NEWS in package ‘emmeans’

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Changes in version 1.7.4

• Added an argument enhance.levels to contrast() that allows better labeling of the levels being contrasted. For example, now (by default) if a factor treat has numeric levels, then comparisons will have levels like treat1 - treat2 rather than 1 - 2. We can request similar behavior with non-numeric levels, but only if we specify which factors.
  • Two new functions comb_facs() and split_fac() for manipulating the factors in an emmGrid.
  • Added an argument wts to eff.emmc and del.eff.emmc, which allows for weighted versions of effect-style contrasts (#346)
  • Made qdrg() more robust in accommodating various manifestations of rank-deficient models.
  • qdrg() now always uses df if provided. Previously forced df = Inf when a link function was provided.
  • Fix to df.error calculation with gls (#347)

Changes in version 1.7.3

• argument change ref_grid(..., transform = ...) now should be ref_grid(..., regrid = ...) to avoid confusing transform with the tran option (which kind of does the opposite). If we match transform and don't match tran, it will still work, but a message is displayed with advice to use regrid instead.
  • Repairs to averaging support (#324). Previous versions were potentially dead wrong except for models created by lm() (and maybe some of those were bad too)
  • Added a which argument to emm() to select which list elements to pass to multcomp::glht()
  • Support for rank-deficient gls models (note that nlme allows such models with gls, but not lme)
  • Bug in lqm / lqmm support (#340)
  • Other minor corrections (e.g. #334)

Changes in version 1.7.2

• Improvements to averaging support (#319)
  • Fixed bug in comparison arrows when by = NULL (#321) (this bug was a subtle byproduct of the name-checking in #305) Note this fixes visible errors in the vignettes for ver 1.7.1-1
  • Patch for gamlss support (#323)
  • Added withAutoprint() to documentation examples with require() clauses, so we see interactive-style results
  • Correction to a logic error in adjustment corrections in summary.emmGrid (#31)
  • Revised summary.emmGrid() so that if we have both a response transformation and a link function, then both transformations are followed through with type = "response". Previously, I took the lazy way out and used summary(regrid(object, transform = "unlink"), type = "response") (see #325)
  • Fix to force_regular() which caused an unintended warning (#326)
  • Fixes to issues in emtrends() (#327)

Changes in version 1.7.1

• Support from multinomial models in mgcv::gam (#303) thanks to Hannes Riebl
  • Bug fix for spaces in by variable names (#305). Related to this are:
    • plot.emmGrid() now forces all names to be syntactically valid
    • In as.data.frame.emmGrid(), we changed the optional argument to check.names (defaulting to TRUE), and it actually has an effect. So by default, the result will have syntactically valid names; this is a change, but only because optional did not work right (because it is an argument for `as.data.frame.list()).
  • Fix for missing column names in linfct from emmeans() (#308)
  • Added gnls support (#313, #314, thanks to Fernando Miguez)
  • Modified glm support so that df.residual is used when the family is gaussian or gamma. Thus, e.g., we match lm results when the model is fitted with a Gaussian family. Previously we ignored the d.f. for all glm objects.
  • New vignette example with percentage differences
  • More graceful handling of comparisons when there is only one mean; and a related FAQ

Changes in version 1.7.0

Notable changes

• New rg.limit option (and argument for ref_grid()) to limit the number of rows in the reference grid (#282, #292). This change could affect existing code that used to work -- but only in fairly extreme situations. Some users report extreme performance issues that can be traced to the size of the reference grid being in the billions, causing memory to be paged, etc. So providing this limit really is necessary. The default is 10,000 rows. I hope that most existing users don't bump up against that too often. The nuisance (or non.nuisance) argument in ref_grid() (see below) can help work around this limit.
  • New nuisance option in ref_grid(), by which we can specify names of factors to exclude from the reference grid (accommodating them by averaging) (#282, #292). These must be factors that don't interact with anything, even other nuisance factors. This provides a remedy for excessive grid sizes.
  • Improvements to and broadening of qdrg():
    • Changed the order of arguments in to something a bit more natural
    • Default for contrasts now object$contrasts when object is specified
    • Detection of multivariate situations
    • Added ordinal.dim argument to support ordinal models
  • New force_regular() function adds invisible rows to an irregular emmGrid to make it regular (i.e., covers all factor combinations)

