AnalyseStableModels_LOO | analyse stability of models from digest |
analyzeImportanceFeatures | Analyze Feature Importance for Machine Learning Models |
analyzeImportanceFeaturesFBM | Analyze and Plot Feature Importance for Feature-Based Models... |
analyzePopulationFeatures | Analyze Features in a Population of Models |
bestModelFeatureStability | analyse stability of models from digest |
bestModelStability | analyse stability of models from digest |
cir_test | Cirhosis stage 2 (frequencies) |
cir_train | Cirhosis stage 1 (frequencies) |
cleanPopulation | cleanPopulation |
computeCardEnrichment | computeCardEnrichment |
computeCoeffSVMLin | Compute other prediction scores such as precision, recall and... |
computeConfusionMatrix | Evaluates the confusion Matrix of the predicted class and the... |
computeEffectSizes | Compute Effect Sizes for Features |
computeFeatureMetrics | Computes different metrics for a given distributions |
computeIntercept | Computes the best intercept for the model while minimizing... |
convergence.test | Test for Convergence in Evolutionary Algorithm Scores |
counter | The counter for the experiment id (used in the clf builders) |
crossing | Generate Children by Crossover from Parent Population |
crossing2 | Generate Offspring by Pairing Parents in a Population |
crossingIndividual_v1 | Create a New Individual by Crossing Genes from Two Parents |
crossingIndividual_v2 | Create a New Individual by Combining Gene Vectors from Two... |
crossingIndividual_v3 | Create a New Individual by Sampling Genes from Two Parents... |
denseVecToModel | denseVecToModel |
digest | Summarize the results from an experiment object |
digestModelCollection | digestModelCollection |
disectModel | Dissects the model by separating positive and negative... |
estimateCoefficientsIndividual | Estimate Model Coefficients for a Subset of Features |
estimateFeatureImportance | Estimates the importance of each feature in the model object |
evaluateAccuracy | Evaluates the accuracy of a model |
evaluateAdditionnalMetrics | Compute other prediction scores such as precision, recall and... |
evaluateAUC | Computes the AUC of a model |
evaluateFeatureImportanceInPopulation | evaluates the feature importance in a population of models |
evaluateFit | Evaluates the fitting score of a model object |
evaluateIntercept | Evaluates the fitting score of a model object |
evaluateModel | Evaluates the fitting score of a model object |
evaluateModelRegression | Evaluates the fitting coefficents of a model object |
evaluatePopulation | evaluatePopulation |
evaluatePrevalence | Evaluate the prevalence of a given model |
evaluateYhat | Computes the predected classification using a given model |
evolve | Evolve a Population of Models Over Generations |
evolve1 | Evolve a Population in an Evolutionary Algorithm |
evolve2m | Evolve a Population with Advanced Selection, Crossover, and... |
evolve3m | Evolve a Population with Advanced Mating and Mutation |
filterFeaturesByPrevalence | Selects the most prevalent features in the dataset baset on... |
filterfeaturesK | Selects a the top k features that are significantly... |
filterNoSignal | filterNoSignal: Omits the variables with no information |
findk | Find the number of weights not yet integer. |
fit | fit: runs the classifier on a dataset |
generateAllCombinations | generateAllCombinations |
generator_metal | #' Computes best model of a metal clf #' #' @description Get... |
getFeaturePrevalence | Evaluates the prevalence of a list of features in the whole... |
getFitIndividual | Get the fitting score of an individual object |
getFitModel | Get the fitting score of a model object |
getFitModels | Get the fitting score of a list a models |
getFitPopulation | Get the fitting score of a list of individuals |
getGraph | getGraph |
getImportanceFeaturesFBMobjects | Extract Important Features and Related Metrics from Final... |
getIndicesIndividual | Get the index of the features in a given individual |
getIndicesPopulation | Get the indices of the features used in a population of... |
