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