Man pages for predomics/predomicspkg
Interpretable Prediction in Omics Data

AnalyseStableModels_LOOanalyse stability of models from digest
analyzeImportanceFeaturesAnalyze Feature Importance for Machine Learning Models
analyzeImportanceFeaturesFBMAnalyze and Plot Feature Importance for Feature-Based Models...
analyzePopulationFeaturesAnalyze Features in a Population of Models
bestModelFeatureStabilityanalyse stability of models from digest
bestModelStabilityanalyse stability of models from digest
cir_testCirhosis stage 2 (frequencies)
cir_trainCirhosis stage 1 (frequencies)
cleanPopulationcleanPopulation
computeCardEnrichmentcomputeCardEnrichment
computeCoeffSVMLinCompute other prediction scores such as precision, recall and...
computeConfusionMatrixEvaluates the confusion Matrix of the predicted class and the...
computeEffectSizesCompute Effect Sizes for Features
computeFeatureMetricsComputes different metrics for a given distributions
computeInterceptComputes the best intercept for the model while minimizing...
convergence.testTest for Convergence in Evolutionary Algorithm Scores
counterThe counter for the experiment id (used in the clf builders)
crossingGenerate Children by Crossover from Parent Population
crossing2Generate Offspring by Pairing Parents in a Population
crossingIndividual_v1Create a New Individual by Crossing Genes from Two Parents
crossingIndividual_v2Create a New Individual by Combining Gene Vectors from Two...
crossingIndividual_v3Create a New Individual by Sampling Genes from Two Parents...
denseVecToModeldenseVecToModel
digestSummarize the results from an experiment object
digestModelCollectiondigestModelCollection
disectModelDissects the model by separating positive and negative...
estimateCoefficientsIndividualEstimate Model Coefficients for a Subset of Features
estimateFeatureImportanceEstimates the importance of each feature in the model object
evaluateAccuracyEvaluates the accuracy of a model
evaluateAdditionnalMetricsCompute other prediction scores such as precision, recall and...
evaluateAUCComputes the AUC of a model
evaluateFeatureImportanceInPopulationevaluates the feature importance in a population of models
evaluateFitEvaluates the fitting score of a model object
evaluateInterceptEvaluates the fitting score of a model object
evaluateModelEvaluates the fitting score of a model object
evaluateModelRegressionEvaluates the fitting coefficents of a model object
evaluatePopulationevaluatePopulation
evaluatePrevalenceEvaluate the prevalence of a given model
evaluateYhatComputes the predected classification using a given model
evolveEvolve a Population of Models Over Generations
evolve1Evolve a Population in an Evolutionary Algorithm
evolve2mEvolve a Population with Advanced Selection, Crossover, and...
evolve3mEvolve a Population with Advanced Mating and Mutation
filterFeaturesByPrevalenceSelects the most prevalent features in the dataset baset on...
filterfeaturesKSelects a the top k features that are significantly...
filterNoSignalfilterNoSignal: Omits the variables with no information
findkFind the number of weights not yet integer.
fitfit: runs the classifier on a dataset
generateAllCombinationsgenerateAllCombinations
generator_metal#' Computes best model of a metal clf #' #' @description Get...
getFeaturePrevalenceEvaluates the prevalence of a list of features in the whole...
getFitIndividualGet the fitting score of an individual object
getFitModelGet the fitting score of a model object
getFitModelsGet the fitting score of a list a models
getFitPopulationGet the fitting score of a list of individuals
getGraphgetGraph
getImportanceFeaturesFBMobjectsExtract Important Features and Related Metrics from Final...
getIndicesIndividualGet the index of the features in a given individual
getIndicesPopulationGet the indices of the features used in a population of...
get_IndividualToBeMutatedRetrieve Individuals Marked for Mutation
getMaxMinPrevalenceModelGet the model that has the highest minimal prevalence in its...
getModelScoreComputes the ^y score of the model
getNBestModelsGet the models from a classifier result for each k-sparsity
get_ParentsRetrieve Selected Individuals as Parents
getSignEvaluates the sign for a given feature this is the old...
glmnetRRSolve with GLMNET and create models
ibdInflammatory Bowel Disease (frequencies) from the MetaHIT...
index2namesindex2names
individualCreates an object individual
individualGetDenseVecConvert an Individual's Sparse Gene Representation to a Dense...
individual_vec_v1Generate a Sparse Individual Vector for Evolutionary...
individual_vec_v2Generate a Sparse Individual Vector with Specified Density
individual_vec_v3Generate Sparse Individual Vector with Indices and...
isClfEvaluates wether an object is a classifier
isclosetests weather two values are close
isExperimentEvaluates wether an object is an experiment
isLearnerSotaEvaluates wether an object is a model SOTA SVM
isModelEvaluates wether an object is a model
isModelBTREvaluates wether an object is a model BTR
isModelCollectionEvaluates wether an object is a model collection objecct
isModelSotaEvaluates wether an object is a model SOTA
isModelSotaGLMNETEvaluates wether an object is a model SOTA GLMNET
isModelSotaRFEvaluates wether an object is a model SOTA RF
isModelSotaSVMEvaluates wether an object is a model SOTA SVM
isModelTerdaEvaluates wether an object is a model BTR Terda
isPopulationEvaluates wether an object is a population of models
listOfDenseVecToListOfModelsBuilds a model object from a list of vector coefficients
listOfDenseVecToModelCollectionBuilds a list of dense vector coefficients from a list of...
listOfModels2ModelCollectionlistOfModels2ModelCollection
listOfModelsToDenseCoefMatrixlistOfModelsToDenseCoefMatrix
listOfModelsToListOfDenseVecBuilds a list of dense vector coefficients from a list of...
