NEWS.md

NEWS for the emmeans package

emmeans 1.3.5

• First steps to take prediction seriously. This includes
  • Addition of a sigma argument to ref_grid() (defaults to sigma(object) if available)
  • Addition of an interval argument in predict.emmGrid()
  • Addition of a likelihood argument in as.mcmc to allow for simulating from the posterior predictive distribution
  • Crude provisions for bias adjustment when back-transforming. This is not really prediction, but it is made possible by availability of sigma in object
• Further steps to lower the profile of cld() and CLD()
• Family size for Tukey adjustment was wrong when using exclude (#107)
• Provided for direct passing of info from recover_data to emm_basis
• Attempts to broaden MCMCglmm support

emmeans 1.3.4

• Un-naming a lot of arguments in do.call(paste, ...) and do.call(order, ...), to prevent problems with factor names like method that are argument names for these functions (#94)
• Fix to a logic error in summary.emmGrid() whereby transformations of class list were ignored.
• Enhancement to update.emmGrid(..., levels = levs) whereby we can easily relabel the reference grid and ensure that the grid and roles slots stay consistent. Added vignette example.
• Clarified ordering rules used by emmeans(). We now ensure that the original order of the reference grid is preserved. Previously, the grid was re-ordered if any numeric or character levels occurred out of order, per order()
• Curbing use of "statistical significance" language. This includes additional vignette material and plans to deprecate CLD() due to its misleading display of pairwise-comparison tests.
• Bug fix for betareg objects, where the wrong terms component was sometimes used.
• Correction to logic error that affected multiplicity adjustments when by variables are present (#98).
• Addition of pwpp() function to plot P values of comparisons
• Improvement to summary(..., adjust = "scheffe"). We now actually compute and use the rank of the matrix of linear functions to obtain the F numerator d.f., rather than trying to guess the likely correct value.
• Removal of vignette on transitioning from lsmeans -- it's been a long enough time now.

emmeans 1.3.3

• Fix to unintended consequence of #71 that caused incorrect ordering of contrast() results if they are later used by emmeans(). This was first noticed with ordinal models in prob mode (#83).
• Improved checking of conformability of parameters -- for models with rank deficiency not handled same way as lm()'s NA convention
• Added basic support for sommer::mmer, MuMIn::averaging, and mice::mira objects
• Fix in nnet::multinom support when there are 2 outcomes (#19)
• Added Satterthwaite d.f. to gls objects
• famSize now correct when exclude or include is used in a contrast function (see #68)
• Stronger warnings of possible bias with aovList objects, in part due to the popularity of afex::aov_ez() which uses these models.
• Updates to FAQs vignette

emmeans 1.3.2

• I decided to enable "optimal digits" display by default. In summaries, we try to show enough---but not too much---precision in estimates and confidence intervals. If you don't like this and want to revert to the old (exaggerated precision) behavior, do emm_options(opt.digits = FALSE)
• Added include argument to most .emmc functions (#67)
• Now allow character values for ref, exclude, and include in .emmc functions (#68)
• Better handling of matrix predictors (#66)
• Fixed over-zealous choice to not pass ... arguments in emmeans() when two-sided formulas are present
• Fix to clm support when model is rank-deficient
• Fix to regrid(..., transform = "log") error when there are existing non-estimable cases (issue #65)
• Improvements to brmsfit support (#43)
• Added support for mgcv::gam and mgcv::gamm models
• .my.vcov() now passes ... to clients
• Removed glmmADMB support. This package appears to be dormant
• Fixed ordering bug for nested models (#71)
• Support for manova object no longer requires data keyword (#72)
• Added support for multivariate response in aovlist models (#73)
• Documentation clarification (#76)
• Fix to CLD fatal error when sort = TRUE (#77)
• Fix to issue with weights and incomplete cases with lme objects (#75)
• Nested fixed-effects yielded NonEsts when two factors are nested in the same factor(s) (#79)

