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handle case where a single contrasts fails in makeContrastsDream()
variancePartition 1.33.3
Dec 5, 2023
in residuals() when dividing by sqrt(1-hatvalues) add small offset to make sure the value is positive
variancePartition 1.33.2
Nov 13, 2023
add augmentPriorCount()
add prior.count argument to voomWithDreamWeights() and feed it to augmentPriorCount()
variancePartition 1.33.1
Nov 2, 2023
move omp_set_num_threads() deeper in nesting
variancePartition 1.31.22
Oct 19, 2023
fix handling of variables with missing data
return fit$genes properly
variancePartition 1.31.21
Oct 16, 2023
handle weights properly when the linear mixed model fails for some genes
lmFit() and
in iterRows() set scale = FALSE as default
in voomWithDreamWeights(), scale in input weights and weights in side fitVarPartModel()
get weights estimated most similar to voomLmFit()
in dream() use rescaleWeights = FALSE to get sigma estimates compatable with lmFit()
variancePartition 1.31.20
Sept 26, 2023
allow weights to be a matrix in voomWithDreamWeights()
variancePartition 1.31.19
Sept 22, 2023
add rescaleWeightsAfter argument to voomWithDreamWeights()
variancePartition 1.31.18
Sept 5, 2023
improved error handling for fitVarPartModel(), fitExtractVarPartModel(), and voomWithDreamWeights()
variancePartition 1.31.16
August 18, 2023
in dream(), if "Kenward-Roger" is specified but gives covariance matrix that has poor condition number or is not positive definite, then fall back to "Satterthwaite" for hypothesis testing in linear mixed models
Update documentation, and reformat code
variancePartition 1.31.15
August 10, 2023
fit = dream() now returns fit$loglik (the log-likelihood for each gene), and fit$edf (the effective degreees of freedom for each gene)
variancePartition 1.31.13
August 7, 2023
fix bug in calcVarPart() where weights was ignored in some cases
add additional tests to check this
variancePartition 1.31.12
July 3, 2023
makeContrastsDream() converts NAcontrasts to NULL
variancePartition 1.31.11
setting voomWithDreamWeights(..., span="auto") now estimates tuning parameter from data using fANCOVA::loess.as()
variancePartition 1.31.10
filterInputData() now ensures EList contains a matrix
variancePartition 1.31.9
Fix issue in mvTest() when specifying features with strings
variancePartition 1.31.8
Fix error message when linear mixed model fails
variancePartition 1.31.7
update mvTest() to run in parallel
variancePartition 1.31.6
update mvTest() to include Hotelling T2 test and LS.empirical()
variancePartition 1.31.1
June 4, 2023
Rename for Bioconductor compatability
variancePartition 2.0.5
May 31, 2023
fix convergence issues
fix initialization of lmer() fit
use 1 OMP thread internally, then restore to original value
variancePartition 2.0.4
May 30, 2023
When running dream(), ensure model convergence using second fitting with Nelder_Mead to avoid edge cases where the approximate hessian from lmerTest::as_lmerModLT() has a negative eigenvalue
fix issue in get_prediction() returning NA values when variables modeled as categorical and levels are omitted
fix issue in voomWithDreamWeights() when some genes don't converge
retry lmer() model fit with another optimizer after it fails convergence test.
variancePartition 2.0.3
May 13, 2023
fix vcov()
variancePartition 2.0.2
May 17, 2023
add matrix argument to mvTest()
variancePartition 2.0.1
May 12, 2023
mvTest() now shrinks covariance using the Schafer-Strimmer method
vcovSqrt() returns the matrix whose cross product gives the vcov() result from fits with dream()
variancePartition 2.0.0
April 20, 2023
Major code refactoring to:
improve code reuse
simplify debugging and maintaining code
simplify addition of new features
improve error handling
some linear mixed model analyses are 50% faster
enable additional features for dreamlet package that depends heavily on variancePartition.
