CHANGES IN VERSION 1.19.20
--------------------------
o fix bug discovered when the number of features is less than the number of chunks in iterBatch()
CHANGES IN VERSION 1.19.19
--------------------------
o simple bug fixes to pass R CMD check
CHANGES IN VERSION 1.19.18
--------------------------
o simplify calcVarPart for lm and lmer. Add compatibility for glm
o Simplify checkModelStatus.merMod to allow formula (A|B) where A is continuous
o remove unused "adjust" arguments for clarity
CHANGES IN VERSION 1.19.17
--------------------------
o add get_prediction() for results of lm()
o improve documentation of get_prediction()
CHANGES IN VERSION 1.19.16
--------------------------
o in canCorPairs() change statistic used to summarize CCA to Cramer's V. The difference is very subtle, but is now based on first principles.
o in dream, check that data is a data.frame
o dream() defaults to computeResiduals=TRUE for compatability with zenith
CHANGES IN VERSION 1.19.14
--------------------------
o fix issue with residuals() where examples fail
CHANGES IN VERSION 1.19.13
--------------------------
o fix issues with residuals()
- https://github.com/GabrielHoffman/variancePartition/issues/18
o fix issue exporting eBayes, topTable, etc
CHANGES IN VERSION 1.19.12
--------------------------
o Improve documentation for contrasts in dream.Rmd
o check that contrasts sum to zero in plotContrasts.
CHANGES IN VERSION 1.19.11
--------------------------
o in voomWithDreamWeights() fix issue with not defining design
- https://github.com/GabrielHoffman/variancePartition/issues/17
CHANGES IN VERSION 1.19.10
--------------------------
o in voomWithDreamWeights() fix issue with returning design matrix
o better error if counts can't be converted to matrix
- https://github.com/GabrielHoffman/variancePartition/issues/15
CHANGES IN VERSION 1.19.7
-------------------------
o Round numbers in plotContrasts()
o fix issues with strings are passed to formula arguments
CHANGES IN VERSION 1.19.6
-------------------------
o New gives meaning full error message for dream(), etc when variable is not found in data.
CHANGES IN VERSION 1.19.5
-------------------------
o Better error catching when running fitVarPartModel() with fxn that fails
o 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))
CHANGES IN VERSION 1.19.4
-------------------------
o Update vignette #3, and update documentation of REML argument
CHANGES IN VERSION 1.19.3
-------------------------
o add new FAQ.Rmd
CHANGES IN VERSION 1.19.2
-------------------------
o canCorPairs() now returns NA correlation when two variables have
no overlapping observed values
o plotCorrMatrix() now handles NA correlation values
CHANGES IN VERSION 1.19.1
-------------------------
o Bump to next Bioconductor version
CHANGES IN VERSION 1.18.3
-------------------------
o Improve documentation
o move location of eBayesFMT code
CHANGES IN VERSION 1.18.2
-------------------------
o Clean up some code and add documentation
o document ebayesFMT
CHANGES IN VERSION 1.18.1
-------------------------
o Clean up some code and add documentation
o compute effective degrees of freedom for each model
CHANGES IN VERSION 1.18.0
-------------------------
o Bioconductor freeze
CHANGES IN VERSION 1.17.10
-------------------------
o fix issue returning residuals from limma
CHANGES IN VERSION 1.17.10
-------------------------
o 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
CHANGES IN VERSION 1.17.9
-------------------------
o Fix issues with compatability with R/4.0.0
CHANGES IN VERSION 1.17.8
-------------------------
o Better error message when response contains missing data
CHANGES IN VERSION 1.17.7
-------------------------
o Better error message when variable in formula does not exist
CHANGES IN VERSION 1.17.6
-------------------------
o comply with new Bioconductor check: _R_CHECK_LENGTH_1_LOGIC2_
CHANGES IN VERSION 1.17.5
-------------------------
o if contrasts for dream() is data.frame, convert to matrix
CHANGES IN VERSION 1.17.4
-------------------------
o Don't print warnings for residuals() when only one argument passed.
