Merge pull request mi-erasmusmc#3 from mi-erasmusmc/development

Latest version

.Rbuildignore

@@ -0,0 +1,11 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^vignettes$
+^output$
+^docs$
+^Meta$
+^README\.Rmd$
+^LICENSE\.md$
+^\.github$
+^_pkgdown\.yml$
+^pkgdown$

.gitignore

@@ -1,5 +1,49 @@
-.Rproj.user
+# History files
 .Rhistory
+
+# Session Data files
 .RData
+.RDataTmp
+
+# User-specific files
 .Ruserdata
-.DS_STORE
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# Produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# R Environment Variables
+.Renviron
+
+# Documents and results
+docs/
+output/
+
+# Mac files
+.DS_STORE
+.idea/
+
+# Compiled Object files
+*.o
+*.obj
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Compiled Static libraries
+*.a
+*.lib
+
+# Other C++ files
+**/__history/
+
+# EXPLORE result files
+*.result

CMakeLists.txt

@@ -3,6 +3,7 @@ project(Explore)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O3")
+set(CMAKE_VERBOSE_MAKEFILE ON)
 
 # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -v -stdlib=libc++")
@@ -28,8 +29,8 @@ include_directories(IOExplore)
 include_directories(include /usr/local/include/)
 link_directories(/usr/local/lib)
 # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ltbb -fprofile-instr-generate -fcoverage-mapping")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ltbb --coverage")
-
+# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ltbb --coverage")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ltbb")
 
 
 # LINUX

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-export(aucrocExplore)
+export(aurocEXPLORE)
 export(changeSetting)
 export(getSetting)
 export(predictExplore)

R/HelperFunctions.R

@@ -25,12 +25,22 @@ changeSetting <- function(settings, parameter, input, default_setting) {
   }
 
   if (!is.null(input)) { # If input has a value -> update parameter in settings
+
+    # if (input=="custom") {
+    #   if (parameter=="Accuracy") {input <- custom_Accuracy()}
+    # }
+
     settings <- sub(current_setting, paste0(parameter, "=", input, ""), settings)
 
   } else if  (grepl(paste0("@",parameter), settings, fixed=TRUE)) { # If value is required in settings, use default value if possible
     # TODO: extend list of patterns that are recognized as required settings
 
     if(!is.na(default_setting)) {
+
+      # if (default_setting=="custom") {
+      #   if (parameter=="Accuracy") {default_setting <- custom_Accuracy()}
+      # }
+
       settings <- sub(current_setting, paste0(parameter, "=", default_setting, ""), settings)
     } else{
       warning(paste0('Default setting for ', parameter, ' is NA, but setting is required to replace @', parameter, "."))

R/MainFunctions.R

@@ -1,6 +1,6 @@
 # TODO: add descriptions for package manual
 
-#' trainExplore
+#' trainExplore This function finds the best decision rule for the given dataset based using EXPLORE. 
 #'
 #' @param output_path 
 #' @param train_data 
@@ -10,6 +10,7 @@
 #'
 #' @return
 #' @export
+#' @import Rcpp RcppParallel
 #'
 #' @examples
 trainExplore <- function(output_path, train_data = NULL, settings_path = NULL, file_name = "train_data", ...) {
@@ -190,7 +191,8 @@ predictExplore <- function(model, test_data) {
 #' @export
 #'
 #' @examples
-aucrocExplore <- function(output_path, train_data, settings_path, file_name, ...) {
+aurocEXPLORE <- function(output_path, train_data, settings_path, file_name, ...) {
+  # TODO: check with latest implementation in PLP
 
   # Range of specificities to check
   specificities <- seq(from = 0.01, to = 0.99, by = 0.02)
@@ -212,8 +214,8 @@ aucrocExplore <- function(output_path, train_data, settings_path, file_name, ...
     sensitivities[s] <- as.numeric(sensitivity)
   }
 
-  aucroc <- simple_auc(TPR = rev(sensitivities), FPR = rev(1 - specificities))
-  plot(1-specificities, sensitivities)
+  auroc <- simple_auc(TPR = rev(sensitivities), FPR = rev(1 - specificities))
+  # plot(1-specificities, sensitivities)
 