emmeans 1.3.1

• "mvt" adjustment ignored by grouping
• contrast() mis-labeled estimates when levels varied among by groups (most prominently this happened in CLD(..., details = TRUE))
• Changed aovlist support so it re-fits the model when non-sum-to-zero contrasts were used
• print.summary_emm() now cleans up numeric columns with zapsmall()
• More robust handling of nesting in ref_grid() and update(), and addition of covnest argument for whether to include covariates when auto-detecting nesting
• Revision of some vignettes
• Fixed bug in hpd.summary() and handoff to it from summary()
• Fixed bug where ref_grid() ignored mult.levs
• Fixes in emmeans where it passes ... where it shouldn't
• CLD() now works for MCMC models (uses frequentist summary)
• Addition of opt.digits option

emmeans 1.3.0

• Deprecated functions like ref.grid() put to final rest, and we no longer support packages that provide recover.data or lsm.basis methods
• Courtesy exports .recover_data() and .emm_basis() to provide access for extension developers to all available methods
• Streamlining of a stored example in inst/extdata
• Fix to .all.vars() that could cause errors when response variable has a function call with character constants.
• Relabeling of differences as ratios when appropriate in regrid() (so results match summary() labeling with type = "response").
• plot.emmGrid(..., comparisons = TRUE, type = "response") produced incorrect comparison arrows; now fixed

emmeans 1.2.4

• Support for model formulas such as df$y ~ df$treat + df[["cov"]]. This had failed previously for two obscure reasons, but now works correctly.
• New simplify.names option for above types of models
• emm_options() with no arguments now returns all options in force, including the defaults. This makes it more consistent with options()
• Bug fix for emtrends(); produced incorrect results in models with offsets.
• Separated the help pages for update.emmGrid() and emm_options()
• New qdrg() function (quick and dirty reference grid) for help with unsupported model objects

emmeans 1.2.3

• S3 methods involving packages multcomp and coda are now dynamically registered, not merely exported as functions. This passes checks when S3 methods are required to be registered.
• cld() has been deprecated in favor of CLD(). This had been a headache. multcomp is the wrong place for the generic to be; it is too fancy a dance to export cld with or without having multcomp installed.
• Added vignette caution regarding interdependent covariates
• Improved glmmADMB support to recover contrasts correctly

emmeans 1.2.2

• Removed ggplot2, multcomp, and coda to Suggests -- thus vastly reducing dependencies
• Added a FAQ to the FAQs vignette
• Modified advice in xtending.Rmd vignette on how to export methods
• Fixes to revpairwise.emmc and cld regarding comparing only 1 EMM
• cld.emm_list now returns results only for object[[ which[1] ]], along with a warning message.
• Deprecated emmeans specs like cld ~ group, a vestige of lsmeans as it did not work correctly (and was already undocumented)

emmeans 1.2.1

• Moved brms to Suggests (dozens and dozens fewer dependencies)

emmeans 1.2

• Index of vignette topics added
• New, improved (to my taste) vignette formats
• Fixed df bug in regrid (#29)
• Fixed annotation bug for nested models (#30)
• Better documentation for lme models in "models" vignette
• Additional fixes for arguments passed to .emmc functions (#22)
• Support added for logical predictors (who knew we could have those? not me)
• Replaced tex/pdf "Extending" vignette with Rmd/html
• Overhauled the faulty logic for df methods in emm_basis.merMod
• Added Henrik to contributors list (long-standing oversight)
• Added exclude argument to most .emmc functions: allows user to omit certain levels when computing contrasts
• New hpd.summary() function for Bayesian models to show HPD intervals rather than frequentist summary. Note: summary() automatically reroutes to it. Also plot() and emmip() play along.
• Rudimentary support for brms package
• Ad hoc Satterthwaite method for nlme::lme models

emmeans 1.1.3

• Formatting corrections in documentation
• Fixed bug for survival models where Surv() was interpreted as a response transformation.
• Fixed bug (issue #19) in multinom support
• Fixed bug (issue #22) in optional arguments with interaction contrasts
• Fixed bug (issue #23) in weighting with character predictors
• Clarifying message when cld() is applied to an emm_list (issue #24)
• Added offset argument to ref_grid() (scalar offset only) and to emmeans() (vector offset allowed) -- (issue #18)
• New optional argument for [.summary_emm to choose whether to retain its class or coerce to a data.frame (relates to issue #14)
• Added reverse option for trt.vs.ctrl and relatives (#27)

