## 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
- 7.2-plGrid.R
- 8.2-ens.R
- Pass along known class values to
ExprsPredict
result
- 9-global.R
- Find optimal import combination
- 9-tidy.R
## 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
- 1.2-methods.R
- 2.1-import.R
- 2.2-misc.R
- Code renamed to file 2.2-process.R
- Fixed warnings and notes
- 3.1-split.R
- 4.1-modSwap.R
- Store mutated annotation as boolean (not factor)
- Fixed warnings and notes
- 4.2-modCluster.R
- 4.3-compare.R
- 5.1-fs-binary.R
- 5.2-build-binary.R
- 5.3-doMulti.R
- 6-predict.R
- 8.1-pipe.R
- 8.2-ens.R
- 9-global.R
## 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