Changes in version 2.0.5
- May 31, 2023
- fix convergence issues
- fix initialization of lmer() fit
- use 1 OMP thread internally, then restore to original value
Changes in version 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.
Changes in version 2.0.3
- May 13, 2023
- fix vcov()
Changes in version 2.0.2
- May 17, 2023
- add matrix argument to mvTest()
Changes in version 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()
Changes in version 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.
Changes in version 1.36.3
- Jan 2, 2025
- examine adding REDUCE = c to bpiterate()
- fix issue mvTest() for test of single coefficient
Changes in version 1.36.2
- Nov 7, 2024
- doc fix
- Nov 7, 2024
- fix docs
Changes in version 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
Changes in version 1.35.5
- June 17, 2024
- fix bug in mvTest() for se value with 1 feature
Changes in version 1.35.4
- June 13, 2024
- fix bug in [.MArrayLM2 dropping residuals to a vector
Changes in version 1.35.3
- June 11, 2024
- in mvTest() with shrink.cov = TRUE uses lambda = 0.01
Changes in version 1.35.2
- June 6, 2024
- in mvTest() return beta and se
Changes in version 1.35.1
- May 31, 2024
- version bump for BioC
Changes in version 1.33.15
- May 16, 2024
- in voomWithDreamWeights(), default changed to rescaleWeightsAfter =
FALSE
Changes in version 1.33.14
- April 19, 2024
- in topTable() resolve issue when specifying multiple coeffs
Changes in version 1.33.13
- April 6, 2024
- in voomWithDreamWeights(), add argument prior.count.for.weights
Changes in version 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
Changes in version 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
Changes in version 1.33.10
- Feb 5, 2024
- in augmentPriorCount() and voomWithDreamWeights(), add argument
scaledByLib=FALSE
Changes in version 1.33.9
- Jan 25, 2024
- bug fix in BIC() and .fitExtractVarPartModel()
Changes in version 1.33.8
- Jan 22, 2024
- add BIC() for result of dream() and lmFit()
Changes in version 1.33.7
- Jan 19, 2024
- add logLik() for result of dream() and lmFit()
Changes in version 1.33.6
- fix issue with subsetting using logicals
Changes in version 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
Changes in version 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()
Changes in version 1.33.3
- Dec 5, 2023
- in residuals() when dividing by sqrt(1-hatvalues) add small offset
to make sure the value is positive
Changes in version 1.33.2
- Nov 13, 2023
- add augmentPriorCount()
- add prior.count argument to voomWithDreamWeights() and feed it to
augmentPriorCount()
Changes in version 1.33.1
- Nov 2, 2023
- move omp_set_num_threads() deeper in nesting
Changes in version 1.31.22
- Oct 19, 2023
- fix handling of variables with missing data
- return fit$genes properly
Changes in version 1.31.21
- Oct 16, 2023
- handle weights properly when the linear mixed model fails for some
genes
- lmFit() and
- in iterRows() set scale = FALSE as default
- in voomWithDreamWeights(), scale in input weights and weights in
side fitVarPartModel()
- get weights estimated most similar to voomLmFit()
- in dream() use rescaleWeights = FALSE to get sigma estimates
compatable with lmFit()
Changes in version 1.31.20
- Sept 26, 2023
- allow weights to be a matrix in voomWithDreamWeights()
Changes in version 1.31.19
- Sept 22, 2023
- add rescaleWeightsAfter argument to voomWithDreamWeights()
Changes in version 1.31.18
- Sept 5, 2023
- improved error handling for fitVarPartModel(),
fitExtractVarPartModel(), and voomWithDreamWeights()
Changes in version 1.31.16
- August 18, 2023
- in dream(), if "Kenward-Roger" is specified but gives covariance
matrix that has poor condition number or is not positive definite,
then fall back to "Satterthwaite" for hypothesis testing in linear
mixed models
- Update documentation, and reformat code
Changes in version 1.31.15
- August 10, 2023
- fit = dream() now returns fit$loglik (the log-likelihood for each
gene), and fit$edf (the effective degreees of freedom for each gene)
Changes in version 1.31.13
- August 7, 2023
- fix bug in calcVarPart() where weights was ignored in some cases