o fix bug with residuals evaluated with only fixed effects
CHANGES IN VERSION 1.17.3
-------------------------
o Allow sparseMatrix for gene expression. Now saves memory by avoiding conversion to matrix. Processing sparseMatrix will be slower, but memory usage will be low.
o dream(..., computeResiduals=TRUE) now computes residuals and allows use of residuals() function
CHANGES IN VERSION 1.17.2
-------------------------
o fix error in voomWithDreamWeights() when design matrix is null
CHANGES IN VERSION 1.17.1
-------------------------
o topTable(...,sort.by=) now is correct when and F-test is used
o fixed issue in classifyTestsF.MArrayLM2, now is much faster
CHANGES IN VERSION 1.15.8
-------------------------
o Replace cat() with message()
o add quiet option to a few functions
o dream() does not call eBayes() when lmFit is used
CHANGES IN VERSION 1.15.7
-------------------------
o Official release to development branch
CHANGES IN VERSION 1.15.6
-------------------------
o fix convergence errror when recycling parameters values from first gene
o add column z.std and F.std to topTable
CHANGES IN VERSION 1.15.4
-------------------------
o Add error message when scale of fixed effects causes a problem
CHANGES IN VERSION 1.15.3
-------------------------
o Try changing order of eBayes
CHANGES IN VERSION 1.15.2
-------------------------
o Update vignette
CHANGES IN VERSION 1.15.0
-------------------------
o Push changes to Bioconductor devel
CHANGES IN VERSION 1.13.11
-------------------------
o Fixed bug in voomWithDreamWeights() with approxfun() with ties
CHANGES IN VERSION 1.13.10
-------------------------
o fix parallel processing issues
CHANGES IN VERSION 1.13.9
-------------------------
o update vignette for new parallel processing backend
CHANGES IN VERSION 1.13.8
-------------------------
o apply empirical Bayes when doing F-test
o hypothesis testing for single coefficients is now included by default, so only need to specify contrast matrix if for more complicated contrasts
o add voomWithDreamWeights() for computing observation weights using random effects
o Add BiocParallel capability with BPPARAM argument
- allows parallel processing with lower memory usage
o dream() is now compatable with gene set enrichments from pinnacle (software comming soon)
CHANGES IN VERSION 1.13.7
-------------------------
o in dream(), add support for genes annotation in DGElist()
o in dream(), automatically evaluate contrasts for all single coefficients
o add future compatability for gene set enrichments method "pinnacle"
CHANGES IN VERSION 1.13.5
-------------------------
o add plotContrasts() to dream vignette
CHANGES IN VERSION 1.13.4
-------------------------
o export classes to fix bug with class "varPartResults" not being defined
o Thanks Megan Behringer
CHANGES IN VERSION 1.13.3
-------------------------
o add plotContrasts()
CHANGES IN VERSION 1.13.2
-------------------------
o Enable random slope models in dream, but not for estimating variance fractions
o Thanks Jonas Zierer
CHANGES IN VERSION 1.13.1
-------------------------
o Add progress bar at ETA
=======
CHANGES IN VERSION 1.12.4
-------------------------
o Update dream vignette
CHANGES IN VERSION 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
CHANGES IN VERSION 1.11.13
-------------------------
o Fix multithreading issue
CHANGES IN VERSION 1.11.11
-------------------------
o dream can handle multiple contrasts at the same time
CHANGES IN VERSION 1.11.10
-------------------------
o fix typos in dream vignette
CHANGES IN VERSION 1.11.8
-------------------------
o Check and stop() if response variable has variance of 0
- in dream(), fitExtractVarPartModel(), and fitVarPartModel()
o add standardized_t_stat() implicitly in eBayes() using MArrayLM2 class
- this transforms moderated t-statistics to have same degrees of freedom
CHANGES IN VERSION 1.11.7
-------------------------
o Simplify object return by dream to be more more similar to lmFit
- now returns MArrayLM instead of MArrayLMM_lmer
o if a fixed effects formula is specified (i.e. not random terms)
- dream call lmFit in the backend
- getContrast() works seamlessly
o dream() now returns gene annotation if passed to function
CHANGES IN VERSION 1.11.6
-------------------------
o add error checing for L in dream
o fix typoes in dream vignette
o fix typoes in theory_practice_random_effects.Rnw
CHANGES IN VERSION 1.11.5
-------------------------
o Add dream function for differential expression for repeated measures with a linear mixed model
CHANGES IN VERSION 1.11.2
-------------------------
o Add warnings to canCorPairs for colinear terms
