Man pages for predomics/predomicspkg
Interpretable Prediction in Omics Data
| 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 |