- add additional tests to check this
Changes in version 1.31.12
- July 3, 2023
- makeContrastsDream() converts NA contrasts to NULL
Changes in version 1.31.11
- setting voomWithDreamWeights(..., span="auto") now estimates tuning
parameter from data using fANCOVA::loess.as()
Changes in version 1.31.10
- filterInputData() now ensures EList contains a matrix
Changes in version 1.31.9
- Fix issue in mvTest() when specifying features with strings
Changes in version 1.31.8
- Fix error message when linear mixed model fails
Changes in version 1.31.7
- update mvTest() to run in parallel
Changes in version 1.31.6
- update mvTest() to include Hotelling T2 test and LS.empirical()
Changes in version 1.31.1
- June 4, 2023
- Rename for Bioconductor compatability
Changes in version 1.29.2
- Rescale weights
Changes in version 1.28.9
- March 14, 2023
- fix rounding error in makeContrastsDream()
- add Pearson residuals to residuals()
Changes in version 1.28.8
- March 8, 2023
- add mvTest() with features as list
Changes in version 1.28.7
- March 7, 2023
- Fix bug in makeContrastsDream() by adding droplevels()
Changes in version 1.28.6
- March 1, 2023
- diffVar() now fits contrasts estimated in first step
Changes in version 1.28.5
- Feb 24, 2023
- Fix error in vcov() when samples are dropped due to covariate having
NA value
Changes in version 1.28.4
- Feb 2, 2023
- Improve documentation for contrasts
Changes in version 1.28.3
- Jan 19, 2023
- Improve checking and documentation for contrasts
Changes in version 1.28.2
- Jan 13, 2023
- canCorPairs() now allows random effects in formula
- but won't change results
Changes in version 1.28.1
- Jan 04, 2023
- bug fixes
Changes in version 1.27.17
- in mvTest(), more consistent return values when one features is used
Changes in version 1.27.16
- bug fix
Changes in version 1.27.15
- fix approximation for vcov()
- add checks for vcov() in test_vcov2()
Changes in version 1.27.14
- fix bug in topTable()
- add deviance()
- update docs
- update sqrtMatrix() to have positive diagonal
Changes in version 1.27.13
- add diffVar() test of differential variance
- dream() now returns formula, data, and hatvalues
- define hatvalues() for result of dream()
Changes in version 1.27.12
- in mvTest():
- default method is now "FE"
Changes in version 1.27.11
- in mvTest():
- return number of features
- return stat.FE and stat.het for RE2C
- return NA for stat if 1 feature
Changes in version 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"
Changes in version 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
Changes in version 1.27.8
- bug fix in mvTest()
Changes in version 1.27.7
- add vcov() for results from dream()
- add mvTest() for multivariate tests on results from dream() using
vcov()
Changes in version 1.27.6
- remove FMT functions
Changes in version 1.27.5
- update dependencies
- make topTable() generic to work with R 4.2.1 and Bioc 3.16
Changes in version 1.27.4
- update dependencies
Changes in version 1.27.3
- update filtering of covariates, especially for when many samples are
dropped
Changes in version 1.27.1
- update plotPercentBars arguments
Changes in version 1.26.1
- patch to update docs
Changes in version 1.25.13
- Fix compatibility issue with lme4 1.1.29
- reported
https://github.com/GabrielHoffman/variancePartition/issues/51
Changes in version 1.25.12
- in makeContrastsDream(), fix issue where terms with colon cause and
error
Changes in version 1.25.11
- fix bug in dream() for variables with NA values
- improve handling of invalid contrasts in makeContrastsDream()
Changes in version 1.25.9
- for getContrast() and makeContrastsDream() make sure formula
argument is a formula and not a string
Changes in version 1.25.8
- small bug fixes
Changes in version 1.25.7
- dream() now drops samples with missing data gracefully
Changes in version 1.25.6
- fix small plotting bug in plotStratify() and plotStratifyBy()
Changes in version 1.25.5
- add getTreat() to evaluate treat()/topTreat() seamlessly on results
of dream()
Changes in version 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()
Changes in version 1.25.3
- add genes argument to plotPercentBars()
Changes in version 1.25.2
