   outfile.close();
   *verbose_out << "Saved forest to file " << filename << "." << std::endl;
 }
+// #nocov end
 
 void Forest::grow() {
 
@@ -732,6 +736,7 @@ void Forest::computeTreePermutationImportanceInThread(uint thread_idx, std::vect
 }
 #endif
 
+// #nocov start
 void Forest::loadFromFile(std::string filename) {
   *verbose_out << "Loading forest from file " << filename << "." << std::endl;
 
@@ -757,6 +762,7 @@ void Forest::loadFromFile(std::string filename) {
 // Create thread ranges
   equalSplit(thread_ranges, 0, num_trees - 1, num_threads);
 }
+// #nocov end
 
 void Forest::setSplitWeightVector(std::vector<std::vector<double>>& split_select_weights) {
 

diff --git a/src/ForestClassification.cpp b/src/ForestClassification.cpp
@@ -187,6 +187,7 @@ void ForestClassification::computePredictionErrorInternal() {
   overall_prediction_error = (double) num_missclassifications / (double) num_predictions;
 }
 
+// #nocov start
 void ForestClassification::writeOutputInternal() {
   *verbose_out << "Tree type:                         " << "Classification" << std::endl;
 }
@@ -323,4 +324,4 @@ void ForestClassification::loadFromFileInternal(std::ifstream& infile) {
     trees.push_back(tree);
   }
 }
-
+// #nocov end
diff --git a/src/ForestProbability.cpp b/src/ForestProbability.cpp
@@ -179,6 +179,7 @@ void ForestProbability::computePredictionErrorInternal() {
   overall_prediction_error /= (double) num_predictions;
 }
 
+// #nocov start
 void ForestProbability::writeOutputInternal() {
   *verbose_out << "Tree type:                         " << "Probability estimation" << std::endl;
 }
@@ -309,4 +310,4 @@ void ForestProbability::loadFromFileInternal(std::ifstream& infile) {
     trees.push_back(tree);
   }
 }
-
+// #nocov end
diff --git a/src/ForestRegression.cpp b/src/ForestRegression.cpp
@@ -154,6 +154,7 @@ void ForestRegression::computePredictionErrorInternal() {
   overall_prediction_error /= (double) num_predictions;
 }
 
+// #nocov start
 void ForestRegression::writeOutputInternal() {
   *verbose_out << "Tree type:                         " << "Regression" << std::endl;
 }
@@ -257,4 +258,4 @@ void ForestRegression::loadFromFileInternal(std::ifstream& infile) {
     trees.push_back(tree);
   }
 }
-
+// #nocov end
diff --git a/src/ForestSurvival.cpp b/src/ForestSurvival.cpp
@@ -198,6 +198,7 @@ void ForestSurvival::computePredictionErrorInternal() {
   overall_prediction_error = 1 - computeConcordanceIndex(data, sum_chf, dependent_varID, status_varID, temp);
 }
 
+// #nocov start
 void ForestSurvival::writeOutputInternal() {
   *verbose_out << "Tree type:                         " << "Survival" << std::endl;
   *verbose_out << "Status variable name:              " << data->getVariableNames()[status_varID] << std::endl;
@@ -349,4 +350,5 @@ void ForestSurvival::loadFromFileInternal(std::ifstream& infile) {
     trees.push_back(tree);
   }
 }
+// #nocov end