variancePartition 1.29.2
Rescale weights
variancePartition 1.28.9
March 14, 2023
fix rounding error in makeContrastsDream()
add Pearson residuals to residuals()
variancePartition 1.28.8
March 8, 2023
add mvTest() with features as list
variancePartition 1.28.7
March 7, 2023
Fix bug in makeContrastsDream() by adding droplevels()
variancePartition 1.28.6
March 1, 2023
diffVar() now fits contrasts estimated in first step
variancePartition 1.28.5
Feb 24, 2023
Fix error in vcov() when samples are dropped due to covariate having NA value
variancePartition 1.28.4
Feb 2, 2023
Improve documentation for contrasts
variancePartition 1.28.3
Jan 19, 2023
Improve checking and documentation for contrasts
variancePartition 1.28.2
Jan 13, 2023
canCorPairs() now allows random effects in formula
but won't change results
variancePartition 1.28.1
Jan 04, 2023
bug fixes
variancePartition 1.27.17
in mvTest(), more consistent return values when one features is used
variancePartition 1.27.16
bug fix
variancePartition 1.27.15
fix approximation for vcov()
add checks for vcov() in test_vcov2()
variancePartition 1.27.14
fix bug in topTable()
add deviance()
update docs
update sqrtMatrix() to have positive diagonal
variancePartition 1.27.13
add diffVar() test of differential variance
dream() now returns formula, data, and hatvalues
define hatvalues() for result of dream()
variancePartition 1.27.12
in mvTest():
default method is now "FE"
variancePartition 1.27.11
in mvTest():
return number of features
return stat.FE and stat.het for RE2C
return NA for stat if 1 feature
variancePartition 1.27.10
Add check for very large weights in voomWithDreamWeights()
fix issues with strings are passed to formula arguments
variancePartition 1.19.6
New gives meaning full error message for dream(), etc when variable is not found in data.
variancePartition 1.19.5
Better error catching when running fitVarPartModel() with fxn that fails
add get_prediction() function
the following code now can be run in parallel
fitList = fitVarPartModel( Y, ~ (1|Batch), data, fxn = function(fit){
B = variancePartition::get_prediction(fit, ~(1|Batch))
fit@resp$y - B
}, BPPARAM=SnowParam(3))
variancePartition 1.19.4
Update vignette #3, and update documentation of REML argument
variancePartition 1.19.3
add new FAQ.Rmd
variancePartition 1.19.2
canCorPairs() now returns NA correlation when two variables have
no overlapping observed values
plotCorrMatrix() now handles NA correlation values
variancePartition 1.19.1
Bump to next Bioconductor version
variancePartition 1.18.3
Improve documentation
move location of eBayesFMT code
variancePartition 1.18.2
Clean up some code and add documentation
document ebayesFMT
variancePartition 1.18.1
Clean up some code and add documentation
compute effective degrees of freedom for each model
variancePartition 1.18.0
Bioconductor freeze
variancePartition 1.17.10
fix issue returning residuals from limma
resolve issue where dream gives error: r[cbind(1L:p, 1L:p)] <- 1 : subscript out of bounds
only occured when no fixed effects were used
variancePartition 1.17.9
Fix issues with compatability with R/4.0.0
variancePartition 1.17.8
Better error message when response contains missing data
variancePartition 1.17.7
Better error message when variable in formula does not exist
variancePartition 1.17.6
comply with new Bioconductor check: R_CHECK_LENGTH_1_LOGIC2
variancePartition 1.17.5
if contrasts for dream() is data.frame, convert to matrix
variancePartition 1.17.4
Don't print warnings for residuals() when only one argument passed.
fix bug with residuals evaluated with only fixed effects
variancePartition 1.17.3
Allow sparseMatrix for gene expression. Now saves memory by avoiding conversion to matrix. Processing sparseMatrix will be slower, but memory usage will be low.
