NEWS.md

In tpq/exprso: Rapid Deployment of Machine Learning Algorithms

exprso 0.6.4

• Update fs. and build. methods
  • Now save the intermediate data to debug

exprso 0.6.3

• Update fs methods
  • Sink progress notes for fsAmalgam and fsPRA
  • Add pre-deployment zero check for fsBalance and fsPRA
  • Add post-deployment zero check for fsAmalgam
  • Fix fsAmalgam error due to missing names
  • Now pass defineCase labels to amalgam

exprso 0.6.2

• Add support for the propr::pra method
  • New fsPRA function performs pairwise log-ratio selection
  • Log-ratio selection now supported by modHistory
  • Add assocaited tests

exprso 0.6.1

• Add support for the amalgam package
  • New fsAmalgam function finds amalgams for training set
  • Amalgams now supported by modHistory
  • Support asSLR = TRUE

exprso 0.6.0

• Update OOP framework
  • Have exprso import function make S4 object at very end
  • Allow [.ExprsPipeline operator to re-order models
• Revised documentation
  • New class, conjoin, and fs tests

exprso 0.5.9

• Update OOP framework
  • Fix bug where printing the model triggers an error
• Update predict modules
  • Fix bug where the ensemble does not save predictions as a factor
• Revised documentation
  • Reviewed 2-conjoin and 3-mod
  • New ens test

exprso 0.5.8

• Update OOP framework
  • New MultiPredict object handles multi-class prediction
• Update build modules
  • Try to make fs. and build. more similar
  • Extend build modules to true multi-class learning
• Update predict modules
  • predict.ExprsMulti now handles true multi-class learning
  • predict.ExprsEnsemble now handles true multi-class learning
• Update pl modules
  • plCV: Use plCV.acc = 'acc' when requested value not found
• Update pipe modules
  • pipeSubset: Remove default colBy argument to guard against improper use
• Remove modules
  • Completely remove plGridMulti module
  • Completely remove doMulti module
• Revised documentation
  • Reviewed 1.1, 1.2, and 1.3
  • New build test

exprso 0.5.7

• Update calc modules
  • Now shows the optimal cutoff point on the ROCR plot
• Update pl modules
  • plCV: New plCV.acc argument allows user to select inner-CV performance metric
  • plCV: New aucSkip argument allows user to calculate ROCR performance
  • plGrid: Arguments aucSkip and plCV.acc now passed to plCV
  • plNested: Simplify code
  • plCV: Simplify code

exprso 0.5.6

• Update calc modules
  • Add precision and F1-score to calcStats

exprso 0.5.5

• Update fs modules
  • Add top argument to fsInclude and fsAnnot (needed for ctrlFeatureSelect)

exprso 0.5.4

• Update mod modules
  • When using modHistory, preFilter = 0 will skip the subset (to speed up model deployment)
  • modHistory now checks for equivalent dimension reduction history
• Update fs modules
  • Reduce amount of history recorded after repeat steps (to reduce RAM overhead)
  • Remove keep argument entirely
• Update build modules
  • Reduce amount of history recorded after repeat steps (to reduce RAM overhead)

exprso 0.5.3

• Update exprso module
  • Now apply make.names to annotation columns too
  • Force stringsAsFactors for all annot columns
  • This is needed for fsAnnot to work
• Update fs modules
  • New fsAnnot pulls in an annotation column as a feature
  • Fix fsCor bug that did not rank by absolute value of correlation
  • Improve documentation for a few modules
• Remove modules
  • Completely remove reRank module

exprso 0.5.2

• Update fs modules
  • New colBy argument for fsRDA triggers constrained RDA
  • Note that fsRDA always returns the unconstrained part of an RDA
  • Remove ... for fsRDA
• Update mod modules
  • Note that modHistory always returns the unconstrained part of an RDA
  • This allows colBy to act as the conditioning matrix

exprso 0.5.1

• Remove fsPathClassRFE and fsSelbal

exprso 0.5.0

• Add helper functions
  • New nfeats returns number of features in object
  • New nsamps returns number of samples in object
• Add split modules
  • New splitBoost up-samples the smaller of two classes
• Add fs modules
  • New fsSelbal performs balance selection using selbal::selbal
  • New fsRDA performs dimension reduction using vegan::rda
  • Remove fsPropd module
• Add suppressWarnings(RNGversion("3.5.0")) to tests