CHANGES IN VERSION 1.11.1
-------------------------
o Add vignette: theory_practice_random_effects.Rnw
CHANGES IN VERSION 1.9.9
-------------------------
o Fix issue when package is autoloaded when starting R
CHANGES IN VERSION 1.9.8
-------------------------
o Fix issue where if info data.frame contained a column name "gene",
fitExtractVarPartModel() would not run
CHANGES IN VERSION 1.9.6
-------------------------
o Fix tximport issue with eval=FALSE
CHANGES IN VERSION 1.9.2
-------------------------
o Fix vignette
CHANGES IN VERSION 1.9.1
-------------------------
o Fix formatting of vignette
o add description of canCorPairs() function
CHANGES IN VERSION 1.5.7
-------------------------
o include splines in foreach .packages
CHANGES IN VERSION 1.5.6
-------------------------
o compatibility with tximport v1.3.5
CHANGES IN VERSION 1.5.5
-------------------------
o Decrease computing time of effective sample size with ESS() by additional ~10x with sparse solver
o fix margins for plotPercentBars()
o Fix bug for getVarianceComponents() when correlated continous variables are included
o compatibility with ggplot2 2.2.0
o center plot titles
o fix order of bars in plotPercentBars()
o legend background to transparent
o set text to be black
o include lme4 in foreach .packages
o change residuals color to not be transparent
o add CITATION information
o plotCorrMatrix now shows dendrogram by default
o Estimate run time for fitExtractVarPartModel() / fitVarPartModel()
o improve warnings for plotPercentBar()
o improve warnings for plotCorrStructure()
o define ylab for plotVarPart()
- add as.matrix.varPartResults() (hidden)
- define isVaryingCoefficientModel() (hidden)
CHANGES IN VERSION 1.3.11
-------------------------
o in canCorPairs() and other functions, convert formula with as.formula()
o improve error messages for canCorPairs()
CHANGES IN VERSION 1.3.10
-------------------------
o Add plotStratify()
o Update documentation
CHANGES IN VERSION 1.3.8
-------------------------
o Add additional examples to vignette
o show projected memory usage of fitVarPartModel()
CHANGES IN VERSION 1.3.7
-------------------------
o fitVarPartModel warns if names in exprObj and data are not identical
o residuals() and other functions deal with missing values properly
CHANGES IN VERSION 1.3.6
-------------------------
o Small changes to vignette
CHANGES IN VERSION 1.3.5
-------------------------
o Fix Bioconductor error
CHANGES IN VERSION 1.3.4
-------------------------
o Fix typos
CHANGES IN VERSION 1.3.3
-------------------------
o Improve documentation
CHANGES IN VERSION 1.1.9
-------------------------
o Update sortCols to handle Measurement.error
o change backend package structure
o set Residuals to be grey by default in plotVarPart() and plotPercentBars()
o add control = lme4::lmerControl(calc.derivs=FALSE, check.rankX="stop.deficient" )
o add plotCorrStructure
CHANGES IN VERSION 1.1.8
-------------------------
o Add ESS.R
o Add fitVarTest.R
o use lmerTest by default
o fix bug checkModelStatus() for variables with backticks in name
CHANGES IN VERSION 1.1.7
-------------------------
o GPL License
CHANGES IN VERSION 1.1.6
-------------------------
o Move packages from Depends to Imports
o For clarity, replace = with <- in parts of examples and vignette
o Stop cluster in examples to solve error on Windows machines
CHANGES IN VERSION 1.1.5
-------------------------
o Stop cluster in vignette to solve error on Windows machines
CHANGES IN VERSION 1.1.4
-------------------------
o Fix Bioconductor check error
CHANGES IN VERSION 1.1.3
-------------------------
o Add details to vignette
o Fix ggplot2 compatibility issues
CHANGES IN VERSION 1.1.2
-------------------------
o Add details to vignette
CHANGES IN VERSION 1.1.1
-------------------------
o add plotPercentBars() to vizualize variance fractions for a subset of genes
o add ESS() to compute effective sample size
o fix x.labels argument in plotStratifyBy(). Previously, this argument was not used correctly
CHANGES IN VERSION 1.0.0
-------------------------
o Release to Bioconductor 3.2
CHANGES IN VERSION 0.99.9
-------------------------
o add legend argument to plotStratifyBy()
o improve warnings / errors for varying coefficient models
o allow user to manually adjust cutoff for determining when design matrix is singular
- changed default cutoff to 0.999 from 0.99
CHANGES IN VERSION 0.99.8
-------------------------
o improve warnings / errors when design matrix is close to or exactly singular
CHANGES IN VERSION 0.99.7
-------------------------
o 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.