dream(..., computeResiduals=TRUE) now computes residuals and allows use of residuals() function
variancePartition 1.17.2
fix error in voomWithDreamWeights() when design matrix is null
variancePartition 1.17.1
topTable(...,sort.by=) now is correct when and F-test is used
fixed issue in classifyTestsF.MArrayLM2, now is much faster
variancePartition 1.15.8
Replace cat() with message()
add quiet option to a few functions
dream() does not call eBayes() when lmFit is used
variancePartition 1.15.7
Official release to development branch
variancePartition 1.15.6
fix convergence errror when recycling parameters values from first gene
add column z.std and F.std to topTable
variancePartition 1.15.4
Add error message when scale of fixed effects causes a problem
variancePartition 1.15.3
Try changing order of eBayes
variancePartition 1.15.2
Update vignette
variancePartition 1.15.0
Push changes to Bioconductor devel
variancePartition 1.13.11
Fixed bug in voomWithDreamWeights() with approxfun() with ties
variancePartition 1.13.10
fix parallel processing issues
variancePartition 1.13.9
update vignette for new parallel processing backend
variancePartition 1.13.8
apply empirical Bayes when doing F-test
hypothesis testing for single coefficients is now included by default, so only need to specify contrast matrix if for more complicated contrasts
add voomWithDreamWeights() for computing observation weights using random effects
Add BiocParallel capability with BPPARAM argument
allows parallel processing with lower memory usage
dream() is now compatable with gene set enrichments from pinnacle (software comming soon)
variancePartition 1.13.7
in dream(), add support for genes annotation in DGElist()
in dream(), automatically evaluate contrasts for all single coefficients
add future compatability for gene set enrichments method "pinnacle"
variancePartition 1.13.5
add plotContrasts() to dream vignette
variancePartition 1.13.4
export classes to fix bug with class "varPartResults" not being defined
Thanks Megan Behringer
variancePartition 1.13.3
add plotContrasts()
variancePartition 1.13.2
Enable random slope models in dream, but not for estimating variance fractions
Thanks Jonas Zierer
variancePartition 1.13.1
Add progress bar at ETA
=======
variancePartition 1.12.4
Update dream vignette
variancePartition 1.12.3
o add plotContrasts()
o Enable random slope models in dream, but not for estimating variance fractions
o export classes to fix bug with class "varPartResults" not being defined
- Thanks Megan Behringer
variancePartition 1.11.13
Fix multithreading issue
variancePartition 1.11.11
dream can handle multiple contrasts at the same time
variancePartition 1.11.10
fix typos in dream vignette
variancePartition 1.11.8
Check and stop() if response variable has variance of 0
in dream(), fitExtractVarPartModel(), and fitVarPartModel()
add standardized_t_stat() implicitly in eBayes() using MArrayLM2 class
this transforms moderated t-statistics to have same degrees of freedom
variancePartition 1.11.7
Simplify object return by dream to be more more similar to lmFit
now returns MArrayLM instead of MArrayLMM_lmer
if a fixed effects formula is specified (i.e. not random terms)
dream call lmFit in the backend
getContrast() works seamlessly
dream() now returns gene annotation if passed to function
variancePartition 1.11.6
add error checing for L in dream
fix typoes in dream vignette
fix typoes in theory_practice_random_effects.Rnw
variancePartition 1.11.5
Add dream function for differential expression for repeated measures with a linear mixed model
variancePartition 1.11.2
Add warnings to canCorPairs for colinear terms
variancePartition 1.11.1
Add vignette: theory_practice_random_effects.Rnw
variancePartition 1.9.9
Fix issue when package is autoloaded when starting R
variancePartition 1.9.8
o Fix issue where if info data.frame contained a column name "gene",
fitExtractVarPartModel() would not run
variancePartition 1.9.6
o Fix tximport issue with eval=FALSE
variancePartition 1.9.2
o Fix vignette
variancePartition 1.9.1
o Fix formatting of vignette
o add description of canCorPairs() function
variancePartition 1.5.7
include splines in foreach .packages
variancePartition 1.5.6
compatibility with tximport v1.3.5
variancePartition 1.5.5
Decrease computing time of effective sample size with ESS() by additional ~10x with sparse solver
fix margins for plotPercentBars()
Fix bug for getVarianceComponents() when correlated continous variables are included
compatibility with ggplot2 2.2.0
center plot titles
fix order of bars in plotPercentBars()
legend background to transparent
set text to be black
include lme4 in foreach .packages
change residuals color to not be transparent
add CITATION information
plotCorrMatrix now shows dendrogram by default
Estimate run time for fitExtractVarPartModel() / fitVarPartModel()