exprso 0.4.9

• Update build modules
  • Set default LASSO argument intercept = FALSE
  • Set default SVM argument kernel = "linear"
• Update calcStats
  • Use R-squared for RegrsPredict accuracy

exprso 0.4.8

• Update mod modules
  • Fix a modCLR bug

exprso 0.4.7

• Update exprso import
  • Correctly apply make.names to feature names
• Improvements to calcStats
  • Add correlation and R-squared measures

exprso 0.4.6

• Update mod modules
  • New modPermute will permute predictor variables
• Update getWeights method
  • Extend support to randomForest objects

exprso 0.4.5

• Update fs modules
  • Extend fsBalance to support sbp.fromPropd

exprso 0.4.4

• Update mod modules
  • Extend modHistory to support balance deployment
• Update fs modules
  • New fsBalance to convert features into balances
  • Uses sbp.subset if ternary or ratios argument is provided
• Package maintenance
  • Turn README into FAQ vignette

exprso 0.4.3

• New getWeights method
  • New method gets LASSO weights for ExprsModel and related objects

exprso 0.4.2

• Update build modules
  • Extend buildGLM to work for any outcome (continuous and factor)
  • New buildLASSO module for LASSO and Ridge regression

exprso 0.4.1

• Update mod modules
  • Add alpha argument to modRatios function

exprso 0.4.0

• Package maintenance
  • Clean up message dump within vignettes
  • Update fsPropd for compatibility with propr version 4.0
  • Update tests for compatibility with e1071 version 1.7
  • Remove the gtools import

exprso 0.3.9

• Update mod modules
  • Simplify modSkew function to add feature based only on alpha
• Update fs modules
  • Add fsPathClassRFE to the ?fs help file

exprso 0.3.8

• Update mod modules
  • New modSkew function skews sample vectors by a factor range

exprso 0.3.7

• Update exprso import
  • Fix bug caused by importing an annotation table

exprso 0.3.6

• General changes
  • exprso can now swap "Control" and "Case" labels with switch argument
  • exprso no longer gives error when importing tabular annotations
  • exprso can now predict any column from tabular annotations

exprso 0.3.5

• Update split modules
  • Add splitBalanced to balance both the training and validation sets

exprso 0.3.4

• Update mod modules
  • Add modInclude function to select specific features from a data set
  • Rename modShuffle to modSample

exprso 0.3.3

• General changes
  • exprso no longer alters labels already called "Control" and "Case"
• Update split modules
  • splitStratify now runs quietly
  • splitSample NULL validation set cat changed to a warning

exprso 0.3.2

• Update fs modules
  • Add keep argument to subset features after performing selection
  • Use of keep can speed up model deployment for lage data sets

exprso 0.3.1

• Update mod modules
  • Add base = exp(1) argument as default for modTransform method
• Update fs modules
  • Add modRatios argument to fsPropd for data provided as ratios
• Update split modules
  • Add splitBy function to split data by user-defined group
• General changes
  • Improve performance by making fewer subsets with fs. and build.
  • Improve performance by making fewer subsets with modHistory

exprso 0.3.0

• Update mod modules
  • Replace modScale with a new procedure that uses runif
  • Extend modScale with another method that uses rnorm
  • Add size argument to modShuffle
• Update fs modules
  • New fsRankProd method ranks features using RankProd package
  • Extend fsStats to use wilcox.test and f.test
  • Add suppressMessages to fsPropd module
• Update build modules
  • Sink printed output from nnet function
  • Tweak default buildANN arguments
• Major verbose = FALSE update
  • Add verbose to toggle defaultArg and forceArg messages
  • Force verbose = FALSE for calcStats calls from plCV
  • Make verbose = FALSE the default for plGrid
• General changes
  • Add progress function to list of global functions
  • Add suppressMessages to plMonteCarlo and plNested calls
  • Embed progress bar in plMonteCarlo and plNested calls
  • Add default arguments to argument handler functions