get_IndividualToBeMutated | Retrieve Individuals Marked for Mutation |
getMaxMinPrevalenceModel | Get the model that has the highest minimal prevalence in its... |
getModelScore | Computes the ^y score of the model |
getNBestModels | Get the models from a classifier result for each k-sparsity |
get_Parents | Retrieve Selected Individuals as Parents |
getSign | Evaluates the sign for a given feature this is the old... |
glmnetRR | Solve with GLMNET and create models |
ibd | Inflammatory Bowel Disease (frequencies) from the MetaHIT... |
index2names | index2names |
individual | Creates an object individual |
individualGetDenseVec | Convert an Individual's Sparse Gene Representation to a Dense... |
individual_vec_v1 | Generate a Sparse Individual Vector for Evolutionary... |
individual_vec_v2 | Generate a Sparse Individual Vector with Specified Density |
individual_vec_v3 | Generate Sparse Individual Vector with Indices and... |
isClf | Evaluates wether an object is a classifier |
isclose | tests weather two values are close |
isExperiment | Evaluates wether an object is an experiment |
isLearnerSota | Evaluates wether an object is a model SOTA SVM |
isModel | Evaluates wether an object is a model |
isModelBTR | Evaluates wether an object is a model BTR |
isModelCollection | Evaluates wether an object is a model collection objecct |
isModelSota | Evaluates wether an object is a model SOTA |
isModelSotaGLMNET | Evaluates wether an object is a model SOTA GLMNET |
isModelSotaRF | Evaluates wether an object is a model SOTA RF |
isModelSotaSVM | Evaluates wether an object is a model SOTA SVM |
isModelTerda | Evaluates wether an object is a model BTR Terda |
isPopulation | Evaluates wether an object is a population of models |
listOfDenseVecToListOfModels | Builds a model object from a list of vector coefficients |
listOfDenseVecToModelCollection | Builds a list of dense vector coefficients from a list of... |
listOfModels2ModelCollection | listOfModels2ModelCollection |
listOfModelsToDenseCoefMatrix | listOfModelsToDenseCoefMatrix |
listOfModelsToListOfDenseVec | Builds a list of dense vector coefficients from a list of... |
listOfModelsToListOfSparseVec | Builds a list of sparse vector coefficients from a list of... |
listOfSparseVecToListOfModels | listOfSparseVecToListOfModels |
loadPopulation | Load a population from a file |
loadResults | Load the results of a fit |
LPO_best_models | Compute the cross-validation of leave one out for test... |
make.counter | Function used to create the counter for building... |
makeFeatureAnnot | Prints as text the detail on a given experiment along with... |
makeFeatureModelPrevalenceNetworkCooccur | Prints as text the detail on a given experiment along with... |
makeFeatureModelPrevalenceNetworkMiic | Prints as text the detail on a given experiment along with... |
mergeMeltBestScoreCV | mergeMeltBestScoreCV |
mergeMeltImportanceCV | mergeMeltImportanceCV |
mergeMeltScoreCV | mergeMeltScoreCV |
mergeMeltScoreEmpirical | mergeMeltScoreEmpirical |
mergeResults | mergeResults |
metal | metal: metal searching algorithm |
modelCollectionToPopulation | Transform a model collection to a population (or list of... |
modelSampling | Generate Training and Validation Sampling Matrices |
modelToDenseVec | Transform the model object onto dense format (long) one |
multipleRR | multipleRR |
multipleRR_par | multipleRR_par |
multiplot | Create Multiple Plots on One Page |
mutate | Mutate Selected Individuals in a Population |
mutate2 | Apply Mutation to a Selected Subset of the Population |
mutator_v1 | Mutate an Individual's Genes in the Population |
mutator_v2 | Mutate an Individual's Genes Based on Feature Evaluation |
myAssert | Asserts a condition and prints a message or stops the block |
myAssertNotNullNorNa | Asserts the existance of an object and prints a message or... |
names2index | names2index |
normModelCoeffs | Normalize Model Coefficients |
obesity | Obesity (frequencies) from the MetaHIT study |
plotAbundanceByClass | Plot Feature Abundance by Class |
