NEWS.md

In GabrielHoffman/variancePartition: Quantify and interpret drivers of variation in multilevel gene expression experiments

variancePartition 1.36.3

• Jan 2, 2025
• examine adding REDUCE = c to bpiterate()
• fix issue mvTest() for test of single coefficient

variancePartition 1.36.2

• Nov 7, 2024
• fix docs

variancePartition 1.36.1

• Nov 5, 2024
• Upgrade to Bioc 3.20
• update generic for eBayes() to be comptabile with legacy parameter added in limma v3.62.0

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

• May 16, 2024
• in voomWithDreamWeights(), default changed to rescaleWeightsAfter = FALSE

variancePartition 1.33.14

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

variancePartition 1.33.13

• April 6, 2024
• in voomWithDreamWeights(), add argument prior.count.for.weights

variancePartition 1.33.12

• March 22, 2024
• Fix use with voomWithDreamWeights() taking raw counts
• https://github.com/GabrielHoffman/variancePartition/issues/97
• in voomWithDreamWeights(), add argument priorWeightsAsCounts=FALSE and prior.count.for.weights

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

• Feb 5, 2024
• in augmentPriorCount() and voomWithDreamWeights(), add argument scaledByLib=FALSE

variancePartition 1.33.9

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

variancePartition 1.33.8

• Jan 22, 2024
• add BIC() for result of dream() and lmFit()

variancePartition 1.33.7

• Jan 19, 2024
• add logLik() for result of dream() and lmFit()

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

• Dec 13, 2023
• fix bug with BiocParallel in Windows
• https://github.com/GabrielHoffman/variancePartition/issues/91
• 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 NA contrasts 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()
• follows bug report: https://github.com/GabrielHoffman/variancePartition/issues/66
• in mvTest() change option "LS" to "FE"

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

• bug fix in mvTest()

variancePartition 1.27.7

• add vcov() for results from dream()
• add mvTest() for multivariate tests on results from dream() using vcov()

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

• Fix compatibility issue with lme4 1.1.29
• reported https://github.com/GabrielHoffman/variancePartition/issues/51

variancePartition 1.25.12

• in makeContrastsDream(), fix issue where terms with colon cause and error

variancePartition 1.25.11

• fix bug in dream() for variables with NA values
• improve handling of invalid contrasts in makeContrastsDream()

variancePartition 1.25.9

• for getContrast() and makeContrastsDream() make sure formula argument is a formula and not a string

variancePartition 1.25.8

• small bug fixes

variancePartition 1.25.7

• dream() now drops samples with missing data gracefully

variancePartition 1.25.6

• fix small plotting bug in plotStratify() and plotStratifyBy()

variancePartition 1.25.5

• add getTreat() to evaluate treat()/topTreat() seamlessly on results of dream()

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

• add genes argument to plotPercentBars()

variancePartition 1.25.2

• change plotPercentBars() to use generic S4

variancePartition 1.25.1

• update handling of weights in voomWithDreamWeights() and add applyQualityWeights()

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

• convert some warnings to errors
• add proper handling of weights to voomWithDreamWeights()

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

• Merge changes to contrast code: https://github.com/GabrielHoffman/variancePartition/pull/32
• Merge improvments to error checking: https://github.com/GabrielHoffman/variancePartition/pull/28
• New warning/error if variables in formula have missing data
• add makeContrastsDream()

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

• variance fractions for fixed effects model is now computed using new method
• fixes subtle issue with previous version where estimates dependend on of terms in the formula
• https://github.com/GabrielHoffman/variancePartition/issues/30
• Update documentation

variancePartition 1.21.3

• Faster aggregration after running multiple threads
• Pulled from https://github.com/GabrielHoffman/variancePartition/pull/27
• by Ryan C. Thompson
• eBayes() now works with dream for linear mixed models
• add rdf.merMod

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

• fix issues with residuals()
• https://github.com/GabrielHoffman/variancePartition/issues/18
• fix issue exporting eBayes, topTable, etc

variancePartition 1.19.12

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

variancePartition 1.19.11

• in voomWithDreamWeights() fix issue with not defining design
• https://github.com/GabrielHoffman/variancePartition/issues/17

variancePartition 1.19.10

• in voomWithDreamWeights() fix issue with returning design matrix
• better error if counts can't be converted to matrix
• https://github.com/GabrielHoffman/variancePartition/issues/15

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)) 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()

variancePartition 0.0.3

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

variancePartition 0.99.0

• Initial version

GabrielHoffman/variancePartition documentation built on Jan. 6, 2025, 6:01 a.m.