improve warnings for plotPercentBar()
improve warnings for plotCorrStructure()
define ylab for plotVarPart()
add as.matrix.varPartResults() (hidden)
define isVaryingCoefficientModel() (hidden)
variancePartition 1.3.11
in canCorPairs() and other functions, convert formula with as.formula()
improve error messages for canCorPairs()
variancePartition 1.3.10
Add plotStratify()
Update documentation
variancePartition 1.3.8
Add additional examples to vignette
show projected memory usage of fitVarPartModel()
variancePartition 1.3.7
fitVarPartModel warns if names in exprObj and data are not identical
residuals() and other functions deal with missing values properly
variancePartition 1.3.6
Small changes to vignette
variancePartition 1.3.5
Fix Bioconductor error
variancePartition 1.3.4
Fix typos
variancePartition 1.3.3
Improve documentation
variancePartition 1.1.9
Update sortCols to handle Measurement.error
change backend package structure
set Residuals to be grey by default in plotVarPart() and plotPercentBars()
add control = lme4::lmerControl(calc.derivs=FALSE, check.rankX="stop.deficient" )
add plotCorrStructure
variancePartition 1.1.8
Add ESS.R
Add fitVarTest.R
use lmerTest by default
fix bug checkModelStatus() for variables with backticks in name
variancePartition 1.1.7
GPL License
variancePartition 1.1.6
Move packages from Depends to Imports
For clarity, replace = with <- in parts of examples and vignette
Stop cluster in examples to solve error on Windows machines
variancePartition 1.1.5
Stop cluster in vignette to solve error on Windows machines
variancePartition 1.1.4
Fix Bioconductor check error
variancePartition 1.1.3
o Add details to vignette
Fix ggplot2 compatibility issues
variancePartition 1.1.2
Add details to vignette
variancePartition 1.1.1
add plotPercentBars() to vizualize variance fractions for a subset of genes
add ESS() to compute effective sample size
fix x.labels argument in plotStratifyBy(). Previously, this argument was not used correctly
variancePartition 1.0.0
Release to Bioconductor 3.2
variancePartition 0.99.9
add legend argument to plotStratifyBy()
improve warnings / errors for varying coefficient models
allow user to manually adjust cutoff for determining when design matrix is singular
changed default cutoff to 0.999 from 0.99
variancePartition 0.99.8
improve warnings / errors when design matrix is close to or exactly singular
variancePartition 0.99.7
added new class varPartResults to store results of fitExtractVarPartModel() and extractVarPart()
the user will not notice any change, only the backend is different
o Allow computation of adjusted ICC in addition to ICC.
add warning when categorical variables are modeled as fixed effects
fix computation of variance fractions for varying coefficient models
add getVarianceComponents() to return variances from lmer() or lm() model fit
showWarnings=FALSE suppresses warning messages
add fxn argument to fitVarPartModel to evaluate any function on the model fit
variancePartition 0.99.6
Update DESCRIPTION information
variancePartition 0.99.5
residuals deals with missing data gracefully and returns a matrix
variancePartition 0.99.4
o add documentation for example datasets
o convert calcVarPart() to S4 from S3 function call
o fix typos in vignette
variancePartition 0.99.3
o fitVarPartModel() and fitExractVarPartModel() use S4 instead of S3 calls
variancePartition 0.99.2
rename sort.varParFrac to sortCols
support ExpressionSet
change options for plotStratifyBy()
variancePartition 0.0.12
add plotStratifyBy()
update documentation
variancePartition 0.0.11
fix sort to work on correct argument
variancePartition 0.0.10
fitExtractVarPartModel() and fitVarPartModel() now take subset argument
throw warning when no Intercept is specified
if using lmer, warning if categorical variable is modeled as fixed effect
fixed calcVarPart bug with reporting too few variances for multicategory fixed effects
add colinearityScore
variancePartition 0.0.9
o function now use the precision weights when specified
remove warning about unspecified weights, when useWeights=TRUE
fix issue with sort with only one variable
add main argument to plotVarPart
variancePartition 0.0.8
o Bug update to vignette and simulated data
variancePartition 0.0.7
remove 'variable' from xlab of plotVarPart
variancePartition 0.0.6
set REML=FALSE to default. This fixes issues of inaccurate variance estiamtes, and makes lmer() results more concordant with lm() results
Fix residuals function when lm or lmer is used
fix useWeights argument error for fitExtractVarPartModel()
variancePartition 0.0.5
o plotVarPart() as ylim=c(0,100) as default, and can be changed by user
fitExtractVarPartModel() labels rows correctly
variancePartition 0.0.4
Add sort() for output of extractVarPart() or fitExtractVarPartModel()