exprso 0.2.9

• Update mod modules
  • New modShuffle function shuffles feature order by random sampling
  • New modScale function scales sample vectors by a factor range
• Update build modules
  • New buildDT function builds decision tree model
    • Add predict.ExprsMachine and predict.RegrsModel support
  • New buildFRB function builds fuzzy rule based model
    • Add predict.ExprsMachine and predict.RegrsModel support
  • New buildLR function builds logistic regression model
    • Add predict.ExprsMachine support
  • New buildLM and buildGLM functions
    • Add predict.RegrsModel support
• General changes
  • plMonteCarlo now accepts a list of ctrlModSet handlers
  • plMonteCarlo now skips fs if ctrlFS = NULL
  • plNested now skips fs if ctrlFS = NULL

exprso 0.2.8

• New modRatios function recasts data as feature ratios

exprso 0.2.7

• General changes
  • Fix bug in show.ExprsPredict method

exprso 0.2.6

• General changes
  • New show method for RegrsArray objects
  • New show method for RegrsModel objects
  • New show method for RegrsPredict objects
  • Review all documentation

exprso 0.2.5

• General changes
  • Validate performance of regression pl pipelines
  • Users can now deploy multi-class classifier ensembles
  • Users can now deploy regression ensembles
  • Trim documentation

exprso 0.2.4

• General changes
  • Move modHistory into script with other mod modules
  • Move predict and calcStats into separate files
• Revise split modules
  • Make splitSample work with RegrsArray objects
  • Note splitStratify is classification only
• Revise build modules
  • Fix bug when making RegrsModel objects
  • Note buildLDA is classification only
  • Note buildNB is classification only
• Revise predict
  • New predict method for RegrsModel objects
  • New calcStats method for RegrsPredict objects
  • Trim documentation

exprso 0.2.3

• Revise build modules
  • All build wrapper functions now support continuous outcomes
• Revise pl modules
  • New ctrlModSet function to handle pre-process arguments
  • Let plMonteCarlo apply pre-process at each bootstrap

exprso 0.2.2

• General changes
  • Have exprso throw error if passed boolean outcomes
  • Add new RegrsPredict class with two slots
• Revise pre-filter modules
  • New modAcomp makes all sample vectors have same total sum
  • New modCLR applies centered log-ratio transformation
• Revise fs modules
  • Pass additional arguments to fsPropd function
  • Make fsStats run a bit faster
• Revise build modules
  • Add RegrsModel support to build. constructor
• Revise pl modules
  • Add default argument to calcMonteCarlo
  • Add default argument to calcNested

exprso 0.2.1

• General changes
  • Fix NOTE associated with magrittr import
  • Revise ?fs and ?build help files
  • Rename ExprsCont class to RegrsArray
  • New RegrsModel class
• Revise fs modules
  • New fsCor function ranks features for RegrsArray objects

exprso 0.2.0

• General changes
  • Remove all "Golub_Merge" use in vignettes
  • Revise the exprso overview figure
  • Completely revise all vignettes
  • Completely revise README file
  • New ?pipe help file
• Revise pre-filter modules
  • modTMM now returns effective library size instead of cpm
• Revise fs modules
  • New fsEdger function ranks features using exact test
  • fsEbayes now uses the correct design matrix
• Revise build modules
  • build modules now have own documentation
  • New ?build help file

exprso 0.1.9

• General changes
  • Reformat NOTES and vignettes for CRAN
  • All Bioconductor packages now listed in Suggests:
  • Remove golubEsets dependency
• Improve data import
  • New exprso function provides x and y style import
  • New ExprsCont class handles continuous outcomes
• Revise pre-filter modules
  • New modTMM function performs TMM normalization
  • Replace formal methods with class checks
  • New ?mod help file
• Revise split modules
  • split now defaults to percent.include = 67
  • split modules now have own documentation
  • New ?split help file
• Revise fs modules
  • New fsPropd function selects features using propr package
  • fs modules now have own documentation
  • New ?fs help file

exprso 0.1.8

• Improvements to arrayExprs
  • Fixed an import error when reading directly from file
• Improvements to calcStats
  • All NaN and NA performance metrics now replaced with 0
• Improvements to fs functions
  • New fsInclude ranks stated features above all others
  • Add fs. check for non-numeric features
• Improvements to pl functions
  • pl functions now store run parameters in results
  • Embedding plMonteCarlo now calculates outer-fold accuracy
  • Embedding plNested now calculates outer-fold accuracy
• Improvements to pipeFilter
  • top now chooses simplest classifier in case of tie
• Added F1000Research citation to inst/CITATION