Bug fixes and tweaks

• Removed dependency on plyr package (#298)
  • Fix to bug in regrid() with nested structures (#287)
  • Fix bug in rbind() which mishandled @grid$.offset.
  • Major repairs to clm and clmm support to fix issues related to rank deficiency and nested models, particularly with mode = "prob" (#300)
  • Allow type to be passed in emmeans() when object is already an emmGrid (incidentally noticed in #287)
  • Code to prevent a warning when an existing factor is coerced to a factor in the model formula -- see SO question
  • Add documentation note for add_grouping with multiple reference factors (#291)

Changes in version 1.6.3

• Clarification of documentation of ref_grid(object, vcov. = ...) (#283)
  • Fix to emmtrends() with covariate formulas (#284)
  • Improved parts of "Basics" vignette - removed "back story", revised guidance on $P$ values and models
  • Allow for > 1 reference factor in add_grouping() (#286)
  • Repairs to contrast() to avoid all-nonEst results in irregular nested structures

Changes in version 1.6.2

• Fixed navigation error in vignette index
  • Discouraging message added to cld() results. Also am providing an emm_list method for emm_list objects.
  • Added mvcontrast() function (#281) and assoc vignette material
  • Added update.summary_emm()

Changes in version 1.6.1

• Fixed a bug in parsing a response transformation (#274)
  • Changed handling of contrast() so that log2 and log10 transformations are handled just like log. (#273) Also disabled making ratios with genlog as it seems ill-advised.
  • Added support for log1p transformation
  • Improved detection of cases where Tukey adjustment is [in]appropriate (#275)
  • Added type = "scale" argument to plot.emmGrid() and emmip(). This is the same as type = "response" except the scale itself is transformed (i.e., a log scale if the log transformation was used). Since the same transformation is used, the appearance of the plot will be the same as with type = "lp", but with an altered axis scale. Currently this is implemented only with engine = "ggplot".
  • Fixed bug whereby Scheffe is ignored when there is only one contrast, even though scheffe.rank > 1 was specified. (#171)
  • Added a subset() method for emmGrid objects
  • Bug fixes for mcmc and mcmc.list objects (#278, #279)
  • test() shows null whenever it is nonzero on the chosen scale (#280)

Changes in version 1.6.0

This version has some changes that affect all users, e.g., not saving .Last.ref_grid, so we incremented the sub-version number.

• Changed handling of logit transformations in contrast(), so that the odds-ratio transformation persists into subsequent contrast() calls e.g., interaction contrasts.
• We also made contrast(..., type = ...) work correctly
• Bug fix so that all p.adjust.methods work (#267)
• Support for mblogit extended to work with mmblogit models (#268) (However, since, mclogit pkg incorporates its own interface)
• Added export option in print.emmGrid() and print.emm_summary()
• Changed default for emm_options(save.ref_grid = FALSE). Years ago, it seemed potentially useful to save the last reference grid, but this is extra overhead, and writes in the user's global environment. The option remains if you want it.
• Added a note advising against using as.data.frame (because we lose potentially important annotations), and information/example on how to see more digits (which I guess is why I'm seeing users do this).
• Further refinement to nesting detection. A model like y ~ A:B detected A %in% B and B %in% A, and hence A %in% A*B and B %in% A*B due to a change in 1.4.6. Now we omit cases where factors are nested in themselves!
• Expansion of cov.reduce formulas to allow use of custom models for predicting mediating covariates