-  return(aucroc)
+  return(auroc)
 }

README.Rmd

@@ -0,0 +1,62 @@
+---
+output: github_document
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(warning = FALSE,
+  collapse = TRUE,
+  comment = "#>",
+fig.path = "man/figures/",
+out.width = "100%"
+)
+```
+
+## Package overview
+Functions to find a short and accurate decision rule in disjunctive normal form using the Exhaustive Procedure for LOgic-Rule Extraction (EXPLORE) algorithm. The application performs and exhaustive search on all Boolean Normal Form decision rules.
+
+## Package installation
+
+You can install the latest version of EXPLORE like so:
+
+```{r, eval=FALSE}
+install.packages("remotes")
+remotes::install_github("mi-erasmusmc/EXPLORE")
+```
+
+Additional instructions: to be added.
+
+
+## Example usage using iris dataset
+```{r}
+library(Explore)
+library(farff)
+```
+
+Load data:
+```{r, eval=FALSE}
+data <- farff::readARFF("inst/examples/iris.arff")
+output_path <- file.path(getwd(), "output/")
+```
+
+Fit model with defaults and/or input parameters:
+```{r, eval=FALSE}
+model <- Explore::trainExplore(output_path = output_path, file_name = "iris", train_data = data, ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
+```
+
+Predict:
+```{r, eval=FALSE}
+prediction <- Explore::predictExplore(model, test_data = data)
+```  
+
+
+Additional documentation includes:
+- Vignette code examples in combination with PLP: [to be added](~/Documents/Git/Explore/vignettes/EXPLORE_withPLP.Rmd) 
+- Package manual: [to be added](~/Documents/Git/Explore/vignettes/Explore_1.0.pdf) 
+
+
+## Development status
+EXPLORE is under active development.
+
+
+## Publication
+Rijnbeek, P.R., Kors, J.A. Finding a short and accurate decision rule in disjunctive normal form by exhaustive search. Machine Learning 80, 33–62 (2010). https://doi.org/10.1007/s10994-010-5168-9

README.md

@@ -1,13 +1,59 @@
-# EXPLORE Package
-Finding a short and accurate decision rule in disjunctive normal form by exhaustive search.
-The application performs and exhaustive search on all Boolean Normal Form decision rules.
 
-## User Documentation
-Available documentation includes:
-- Package manual: to be added.
+## Package overview
+
+Functions to find a short and accurate decision rule in disjunctive
+normal form using the Exhaustive Procedure for LOgic-Rule Extraction
+(EXPLORE) algorithm. The application performs and exhaustive search on
+all Boolean Normal Form decision rules.
+
+## Package installation
+
+You can install the latest version of EXPLORE like so:
+
+``` r
+install.packages("remotes")
+remotes::install_github("mi-erasmusmc/EXPLORE")
+```
+
+Additional instructions: to be added.
+
+## Example usage using iris dataset
+
+``` r
+library(Explore)
+library(farff)
+```
+
+Load data:
+
+``` r
+data <- farff::readARFF("inst/examples/iris.arff")
+output_path <- file.path(getwd(), "output/")
+```
+
+Fit model with defaults and/or input parameters:
+
+``` r
+model <- Explore::trainExplore(output_path = output_path, file_name = "iris", train_data = data, ClassFeature = "'class'", PositiveClass = '"Iris-versicolor"')
+```
+
+Predict:
+
+``` r
+prediction <- Explore::predictExplore(model, test_data = data)
+```
+
+Additional documentation includes: - Vignette code examples in
+combination with PLP: [to be
+added](~/Documents/Git/Explore/vignettes/EXPLORE_withPLP.Rmd) - Package
+manual: [to be added](~/Documents/Git/Explore/vignettes/Explore_1.0.pdf)
 
 ## Development status
+
 EXPLORE is under active development.
 
 ## Publication
-Rijnbeek, P.R., Kors, J.A. Finding a short and accurate decision rule in disjunctive normal form by exhaustive search. Mach Learn 80, 33–62 (2010). https://doi.org/10.1007/s10994-010-5168-9
+
+Rijnbeek, P.R., Kors, J.A. Finding a short and accurate decision rule in
+disjunctive normal form by exhaustive search. Machine Learning 80, 33–62
+(2010). <https://doi.org/10.1007/s10994-010-5168-9>

inst/examples/iris.project

@@ -1,9 +1,9 @@
 [General]
 Name=test
 Remarks=test
-DataFile=/Users/aniekmarkus/Documents/Git/Explore/data/iris.arff
+DataFile=/Users/aniekmarkus/Documents/Git/Explore/inst/examples/iris.arff
 Output=File
-OutputFile=/Users/aniekmarkus/Documents/Git/Explore/tests/iris.result
+OutputFile=@OutputFile
 IncrementalOutputFile=false
 [Setup]
 PartitionMethod=RESUBSTITUTION
@@ -14,20 +14,20 @@ LearnRatio=0.8
 NumberofPartitions=1
 OperatorMethod=EXHAUSTIVE
 CutoffMethod=RVAC
-CutoffFile=/Users/aniekmarkus/Documents/Git/Explore/test/iris.cutoff
+CutoffFile=/Users/aniekmarkus/Documents/Git/Explore/inst/examples/iris.cutoff
 ClassFeature=class
 PositiveClass=Iris-versicolor
 [Restrictions]
 Rule=
-FeatureInclude=''
+FeatureInclude=
 FeatureRule=
 [Constraints]
 Maximize=ACCURACY
 Accuracy=
 Specificity=
 [Output]
 OutputMethod=BEST
-PrintSettings=no
+PrintSettings=yes
 PrintPartitions=no
 PrintFeatureOperators=no
 PrintCutoffMethod=no
@@ -37,14 +37,12 @@ PrintOperatorValues=no
 PrintCombinations=no
 PrintFeatureSets=no
 PrintCutoffSets=no
-PrintCutoffSetsBestLength=no
-PrintPerformance=no
+PrintCutOffsetsBestLength=no
+PrintPerformance=yes
 PrintSets=no
 SavePartitions=no
 [Run]
 OptimizeRules=yes
 Subsumption=yes
 BranchBound=yes
-
-
-
+Parallel=no