exprso 0.1.7

• 2.1-import.R
  • Make Biobase and GEOquery optional packages
• 5.1-fs.R
  • Make limma an optional package
  • Renamed from 5.1-fs-binary.R
  • Add fsNULL method to return feature input unaltered
  • Add fsANOVA feature selection method
• 5.2-build.R
  • Renamed from 5.2-build-binary.R
• 7.2-plGrid.R
  • Add back-end argument handler makeGridFromArgs
  • Add default arguments for how = buildSVM
• 7.3-plGridMulti.R
  • New function for 1-vs.all classification with ctrlFS
• 7.4-plMonteCarlo.R
  • Renamed from 7.3-plMonteCarlo.R
  • ctrlGS will now accept any pl function
  • Use rbind.fill instead of rbind to prevent error
• 7.5-plNested.R
  • Renamed from 7.4-plNested.R
  • ctrlGS will now accept any pl function
  • Use rbind.fill instead of rbind to prevent error
  • Add plGridMulti check to check.ctrlGS

exprso 0.1.6

• 1.2-methods.R
  • Rename getProbeSet to getFeatures
• 2.1-import.R
  • Rename probes.begin argument to begin
• 4.1-modSwap.R
  • Have fsPrcomp use top argument
• 4.2-modCluster.R
  • Change probes argument to top
• 5.1-fs-binary.R
  • Change probes argument to top
  • Make fsSample an ExprsArray method
• 5.2-build-binary.R
  • Change probes argument to top
  • Add ExprsArray signature to all build methods
  • Add doMulti call to build. function
• 5.3-doMulti.R
  • Change probes argument to top
  • Change what agument to method to allow for do.call
  • Use NA instead of NULL for empty ExprsMachine
  • Remove ExprsMulti method for fsSample
  • Remove ExprsMulti method for fsStats
• 6-predict.R
  • Use NA instead of NULL for empty ExprsMachine
  • Fix ExprsMulti tie breaker warning
• 7.1-plCV.R
  • Change probes argument to top
• 7.2-plGrid.R
  • Change probes argument to top
• 7.3-plMonteCarlo.R
  • Change probes argument to top
• 8.1-pipe.R
  • Change top.N argument to top
• 8.2-ens.R
  • Change top.N argument to top
• 9-global.R
  • Add documentation for data

exprso 0.1.5

• 1.1-classes.R
  • Add actual slot to ExprsPredict object
• 1.2-methods.R
  • Add 2D plotting to plot method
• 2.1-import.R
  • Force stringsAsFactors = FALSE
• 4.1-modSwap.R
  • Clean up plot calls using new plot method
• 6-predict.R
  • Add class check for modHistory @reductionModel
  • Add class check for predict @mach
  • Pass along known class values to ExprsPredict result
  • Remove calcStats array argument
• 7.1-plCV.R
  • Tidy calcStats calls
• 7.2-plGrid.R
  • Tidy calcStats calls
• 8.2-ens.R
  • Pass along known class values to ExprsPredict result
• 9-global.R
  • Find optimal import combination
• 9-tidy.R
  • Add pipeSubset function

exprso 0.1.4

• 2.1-import.R
  • Deprecated arrayRead and arrayEset functions
  • New arrayExprs function adds data.frame support
• 3.1-split.R
  • Remove splitSample warning
  • Add details to the "Please Read" vignette
• 4.2-cluster.R
  • Add support for numeric vector probes
• 4.3-compare.R
  • Convert compare warning into error
• 5.1-fs-binary.R
  • Add imports to NAMESPACE
  • Add fs. method to wrap repetitive code
  • Add support for numeric vector probes
  • Remove the fsStats "ks-boot" method
  • Remove fsPenalizedSVM
• 5.2-build-binary.R
  • Add imports to NAMESPACE
  • Add build. method to wrap repetitive code
  • Add support for numeric vector probes
• 7.1-plCV.R
  • Remove plCV warning
  • Add details to the "Please Read" vignette
• 7.2-plGrid.R
  • Convert plGrid warning into a message
  • Consolidate numeric probes handling
  • Add handling for a list of numeric or character probes
  • Add details to the "Please Read" vignette
• 8.1-pipe.R
  • Convert pipeFilter warning into a message
  • Add details to the "Please Read" vignette
• 9-deprecated.R
  • Contains deprecated functions
• 9-tidy.R
  • Add getArgs, defaultArg, and forceArg functions
  • Add trainingSet, validationSet, and testSet functions
  • Add modSubset wrapper for subset method

