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Changelog

Source: NEWS.md

variancePartition 1.35.5

  • June 17, 2024
  • fix bug in mvTest() for se value with 1 feature

variancePartition 1.35.4

  • June 13, 2024
  • fix bug in [.MArrayLM2 dropping residuals to a vector

variancePartition 1.35.3

  • June 11, 2024
  • in mvTest() with shrink.cov = TRUE uses lambda = 0.01

variancePartition 1.35.2

  • June 6, 2024
  • in mvTest() return beta and se

variancePartition 1.35.1

  • May 31, 2024
  • version bump for BioC

variancePartition 1.33.15

variancePartition 1.33.14

  • April 19, 2024
  • in topTable() resolve issue when specifying multiple coeffs

variancePartition 1.33.13

variancePartition 1.33.12

variancePartition 1.33.11

  • Feb 7, 2024
  • fix bug in dream(...,ddf="Kenward-Roger") that gave false positives and negatives
    • scaled weights properly to fix this issue, since df in lmerTest::contest() assumes mean of weights is 1.
    • old code used unscaled weights, so df values were too large

variancePartition 1.33.10

variancePartition 1.33.9

  • Jan 25, 2024
  • bug fix in BIC() and .fitExtractVarPartModel()

variancePartition 1.33.8

variancePartition 1.33.7

variancePartition 1.33.6

  • fix issue with subsetting using logicals

variancePartition 1.33.5

  • Dec 21, 2023
  • fix issue with ddf always calling "Satterthwaite"
  • enforce subsetting of residuals in assign( "[.MArrayLM2",)
    • this comes with when rdf < 1

variancePartition 1.33.4

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

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

variancePartition 1.31.19

variancePartition 1.31.18

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

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

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

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

variancePartition 1.28.8

  • March 8, 2023
  • add mvTest() with features as list

variancePartition 1.28.7

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

variancePartition 1.27.13

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

variancePartition 1.27.9

  • bug fix in mvTest() for contrasts
    • extensive changes to vcov() in order to handle contrasts
  • fix by in subsetting MArrayLM2 object. cov.coefficients.list are now named based on gene names

variancePartition 1.27.8

variancePartition 1.27.7

variancePartition 1.27.6

  • remove FMT functions

variancePartition 1.27.5

  • update dependencies
  • make topTable() generic to work with R 4.2.1 and Bioc 3.16

variancePartition 1.27.4

  • update dependencies

variancePartition 1.27.3

  • update filtering of covariates, especially for when many samples are dropped

variancePartition 1.27.1

  • update plotPercentBars arguments

variancePartition 1.26.1

  • patch to update docs

variancePartition 1.25.13

variancePartition 1.25.12

variancePartition 1.25.11

variancePartition 1.25.9

variancePartition 1.25.8

  • small bug fixes

variancePartition 1.25.7

  • dream() now drops samples with missing data gracefully

variancePartition 1.25.6

variancePartition 1.25.5

variancePartition 1.25.4

  • in dream() set default ddf = "adaptive", which uses “KR” for less than 12 samples
  • all functions default tp BPPARAM=SerialParam()
  • add eBayes() to vignette for dream()

variancePartition 1.25.3

variancePartition 1.25.2

variancePartition 1.25.1

variancePartition 1.23.6

  • update calcVarPart() with argument scale=TRUE allowing the user to disable scaling to fractions

variancePartition 1.23.5

  • use RhpcBLASctl::omp_set_num_threads(1) to use only 1 OpenMP thread for linear algebra within each BiocParallel process
  • update dream() so useWeights=FALSE works with lmFit()

variancePartition 1.23.4

variancePartition 1.23.3

  • add calcVarPart() support for a range of GLM/GLMM’s

variancePartition 1.23.2

  • add flag to checkModelStatus() so warnings are thrown immediately
  • fix export of as.data.frame
  • fixed issues where messages were printed even if quiet=TRUE

variancePartition 1.23.1

  • New freeze for Bioconductor devel branch

variancePartition 1.21.10

  • add suppressWarnings flag to makeContrastsDream()
  • ensure that z.std is finite

variancePartition 1.21.9

  • fix bug with makeContrastsDream()

variancePartition 1.21.8

  • update dream vignette
  • update documentation for makeContrastsDream()
  • fix error in rdf_from_matrices() with eigen() failing

variancePartition 1.21.7

variancePartition 1.21.6

  • in dream() allow L to be NULL

variancePartition 1.21.5

  • Fix roxygen2 documentation to pass R CMD check

variancePartition 1.21.4

variancePartition 1.21.3

variancePartition 1.21.2

  • Reduce size of data passed to each thread by only including variables used in the formula. Applies to multiple functions
  • add more unit tests

variancePartition 1.21.1

  • fix issue with dream and random slopes

variancePartition 1.19.20

  • fix bug discovered when the number of features is less than the number of chunks in iterBatch()

variancePartition 1.19.19

  • simple bug fixes to pass R CMD check

variancePartition 1.19.18

  • simplify calcVarPart for lm and lmer. Add compatibility for glm
  • Simplify checkModelStatus.merMod to allow formula (A|B) where A is continuous
  • remove unused “adjust” arguments for clarity

variancePartition 1.19.17

  • add get_prediction() for results of lm()
  • improve documentation of get_prediction()

variancePartition 1.19.16

  • in canCorPairs() change statistic used to summarize CCA to Cramer’s V. The difference is very subtle, but is now based on first principles.
  • in dream, check that data is a data.frame
  • dream() defaults to computeResiduals=TRUE for compatability with zenith

variancePartition 1.19.14

  • fix issue with residuals() where examples fail

variancePartition 1.19.13

variancePartition 1.19.12

  • Improve documentation for contrasts in dream.Rmd
  • check that contrasts sum to zero in plotContrasts.

variancePartition 1.19.11

variancePartition 1.19.10

variancePartition 1.19.7

  • Round numbers in plotContrasts()
  • 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)) $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()

variancePartition 0.0.3

  • add residuals function
  • add fitExtractVarPartModel()
  • foreach loops us iterators

variancePartition 0.99.0

  • Initial version