emmeans 1.1.2

• Changed the way terms is accessed with lme objects to make it more robust
• emmeans:::convert_scripts() renames output file more simply
• Added [ method for class summary_emm
• Added simple argument for contrast - essentially the complement of by
• Improved estimability handling in joint_tests()
• Made ref_grid() accept ylevs list of length > 1; also slight argument change: mult.name -> mult.names
• Various bug fixes, bullet-proofing
• Fixes to make Markdown files render better

emmeans 1.1

• Fixed a bug in emmeans() wherein weights was ignored when specs is a list
• Coerce data argument, if supplied to a data.frame (recover_data() doesn't like tibbles...)
• Added as.data.frame method for emmGrid objects, making it often possible to pass it directly to other functions as a data argument.
• Fixed bug in contrast() where by was ignored for interaction contrasts
• Fixed bug in as.glht() where it choked on df = Inf
• Fixed bug occurring when a model call has no data or subset
• New joint_tests() function tests all [interaction] contrasts

emmeans 1.0

• Added preliminary support for gamlss objects (but doesn't support smoothing). Additional argument is what = c("mu", "sigma", "nu", "tau") It seems to be flaky when the model of interest is just ~ 1.
• Improved support for models with fancy variable names (containing spaces and such)
• Fixed a bug whereby emmeans() might pass data to contrast()
• Added some missing documentation for summary.emmGrid()
• Repaired handling of emm_options(summary = ...) to work as advertised.
• Changed many object names in examples and vignettes from xxx.emmGrid to xxx.emm (result of overdoing the renaming the object class itself)
• Changed emmGrid() function to emm() as had been intended as alternative to mcp() in multcomp::glht() (result of ditto).
• Fixed error in exporting cld.emm_list()
• Fixed a bug whereby all CIs were computed using the first estimate's degrees of freedom.
• Now using Inf to display d.f. for asymptotic (z) tests. (NA will still work too but Inf is a better choice for consistency and meaning.)
• Bug fix in nesting-detection code when model has only an intercept

emmeans 0.9.1

• Documentation corrections (broken links, misspellings, mistakes)
• More sophisticated check for randomized data in recover_data() now throws an error when it finds recovered data not reproducible
• Added support for gam::gam objects
• Fixes to vcov() calls to comply with recent R-devel changes

emmeans 0.9

This is the initial major version that replaces the lsmeans package. Changes shown below are changes made to the last real release of lsmeans (version 2.27-2). lsmeans versions greater than that are transitional to that package being retired.

• We now emphasize the terminology "estimated marginal means" rather than "least-squares means"
• The flagship functions are now emmeans(), emtrends(), emmip(), etc. But lsmeans(), lstrends(), etc. as well as pmmeans() etc. are mapped to their corresponding emxxxx() functions.
• In addition, we are trying to avoid names that could get confused as S3 methods. So, ref.grid -> ref_grid, lsm.options -> emm_options, etc.
• Classes ref.grid and lsmobj are gone. Both are replaced by class emmGrid. An as.emmGrid() function is provided to convert old objects to class emmGrid.
• I decided to revert back to "kenward-roger" as the default degrees-of-freedom method for lmerMod models. Also added options disable.lmerTest and lmerTest.limit, similar to those for pbkrtest.
• Documentation and NAMESPACE are now "ROxygenated"
• Additional neuralgia and pigs datasets
• Dispatching of emmmeans() methods is now top-down rather than convoluted intermingling of S3 methods
• Improved display of back-transformed contrasts when log or logit transformation was used: We change any -s in labels to /s to emphasize that thnese results are ratios.
• A message is now displayed when nesting is auto-detected in ref_grid. (Can be disabled via emm_options())
• Options were added for several messages that users may want to suppress, e.g., ones about interactions and nesting.
• Greatly overhauled help page for models. It is now a vignette, with a quick reference chart linked to details, and is organized by similarities instead of packages.
• Support for 'mer' objects (lme4.0 package) removed.
• A large number of smaller interlinked vignettes replaces the one big one on using the package. Several vignettes are linked in the help pages.
• Graphics methods plot() and emmip() are now ggplot2-based. Old lattice-based functionality is still available too, and there is a graphics.engine option to choose the default.
• Non-exported utilities convert_workspace() and convert_scripts() to help with transition
• Moved Suggests pkgs to Enhances when not needed for building/testing

NOTE: emmeans is a continuation of the lsmeans package.

New developments will take place in emmeans, and lsmeans will remain static and eventually will be archived.