NEWS
- Maintenance release to fix minor issues with function documentation
- Fix #130 by avoiding conflict with
vcov in the merDeriv package
- Upgrade package test infrastructure to 3e testthat specification
- Maintenance release to keep package listed on CRAN
- Fix a small bug where parallel code path is run twice (#126)
- Update plotting functions to avoid deprecated
aes_string() calls (#127)
- Fix (#115) in description
- Speed up PI using @bbolker pull request (#120)
- Updated package maintainer contact information
- Streamline vignette building to be precompiled and move tests to limit burden on CRAN check
- Switch dependency from
broom to broom.mixed because of upstream package reorganization
Bug fixes
- Fixed an issue where
averageObs could not be calculated when model weights were specified in the original model (closes #110)
New Features
subBoot now works with glmerMod objects as wellreMargins a new function that allows the user to marginalize the prediction over breaks in the distribution of random effect distributions, see ?reMargins and the new reMargins vignette (closes #73)
Bug fixes
- Fixed an issue where known convergence errors were issuing warnings and causing the test suite to not work
- Fixed an issue where models with a random slope, no intercept, and no fixed term were unable to be predicted (#101)
- Fixed an issue with shinyMer not working with substantive fixed effects (#93)
New Features
- Parallel fitting of
merModLists is now supported using the future.apply package and the future_lapply functions, optionally
- Reduced package installation surface by eliminating unnecessary packages in the
Suggests field
Bug fixes
- Fixed a bug (#94) where
predictInterval() would return a data.frame of the wrong dimensions when predicting a single row of observations for a glm
- Fixed a bug (#96) related to
rstanarm dependencies in the package vignette
- Switched from
dontrun to donttest for long-running examples (CRAN compliance)
- Fixed and made more clear the generics applying to
merModList objects (#92)
New Features
- Standard errors reported by
merModList functions now apply the Rubin correction for multiple imputation
Bug fixes
- Contribution by Alex Whitworth (@alexWhitworth) adding error checking to plotting functions
- The vignettes have been shortened and unit tests reorganized to facilitate Travis-CI builds and reduce CRAN build burden
New Features
- Added vignette on using multilevel models with multiply imputed data
- Added
fixef and ranef generics for merModList objects
- Added
fastdisp generic for merModList
- Added
summary generic for merModList
- Added
print generic for merModList
- Documented all generics for
merModList including examples and a new imputation vignette
- Added
modelInfo generic for merMod objects that provides simple summary stats about a whole model
Bug Fixes
- Fix bug that returned NaN for
std.error of a multiply imputed merModList when calling modelRandEffStats
- Fixed bug in
REimpact where some column names in newdata would prevent the prediction intervals from being computed correctly. Users will now be warned.
- Fixed bug in
wiggle where documentation incorrectly stated the arguments to the function and the documentation did not describe function correctly
- Update the
readme.rmd to package graphics with the R package, per CRAN
- Improve handling of formulas. If the original
merMod has functions specified in the formula, the draw and wiggle functions will check for this and attempt to respect these variable transformations. Where this is not possible a warning will be issued. Most common transformations are respected as long as the the original variable is passed untransformed to the model.
- Change the calculations of the residual variance. Previously residual variance was used to inflate both the variance around the fixed parameters and around the predicted values themselves. This was incorrect and resulted in overly conservative estimates. Now the residual variance is appropriately only used around the final predictions
- Rebuilt the readme.md to include new information about new features
- New option for
predictInterval that allows the user to return the full interval, the fixed component, the random component, or the fixed and each random component separately for each observation
- Fixed a bug with slope+intercept random terms that caused a miscalculation of the random component
- Add comparison to
rstanarm to the Vignette
- Make
expectedRank output more tidy like and allow function to calculate expected rank for all terms at once
- Note, this breaks the API by changing the names of the columns in the output of this function
- Remove tests that test for timing to avoid issues with R-devel JIT compiler
- Remove
plyr and replace with dplyr
- Fix issue #62
varList will now throw an error if == is used instead of =
- Fix issue #54
predictInterval did not included random effects in calculations when newdata had more than 1000 rows and/or user specified parallel=TRUE. Note: fix was to disable the .paropts option for predictInterval … user can still specify for temporary backward compatibility but this should be either removed or fixed in the permanent solution.
- Fix issue #53 about problems with
predictInterval when only specific levels of a grouping factor are in newdata with the colon specification of interactions
- Fix issue #52 ICC wrong calculations … we just needed to square the standard deviations that we pulled
- Fix dependency on
lme4 to ensure compatibility with latest changes.
Bug fixes
- Coerce
dplyr tbl and tbl_df objects to data.frames when they are passed to predictInterval and issue a warning
- Try to coerce other data types passed to
newdata in predictInterval before failing if coercion is unsuccessful
- Numeric stabilization of unit tests by including seed values for random tests
- Fix handling of models with nested random effect terms (GitHub #47)
- Fix vignette images
New Functionality
- Substantial performance enhancement for
predictInterval which includes better handling of large numbers of parameters and simulations, performance tweaks for added speed (~10x), and parallel backend support (currently not optimized)
- Add support for
probit models and limited support for other glmm link functions, with warning (still do not know how to handle sigma parameter for these)
- Add ability for user-specified seed for reproducibility
- Add support for
blmer objects from the blme package
- Add a
merModList object for lists of merMod objects fitted to subsets of a dataset, useful for imputation or for working with extremely large datasets
- Add a
print method for merModList to mimic output of summary.merMod
- Add a
VarCorr method for merModList
- Add new package data to demonstrate replication from selected published texts on multilevel modeling using different software (1982 High School and Beyond Survey data)
Other changes
- Changed the default
n.sims for the predictInterval function from 100 to 1,000 to give better coverage and reflect performance increase
- Changed the default for
level in predictInterval to be 0.8 instead of 0.95 to reflect that 0.95 prediction intervals are more conservative than most users need
Future changes
- For the next release (1.0) we are considering a permanent switch to C++ RMVN sampler courtesy of Giri Gopalan ’s excellent FastGP
New Functions
- Provides
predictInterval to allow prediction intervals from glmer and lmer objects
- Provides
FEsim and REsim to extract distributions of model parameters
- Provides
shinyMer an interactive shiny application for exploring lmer and glmer models
- Provides
expectedRank function to interpret the ordering of effects
- Provides
REimpact to simulate the impact of grouping factors on the outcome
- Provides
draw function to allow user to explore a specific observation
- Provides
wiggle function for user to build a simulated set of counterfactual cases to explore