o add warning when categorical variables are modeled as fixed effects
o fix computation of variance fractions for varying coefficient models
o add getVarianceComponents() to return variances from lmer() or lm() model fit
o showWarnings=FALSE suppresses warning messages
o add fxn argument to fitVarPartModel to evaluate any function on the model fit
CHANGES IN VERSION 0.99.6
-------------------------
o Update DESCRIPTION information
CHANGES IN VERSION 0.99.5
-------------------------
o residuals deals with missing data gracefully and returns a matrix
CHANGES IN VERSION 0.99.4
-------------------------
o add documentation for example datasets
o convert calcVarPart() to S4 from S3 function call
o fix typos in vignette
CHANGES IN VERSION 0.99.3
-------------------------
o fitVarPartModel() and fitExractVarPartModel() use S4 instead of S3 calls
CHANGES IN VERSION 0.99.2
-------------------------
o rename sort.varParFrac to sortCols
o support ExpressionSet
o change options for plotStratifyBy()
# Before Bioconductor submission
CHANGES IN VERSION 0.0.12
-------------------------
o add plotStratifyBy()
o update documentation
CHANGES IN VERSION 0.0.11
-------------------------
o fix sort to work on correct argument
CHANGES IN VERSION 0.0.10
-------------------------
o fitExtractVarPartModel() and fitVarPartModel() now take subset argument
o throw warning when no Intercept is specified
o if using lmer, warning if categorical variable is modeled as fixed effect
o fixed calcVarPart bug with reporting too few variances for multicategory fixed effects
o add colinearityScore
CHANGES IN VERSION 0.0.9
-------------------------
o function now use the precision weights when specified
o remove warning about unspecified weights, when useWeights=TRUE
o fix issue with sort with only one variable
o add main argument to plotVarPart
CHANGES IN VERSION 0.0.8
-------------------------
o Bug update to vignette and simulated data
CHANGES IN VERSION 0.0.7
-------------------------
o remove 'variable' from xlab of plotVarPart
CHANGES IN VERSION 0.0.6
-------------------------
o set REML=FALSE to default. This fixes issues of inaccurate variance estiamtes, and makes lmer() results more concordant with lm() results
o Fix residuals function when lm or lmer is used
o fix useWeights argument error for fitExtractVarPartModel()
CHANGES IN VERSION 0.0.5
-------------------------
o plotVarPart() as ylim=c(0,100) as default, and can be changed by user
o fitExtractVarPartModel() labels rows correctly
CHANGES IN VERSION 0.0.4
-------------------------
o Add sort() for output of extractVarPart() or fitExtractVarPartModel()
CHANGES IN VERSION 0.0.3
-------------------------
o add residuals function
o add fitExtractVarPartModel()
o foreach loops us iterators
CHANGES IN VERSION 0.99.0
-------------------------
o Initial version