exprso 0.1.3

• 1.1-classes.R
  • Fixed warnings and notes
• 1.2-methods.R
  • Fixed warnings and notes
• 2.1-import.R
  • Fixed warnings and notes
• 2.2-misc.R
  • Code renamed to file 2.2-process.R
  • Fixed warnings and notes
• 3.1-split.R
  • Fixed warnings and notes
• 4.1-modSwap.R
  • Store mutated annotation as boolean (not factor)
  • Fixed warnings and notes
• 4.2-modCluster.R
  • Fixed warnings and notes
• 4.3-compare.R
  • Fixed warnings and notes
• 5.1-fs-binary.R
  • Fixed warnings and notes
• 5.2-build-binary.R
  • Fixed warnings and notes
• 5.3-doMulti.R
  • Fixed warnings and notes
• 6-predict.R
  • Fixed warnings and notes
• 8.1-pipe.R
  • Fixed warnings and notes
• 8.2-ens.R
  • Fixed warnings and notes
• 9-global.R
  • Contains global imports

exprso 0.1.2

• 1.2-methods.R
  • Added subset method for ExprsArray objects
  • Added subset method for ExprsPipeline objects
• 3-split.R
  • Code renamed to file 3.1-split.R
• 4-conjoin.R
  • Code renamed to file 3.2-conjoin.R
  • modMutate merged with modSwap as 4.1-modSwap.R
  • modCluster method added as 4.2-modCluster.R
  • compare method added as 4.3-compare.R
  • compare now handles ExprsMulti objects
  • compare test added to validate method
• 5.1-fs-binary.R
  • fsStats has tryCatch to address rare error

exprso 0.1.1

• 1.2-methods.R
  • summary method now accommodates lists of vector arguments
• 5.2-build-binary.R
  • Added buildDNN.ExprsBinary method
  • Removed e1071 cross-validation
• 5.3-doMulti.R
  • Added buildDNN.ExprsMulti method
• 6-build.R
  • Added buildDNN predict clause
• 7.2-plGrid.R
  • plGrid method now accommodates lists of vector arguments
  • Removed e1071 cross-validation

exprso 0.1.0

• Project now organized in a package distribution format
• 0-misc.R
  • Temporarily removed compare function
  • Code renamed to file 2.2-misc.R
• 1-classes.R
  • Code divided into files 1.1-classes.R and 1.2-methods.R
  • Remaining 1-classes.R code renamed to 4-conjoin.R
  • Removed getCases and getConts. Use [ and $ instead
  • getProbeSet extended to replace getProbeSummary
• 2-import.R
  • Code renamed to file 2.1-import.R
• 3-split.R
  • arraySubset replaced with [ and $ in 1.1-classes.R
  • splitSample code heavily edited, including an all.in bug fix
  • splitStratify now handles ExprsMulti objects
• 4-speakEasy.R
  • Temporarily removed speakEasy and abridge functions
• 5-fs.R
  • Code renamed to file 5.1-fs-binary.R
• 6-build.R
  • reRank function serializes doMulti fs added to 5.3-doMulti.R
  • fsSample and fsStats now have ExprsMulti methods
  • Some code move to 5.2-build-binary.R and 5.3-doMulti.R
  • Remaining 6-build.R code renamed to 6-predict.R
• 7-pl.R
  • Code divided into a separate file for each pl method
  • Replaced ctrlGS (ctrlGridSearch) with ctrlPL (ctrlPipeLine)
  • plCV, fixed "1-subject artifact"" with drop = FALSE
  • plNested, fixed "1-subject artifact" with drop = FALSE
  • plNested argument checks moved to separate function
• 8-ens.R
  • Code divided into files 8.1-pipe.R and 8.2-ens.R
  • Removed pipeSubset. Use [ and $ instead

tpq/exprso documentation built on July 27, 2019, 8:44 a.m.