listOfModelsToListOfSparseVecBuilds a list of sparse vector coefficients from a list of...
listOfSparseVecToListOfModelslistOfSparseVecToListOfModels
loadPopulationLoad a population from a file
loadResultsLoad the results of a fit
LPO_best_modelsCompute the cross-validation of leave one out for test...
make.counterFunction used to create the counter for building...
makeFeatureAnnotPrints as text the detail on a given experiment along with...
makeFeatureModelPrevalenceNetworkCooccurPrints as text the detail on a given experiment along with...
makeFeatureModelPrevalenceNetworkMiicPrints as text the detail on a given experiment along with...
mergeMeltBestScoreCVmergeMeltBestScoreCV
mergeMeltImportanceCVmergeMeltImportanceCV
mergeMeltScoreCVmergeMeltScoreCV
mergeMeltScoreEmpiricalmergeMeltScoreEmpirical
mergeResultsmergeResults
metalmetal: metal searching algorithm
modelCollectionToPopulationTransform a model collection to a population (or list of...
modelSamplingGenerate Training and Validation Sampling Matrices
modelToDenseVecTransform the model object onto dense format (long) one
multipleRRmultipleRR
multipleRR_parmultipleRR_par
multiplotCreate Multiple Plots on One Page
mutateMutate Selected Individuals in a Population
mutate2Apply Mutation to a Selected Subset of the Population
mutator_v1Mutate an Individual's Genes in the Population
mutator_v2Mutate an Individual's Genes Based on Feature Evaluation
myAssertAsserts a condition and prints a message or stops the block
myAssertNotNullNorNaAsserts the existance of an object and prints a message or...
names2indexnames2index
normModelCoeffsNormalize Model Coefficients
obesityObesity (frequencies) from the MetaHIT study
plotAbundanceByClassPlot Feature Abundance by Class
plotAUCPlot AUC and ROC Curve with Confidence Intervals
plotAUCgPlot AUC with ROC Curve and Confidence Intervals
plotComparativeBestCVPlot Comparative Best Cross-Validation (CV) Performance for...
plotComparativeCVPlot Comparative Cross-Validation (CV) Performance for...
plotComparativeEmpiricalScorePlot Comparative Empirical Score for Multiple Methods
plotComparativeResultsPlot Comparative Results for Multiple Methods and...
plotComparativeResultsBestPlot Comparative Results for Best Performance Across Multiple...
plotFeatureModelCoeffsPlot Feature Model Coefficients
plotImportanceFeaturesFBMobjectsPlot Feature Importance, Prevalence, and Effect Sizes from...
plotMGSQualityPlot MGS Quality for Genes
plotModelPlot Model Coefficients and Importance
plotModelScorePlot Model Performance Scores
plotPopulationPlot Population of Models
plotPrevalencePlot Feature Prevalence and Enrichment
plotScoreBarcodePlot a barcode representation of model scores
populationGenerate a Population with Controlled Sparsity and Unique...
population2Generate and Initialize a Population for Evolutionary...
populationDenseVecGenerate a Population with Controlled Sparsity Using Dense...
populationGet_XGet the best model from a classifier result
populationSet_XSet models with a given liist of objects
populationToDataFramepopulationToDataFrame
predictPopulationPredicts the outcomes of a population of models in a dataset.
printClassifierPrint Information about a Classifier Object
printExperimentPrint Information about an Experiment Object
printModelPrint Model Information
printModelCollectionPrint Information about a Model Collection
printPopulationPrint Information about a Population of Models
printyPrint Summary of Predomics Object
rankFeaturesRank Features Based on Model Fitness
resetTagsReset Tags for All Individuals in a Population
runClassifierRuns the learning on a dataset
runCrossvalCompute the cross-validation emprirical and generalization...
savePopulationSave a population to a file
saveResultsSave the results of the fit function
scoreRatioComputes the ^y score of the model as a ratio
selectSelect Individuals from a Population Using Multiple Selection...
selectBestPopulationSelect the top significant best part of the population
selectEliteSelect Elite Individuals Based on Evaluation Scores
selectIndividualToKeepSelect the Best Individual by Sparsity Level from a...
selectMixedSelect Individuals Using Mixed Elite and Tournament Selection
selector_v1Select Top Individuals from a Population Based on Fitness
selector_v2Randomly Select Individuals from a Population
selectTournoiSelect Individuals Using Tournament Selection
sim_intercompare stability of different modeles (inter k)
sim_intracompare stability of different modeles (intra k)
sortPopulationsortPopulation
sota.glmnetsota.glmnet
sota.rfsota.rf
sota.svmsota.svm
sparseVecToModelsparseVecToModel
summarySEPlot performance scores for multiple learners.
t2dType 2 diabetes (frequencies) BGI
t2dwType 2 diabetes (frequencies) Women Sweden
tableBestModelsGenerate a Summary Table of Best Models
tag_CouplesPair Individuals in Population as Mating Couples
tag_selectSelect and Tag Individuals in a Population for Evolutionary...
tag_SelectEliteSelect Elite Individuals in a Population
tag_SelectRandomRandomly Select Individuals in a Population
tag_ToBeMutatedTag Individuals for Mutation in a Population
terBeamterbeam
terdaterda
terga1terga1
terga1_fitFit a Model Using an Evolutionary Algorithm with Controlled...
terga2Model search algorithm based on genetic algorithms (GA).
terga2_fitFit a Model Using an Evolutionary Algorithm with Controlled...
updateModelIndexupdateModelIndex
updateObjectIndexupdateObjectIndex
predomics/predomicspkg documentation built on Dec. 11, 2024, 11:06 a.m.