Opt v0.99 -Optimizations and New Features for Main GA Loop

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: BioGA
 Title: Bioinformatics Genetic Algorithm (BioGA)
-Version: 0.99.6
+Version: 0.99.17
 Authors@R: 
     person("Dany", "Mukesha", , "danymukesha@gmail.com", 
             role = c("aut", "cre"),
@@ -20,20 +20,38 @@ Imports:
     ggplot2,
     graphics,
     Rcpp,
+    RcppParallel,
     SummarizedExperiment,
     animation,
     rlang,
     biocViews,
     sessioninfo,
-    BiocStyle
+    BiocStyle,
+    BiocParallel,
+    GEOquery,
+    caret,
+    caretEnsemble,
+    doParallel,
+    dplyr,
+    iml,
+    lattice,
+    lime,
+    pROC,
+    pheatmap,
+    randomForest,
+    survival,
+    survminer,
+    timeROC,
+    xgboost
 Depends: 
     R (>= 4.4)
 Suggests: 
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
 LinkingTo: 
-    Rcpp
+    Rcpp,
+    RcppParallel
 VignetteBuilder: 
     knitr
 biocViews: ExperimentalDesign, Technology

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(bioga_main_cpp)
 export(crossover_cpp)
 export(evaluate_fitness_cpp)
 export(initialize_population_cpp)
@@ -9,19 +10,61 @@ export(plot_fitness_history)
 export(plot_population)
 export(replacement_cpp)
 export(selection_cpp)
+import(RcppParallel)
+importFrom(BiocParallel,bplapply)
+importFrom(BiocParallel,bpmapply)
+importFrom(BiocParallel,register)
 importFrom(BiocStyle,html_document)
+importFrom(GEOquery,getGEO)
 importFrom(Rcpp,evalCpp)
 importFrom(Rcpp,sourceCpp)
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(animation,saveGIF)
 importFrom(biocViews,getBiocViews)
+importFrom(caret,createDataPartition)
+importFrom(caret,train)
+importFrom(caret,trainControl)
+importFrom(caretEnsemble,caretEnsemble)
+importFrom(caretEnsemble,caretList)
+importFrom(doParallel,registerDoParallel)
+importFrom(doParallel,stopImplicitCluster)
+importFrom(dplyr,arrange)
+importFrom(dplyr,distinct)
+importFrom(dplyr,filter)
+importFrom(dplyr,mutate)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+importFrom(dplyr,summarise)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(graphics,boxplot)
 importFrom(graphics,hist)
 importFrom(graphics,par)
+importFrom(iml,FeatureImp)
+importFrom(iml,Predictor)
+importFrom(lattice,bwplot)
+importFrom(lattice,histogram)
+importFrom(lattice,xyplot)
+importFrom(lime,explain)
+importFrom(pROC,ci.auc)
+importFrom(pROC,plot.roc)
+importFrom(pROC,roc)
+importFrom(parallel,detectCores)
+importFrom(parallel,makeCluster)
+importFrom(pheatmap,pheatmap)
+importFrom(randomForest,combine)
+importFrom(randomForest,randomForest)
 importFrom(rlang,local_options)
 importFrom(sessioninfo,session_info)
+importFrom(survival,Surv)
+importFrom(survival,cluster)
+importFrom(survival,coxph)
+importFrom(survival,survfit)
+importFrom(survminer,ggsurvplot)
+importFrom(timeROC,timeROC)
+importFrom(xgboost,slice)
+importFrom(xgboost,xgb.DMatrix)
+importFrom(xgboost,xgb.train)
 useDynLib(BioGA, .registration = TRUE)