plotAUC | Plot AUC and ROC Curve with Confidence Intervals |
plotAUCg | Plot AUC with ROC Curve and Confidence Intervals |
plotComparativeBestCV | Plot Comparative Best Cross-Validation (CV) Performance for... |
plotComparativeCV | Plot Comparative Cross-Validation (CV) Performance for... |
plotComparativeEmpiricalScore | Plot Comparative Empirical Score for Multiple Methods |
plotComparativeResults | Plot Comparative Results for Multiple Methods and... |
plotComparativeResultsBest | Plot Comparative Results for Best Performance Across Multiple... |
plotFeatureModelCoeffs | Plot Feature Model Coefficients |
plotImportanceFeaturesFBMobjects | Plot Feature Importance, Prevalence, and Effect Sizes from... |
plotMGSQuality | Plot MGS Quality for Genes |
plotModel | Plot Model Coefficients and Importance |
plotModelScore | Plot Model Performance Scores |
plotPopulation | Plot Population of Models |
plotPrevalence | Plot Feature Prevalence and Enrichment |
plotScoreBarcode | Plot a barcode representation of model scores |
population | Generate a Population with Controlled Sparsity and Unique... |
population2 | Generate and Initialize a Population for Evolutionary... |
populationDenseVec | Generate a Population with Controlled Sparsity Using Dense... |
populationGet_X | Get the best model from a classifier result |
populationSet_X | Set models with a given liist of objects |
populationToDataFrame | populationToDataFrame |
predictPopulation | Predicts the outcomes of a population of models in a dataset. |
printClassifier | Print Information about a Classifier Object |
printExperiment | Print Information about an Experiment Object |
printModel | Print Model Information |
printModelCollection | Print Information about a Model Collection |
printPopulation | Print Information about a Population of Models |
printy | Print Summary of Predomics Object |
rankFeatures | Rank Features Based on Model Fitness |
resetTags | Reset Tags for All Individuals in a Population |
runClassifier | Runs the learning on a dataset |
runCrossval | Compute the cross-validation emprirical and generalization... |
savePopulation | Save a population to a file |
saveResults | Save the results of the fit function |
scoreRatio | Computes the ^y score of the model as a ratio |
select | Select Individuals from a Population Using Multiple Selection... |
selectBestPopulation | Select the top significant best part of the population |
selectElite | Select Elite Individuals Based on Evaluation Scores |
selectIndividualToKeep | Select the Best Individual by Sparsity Level from a... |
selectMixed | Select Individuals Using Mixed Elite and Tournament Selection |
selector_v1 | Select Top Individuals from a Population Based on Fitness |
selector_v2 | Randomly Select Individuals from a Population |
selectTournoi | Select Individuals Using Tournament Selection |
sim_inter | compare stability of different modeles (inter k) |
sim_intra | compare stability of different modeles (intra k) |
sortPopulation | sortPopulation |
sota.glmnet | sota.glmnet |
sota.rf | sota.rf |
sota.svm | sota.svm |
sparseVecToModel | sparseVecToModel |
summarySE | Plot performance scores for multiple learners. |
t2d | Type 2 diabetes (frequencies) BGI |
t2dw | Type 2 diabetes (frequencies) Women Sweden |
tableBestModels | Generate a Summary Table of Best Models |
tag_Couples | Pair Individuals in Population as Mating Couples |
tag_select | Select and Tag Individuals in a Population for Evolutionary... |
tag_SelectElite | Select Elite Individuals in a Population |
tag_SelectRandom | Randomly Select Individuals in a Population |
tag_ToBeMutated | Tag Individuals for Mutation in a Population |
terBeam | terbeam |
terda | terda |
terga1 | terga1 |
terga1_fit | Fit a Model Using an Evolutionary Algorithm with Controlled... |
terga2 | Model search algorithm based on genetic algorithms (GA). |
terga2_fit | Fit a Model Using an Evolutionary Algorithm with Controlled... |
updateModelIndex | updateModelIndex |
updateObjectIndex | updateObjectIndex |
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