- change plotPercentBars() to use generic S4
Changes in version 1.25.1
- update handling of weights in voomWithDreamWeights() and add
applyQualityWeights()
Changes in version 1.23.6
- update calcVarPart() with argument scale=TRUE allowing the user to
disable scaling to fractions
Changes in version 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()
Changes in version 1.23.4
- convert some warnings to errors
- add proper handling of weights to voomWithDreamWeights()
Changes in version 1.23.3
- add calcVarPart() support for a range of GLM/GLMM's
Changes in version 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
Changes in version 1.23.1
- New freeze for Bioconductor devel branch
Changes in version 1.21.10
- add suppressWarnings flag to makeContrastsDream()
- ensure that z.std is finite
Changes in version 1.21.9
- fix bug with makeContrastsDream()
Changes in version 1.21.8
- update dream vignette
- update documentation for makeContrastsDream()
- fix error in rdf_from_matrices() with eigen() failing
Changes in version 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()
Changes in version 1.21.6
- in dream() allow L to be NULL
Changes in version 1.21.5
- Fix roxygen2 documentation to pass R CMD check
Changes in version 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
Changes in version 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
Changes in version 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
Changes in version 1.21.1
- fix issue with dream and random slopes
Changes in version 1.19.20
- fix bug discovered when the number of features is less than the
number of chunks in iterBatch()
Changes in version 1.19.19
- simple bug fixes to pass R CMD check
Changes in version 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
Changes in version 1.19.17
- add get_prediction() for results of lm()
- improve documentation of get_prediction()
Changes in version 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
Changes in version 1.19.14
- fix issue with residuals() where examples fail
Changes in version 1.19.13
- fix issues with residuals()
- https://github.com/GabrielHoffman/variancePartition/issues/18
- fix issue exporting eBayes, topTable, etc
Changes in version 1.19.12
- Improve documentation for contrasts in dream.Rmd
- check that contrasts sum to zero in plotContrasts.
Changes in version 1.19.11
- in voomWithDreamWeights() fix issue with not defining design
- https://github.com/GabrielHoffman/variancePartition/issues/17
Changes in version 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
Changes in version 1.19.7
- Round numbers in plotContrasts()
- fix issues with strings are passed to formula arguments
Changes in version 1.19.6
- New gives meaning full error message for dream(), etc when variable
is not found in data.
Changes in version 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))
Changes in version 1.19.4
- Update vignette #3, and update documentation of REML argument
Changes in version 1.19.3
- add new FAQ.Rmd
Changes in version 1.19.2
- canCorPairs() now returns NA correlation when two variables have no
overlapping observed values
- plotCorrMatrix() now handles NA correlation values
Changes in version 1.19.1
- Bump to next Bioconductor version
Changes in version 1.18.3
- Improve documentation
- move location of eBayesFMT code
Changes in version 1.18.2
- Clean up some code and add documentation
- document ebayesFMT
Changes in version 1.18.1
- Clean up some code and add documentation
- compute effective degrees of freedom for each model
Changes in version 1.18.0
- Bioconductor freeze
Changes in version 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
Changes in version 1.17.9
- Fix issues with compatability with R/4.0.0
Changes in version 1.17.8
- Better error message when response contains missing data
Changes in version 1.17.7
- Better error message when variable in formula does not exist
Changes in version 1.17.6
- comply with new Bioconductor check: R_CHECK_LENGTH_1_LOGIC2
Changes in version 1.17.5
- if contrasts for dream() is data.frame, convert to matrix
Changes in version 1.17.4
- Don't print warnings for residuals() when only one argument passed.