NEWS.md

@@ -1,3 +1,205 @@
+# BioGA 0.99.17
+
+Added:
+- Demo vignette for BioGA.
+- Mathematical background vignette for BioGA.
+
+Updated:
+- BioGA vignettes with new examples and explanations.
+- `selection_cpp` function for improved performance and bug fixes.
+
+# BioGA 0.99.16
+
+*UPDATE: test_crossover_cpp*
+
+The test verifies dimensions, value ranges, and new parameters.
+
+Changes:
+- Added tests for new parameters (`crossover_rate`, `eta_c`).
+- Verified that offspring values lie within parent ranges (due to SBX).
+- Included edge case test for single parent and zero crossover rate.
+- Simplified error/warning checks.
+
+*UPDATE: test_selection_cpp*
+The test checks dimensions, parent selection, and compatibility with multi-objective fitness.
+
+Changes:
+- Updated to handle multi-objective fitness matrix.
+- Verified that selected parents are exact copies of population rows.
+- Added edge case test for single individual and single objective.
+- Removed redundant fitness evaluation test (already covered in `evaluate_fitness_cpp`).
+
+*UPDATE: test_mutation_cpp*
+The test checks dimensions, mutation effects, and new parameters.
+
+Changes:
+- Added tests for new parameters (`iteration`, `max_iterations`, `network`).
+- Verified that zero mutation rate preserves offspring.
+- Tested network constraints with extreme cases (zero and full constraints).
+- Simplified error/warning checks.
+
+*UPDATE/ADDED: test_replacement_cpp*
+
+The test checks dimensions, elite preservation, and diversity.
+
+Changes:
+- Added test for new function signature (requires fitness matrices).
+- Verified elite preservation based on first objective.
+- Included edge case test for zero replacements.
+- Added checks for dimensions and error-free execution.
+
+*UPDATE: test_initialize_population_cpp*
+
+The test checks dimensions, value validity, and new parameters.
+
+Changes:
+- Added test for `seed` parameter to ensure reproducibility.
+- Included test for `clusters` parameter to verify correct initialization.
+- Maintained tests for dimensions and value validity.
+- Added edge case test for minimal input.
+
+*UPDATE: test_bioga_main_cpp* {PROVISIONAL}
+
+New test file is created to verify the main GA loop.
+
+Feature:
+- Tests the output structure (list with population and fitness).
+- Verifies dimensions of population and fitness matrices.
+- Checks optional parameters (`clusters`, `network`).
+- Includes edge case test for minimal input.
+
+*Test for Package (test-BioGA-package.R)*
+
+Created a new version to test the overall package integrity and ensure all functions are exported correctly.
+
+Feature:
+- Tests package loading and function exports.
+- Verifies a complete GA workflow without errors.
+- Ensures compatibility with the optimized functions.
+
+# BioGA 0.99.15
+
+*UPDATE: test_evaluate_fitness_cpp* 
+The test checks dimensions, values, and error-free execution.
+
+Changes:
+
+* Updated to test the new matrix output (multiple objectives).
+* Added checks for non-negative fitness values (appropriate for expression difference and sparsity).
+* Included edge case test for minimal input.
+* Removed redundant `tryCatch` and simplified error/warning checks.
+
+# BioGA 0.99.14
+
+*Commit -m "New Feature - Main GA Loop"*
+
+adding a main GA loop function that integrates all components 
+and supports multi-objective optimization and parallelization.
+
+Features:
+
+* Integrates all optimized components into a cohesive GA loop.
+* Supports multi-objective optimization, gene networks, and clustering.
+* Returns both final population and fitness scores for analysis.
+
+# BioGA 0.99.13
+
+*Commit -m "Optimized initialize_population.cpp"*
+
+Improvements:
+
+* Add option for biologically informed initialization using gene clusters.
+* Improve random seed handling for reproducibility.
+
+Changes:
+
+* Added optional random seed for reproducibility.
+* Included support for gene clustering to initialize biologically relevant populations.
+* Improved code readability and documentation.
+
+# BioGA 0.99.12
+
+*Commit -m "Optimized replacement.cpp"*
+
+indentation adjustments
+
+# BioGA 0.99.11
+
+*Commit -m "Optimized replacement.cpp"*
+
+Improvements:
+
+* Implement elitism to preserve best individuals.
+* Add diversity-based replacement to avoid premature convergence.
+
+Changes:
+
+* Added elitism to preserve the best individual.
+* Included diversity-based replacement to maintain population diversity.
+* Updated to use multi-objective fitness matrix.
+
+# BioGA 0.99.10
+
+*Commit -m "Optimized mutation.cpp"*
+
+Improvements:
+
+* Add adaptive mutation rate based on iteration or fitness stagnation.
+* Incorporate gene network constraints (placeholder for user-provided network).
+
+Changes:
+
+* Added adaptive mutation rate based on iteration progress.
+* Included optional gene network constraints to ensure biologically relevant mutations.
+* Maintained compatibility with existing functionality.
+
+# BioGA 0.99.9
+
+*Commit -m "Optimized selection.cpp"*
+
+Improvements:
+
+* Implement NSGA-II non-dominated sorting for multi-objective optimization.
+* Add tournament selection for better diversity.
+
+Changes:
+
+* Implemented NSGA-II non-dominated sorting for multi-objective selection.
+* Added tournament selection to maintain diversity.
+* Updated to handle multi-objective fitness matrix.
+
+# BioGA 0.99.8
+
+*Commit -m "Optimized crossover.cpp"*
+"
+Improvements:
+
+* Implement simulated binary crossover (SBX) for better exploration.
+* Add adaptive crossover rate based on population diversity.
+
+Changes:
+
+* Replaced simple averaging with SBX crossover for better exploration.
+* Added adaptive crossover rate based on population diversity.
+* Included parameters for crossover rate and distribution index.
+
+# BioGA 0.99.7
+
+*Commit -m "Optimized evaluate_fitness.cpp"*
+
+Improvements:
+
+* Add multi-objective fitness evaluation (e.g., minimize expression difference and maximize gene sparsity).
+* Use vectorized operations for faster computation.
+* Add parallelization with RcppParallel for large datasets.
+
+Changes:
+
+* Added multi-objective support (expression difference and sparsity).
+* Used `RcppParallel` for parallel computation.
+* Returned a matrix of fitness scores for each objective.
+* Added weights parameter for flexible objective prioritization.
+
 # BioGA 0.99.6
 
 * add the authors and date in the vignettes?

R/BioGA-package.R

@@ -11,6 +11,24 @@
 #' @importFrom animation saveGIF
 #' @importFrom rlang local_options
 #' @importFrom BiocStyle html_document
+#' @import RcppParallel
+#' @importFrom GEOquery getGEO
+#' @importFrom caret train trainControl createDataPartition
+#' @importFrom lattice xyplot bwplot histogram
+#' @importFrom BiocParallel bplapply bpmapply register
+#' @importFrom caretEnsemble caretList caretEnsemble
+#' @importFrom parallel detectCores makeCluster
+#' @importFrom doParallel registerDoParallel stopImplicitCluster
+#' @importFrom dplyr filter select mutate arrange summarise rename distinct
+#' @importFrom iml Predictor FeatureImp
+#' @importFrom lime explain
+#' @importFrom pROC roc ci.auc plot.roc
+#' @importFrom pheatmap pheatmap
+#' @importFrom randomForest combine randomForest
+#' @importFrom survival cluster Surv coxph survfit
+#' @importFrom survminer ggsurvplot
+#' @importFrom timeROC timeROC
+#' @importFrom xgboost slice xgb.DMatrix xgb.train
 #' @useDynLib BioGA, .registration = TRUE
 ## usethis namespace: end
 NULL