NEWS
- Maintenance release to fix crossreference issues with function
documentation
- 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