- fix bug with residuals evaluated with only fixed effects
Changes in version 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
Changes in version 1.17.2
- fix error in voomWithDreamWeights() when design matrix is null
Changes in version 1.17.1
- topTable(...,sort.by=) now is correct when and F-test is used
- fixed issue in classifyTestsF.MArrayLM2, now is much faster
Changes in version 1.15.8
- Replace cat() with message()
- add quiet option to a few functions
- dream() does not call eBayes() when lmFit is used
Changes in version 1.15.7
- Official release to development branch
Changes in version 1.15.6
- fix convergence errror when recycling parameters values from first
gene
- add column z.std and F.std to topTable
Changes in version 1.15.4
- Add error message when scale of fixed effects causes a problem
Changes in version 1.15.3
- Try changing order of eBayes
Changes in version 1.15.2
- Update vignette
Changes in version 1.15.0
- Push changes to Bioconductor devel
Changes in version 1.13.11
- Fixed bug in voomWithDreamWeights() with approxfun() with ties
Changes in version 1.13.10
- fix parallel processing issues
Changes in version 1.13.9
- update vignette for new parallel processing backend
Changes in version 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)
Changes in version 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"
Changes in version 1.13.5
- add plotContrasts() to dream vignette
Changes in version 1.13.4
- export classes to fix bug with class "varPartResults" not being
defined
- Thanks Megan Behringer
Changes in version 1.13.3
- add plotContrasts()
Changes in version 1.13.2
- Enable random slope models in dream, but not for estimating variance
fractions
- Thanks Jonas Zierer
Changes in version 1.13.1
- Add progress bar at ETA =======
Changes in version 1.12.4
- 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
- Fix multithreading issue
Changes in version 1.11.11
- dream can handle multiple contrasts at the same time
Changes in version 1.11.10
- fix typos in dream vignette
Changes in version 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
Changes in version 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
Changes in version 1.11.6
- add error checing for L in dream
- fix typoes in dream vignette
- fix typoes in theory_practice_random_effects.Rnw
Changes in version 1.11.5
- Add dream function for differential expression for repeated measures
with a linear mixed model
Changes in version 1.11.2
- Add warnings to canCorPairs for colinear terms
Changes in version 1.11.1
- Add vignette: theory_practice_random_effects.Rnw
Changes in version 1.9.9
- 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
- include splines in foreach .packages
Changes in version 1.5.6
- compatibility with tximport v1.3.5
Changes in version 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)
Changes in version 1.3.11
- in canCorPairs() and other functions, convert formula with
as.formula()
- improve error messages for canCorPairs()
Changes in version 1.3.10
- Add plotStratify()
- Update documentation
Changes in version 1.3.8
- Add additional examples to vignette
- show projected memory usage of fitVarPartModel()
Changes in version 1.3.7
- fitVarPartModel warns if names in exprObj and data are not identical
- residuals() and other functions deal with missing values properly
Changes in version 1.3.6
- Small changes to vignette
Changes in version 1.3.5
- Fix Bioconductor error
Changes in version 1.3.4
- Fix typos
Changes in version 1.3.3
- Improve documentation
Changes in version 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
Changes in version 1.1.8
- Add ESS.R
- Add fitVarTest.R
- use lmerTest by default
- fix bug checkModelStatus() for variables with backticks in name
Changes in version 1.1.7
- GPL License
Changes in version 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
Changes in version 1.1.5
- Stop cluster in vignette to solve error on Windows machines
Changes in version 1.1.4
- Fix Bioconductor check error
Changes in version 1.1.3
o Add details to vignette
- Fix ggplot2 compatibility issues
Changes in version 1.1.2
- Add details to vignette
Changes in version 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
Changes in version 1.0.0
- Release to Bioconductor 3.2
Changes in version 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
Changes in version 0.99.8
- improve warnings / errors when design matrix is close to or exactly
singular
Changes in version 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
Changes in version 0.99.6
- Update DESCRIPTION information
Changes in version 0.99.5
- 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
- rename sort.varParFrac to sortCols
- support ExpressionSet
- change options for plotStratifyBy()
Changes in version 0.99.0
- Initial version
Changes in version 0.0.12
- add plotStratifyBy()
- update documentation
Changes in version 0.0.11
- fix sort to work on correct argument
Changes in version 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
Changes in version 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
Changes in version 0.0.8
o Bug update to vignette and simulated data
Changes in version 0.0.7
- remove 'variable' from xlab of plotVarPart
Changes in version 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()
Changes in version 0.0.5
o plotVarPart() as ylim=c(0,100) as default, and can be changed by user
- fitExtractVarPartModel() labels rows correctly
Changes in version 0.0.4
- Add sort() for output of extractVarPart() or
fitExtractVarPartModel()
Changes in version 0.0.3
- add residuals function
- add fitExtractVarPartModel()
- foreach loops us iterators