Changes in version 1.5.5

• The multinom "correction" in version 1.5.4 was actually an "incorrection." It was right before, and I made it wrong! If analyzing multinom models, use a version other than 1.5.4
  • Repairs to support for mblogit models
  • Bug fix for survreg support (#258) -- survreg() doesn't handle missing factor levels the same way as lm(). This also affects results from coxph(), AER::tobit(), ...
  • Addition of a note in help auto.noise dataset, and changing that example and vignette example to have noise/10 as the response variable. (Thanks to speech and hearing professor Stuart Rosen for pointing out this issue in an e-mail comment.)
  • Bug fix for appx-satterthwaite mode in gls/lme models (#263)
  • Added mode = "asymptotic" for gls/lme models.
  • Added facetlab argument to emmip_ggplot() so user can control how facets are labeled (#261)
  • Efficiency improvements in joint_tests() (#265)
  • Bug fixes in joint_tests() and interaction contrasts for nested models (#266)
  • Improvement to multinom support suggested by this SO question

Changes in version 1.5.4

• Fix to bug in rbind.emm_list() to default for which
  • Fix for a glitch in recovering data for gee models (#249)
  • Support for svyglm objects (#248)
  • Better support for lqm, lqmm, and added support for rq & rqs objects (quantreg package). User may pass summary or boot arguments such as method, se, R, ... (#250)
  • Correction to multinom objects (SEs were previously incorrect) and addition of support for related mclogit::mblogit objects. If at all possible, users should re-run any pre-1.5.4 analyses of multinomial models
    Note: This correction was wrong! If using multinomial models, you should use some version other than 1.5.4!
  • Change to less misleading messages and documentation related to the N.sim argument of regrid(). We are no longer calling this a posterior sample because this is not really a Bayesian method, it is just a simulated set of regression coefficients.

Changes in version 1.5.3

• Per long-time threats, we really are removing CLD() once and for all. We tried in version 1.5.0, but forced to cave due to downstream problems.
  • Addition of levels<- method that maps to update(... levels =) (#237)
  • Fix cld() so it works with nested cases (#239)
  • Enable coef() method to work with contrasts of nested models. This makes it possible for pwpp() to work (#239)
  • Fixed a coding error in plot() that occurs if we use `type = "response" but there is in fact no transformation (reported on StackOverflow)
  • Added "log10" and "log2" as legal transformations in regrid()
  • Revised vignette example for MCMC models, added example with bayestestR
  • Expanded support for ordinal models to all link functions available in ordinal (errors-out if ordinal not installed and link not available in stats::make.link())
  • Cleaned-up emmip() to route plot output to rendering functions emmip_ggplot() and emmip_lattice(). These functions allow more customization to the plot and can also be called independently. (To do later, maybe next update: the same for plot.emmGrid(). What to name rendering functions?? -- suggestions?)
  • Cleaned up code for .emmc functions so that parenthesization of levels does not get in the way of ref, exclude, or include arguments (#246)
  • Fix to bug in emtrends() when data is specified (#247)
  • Tries harder to recover original data when available in the object (#247). In particular, sometimes this is available, e.g., in $model slot in a lm object, as long as there are no predictor transformations. This provides a little bit more safety in cases the data have been removed or altered.
  • Tweaks to rbind.emm_list() to allow subsetting. (Also documentation & example)

Changes in version 1.5.2

• Change to plot.emmGrid(... comparisons = TRUE) where we determine arrow bounds and unnecessary-arrow deletions separately in each by group. See also Stack Overflow posting
  • emmeans() with contrasts specified ignores adjust and passes to contrast() instead. Associated documentation improved (I hope)
  • Bug-fix for missing cases in plot(..., comparisons = TRUE) (#228)
  • Robustified plot.emmGrid() so that comparison arrows work correctly with back-transformations. (Previously we used regrid() in that case, causing different CIs and PIs depending on comparisons) (#230)
  • Bug fixes in support for stan_polr models.
  • Bug fix for incorrect (and relatively harmless) warning in several models (#234)
  • Lower object size via removing unnecessary environment deps (#232)
  • Repairs to as.list() and as.emmGrid() to fully support nesting and submodels.

Changes in version 1.5.1

• Additional checking for potential errors (e.g. memory overload) connected with submodel support. Also, much more memory-efficient code therein (#218, #219)
  • A new option enable.submodel so user can switch off submodel support when unwanted or to save memory.
  • multinom support for N.sim option
  • Modification to internal dispatching of recover_data and emm_basis so that an external package's methods are always found and given priority whether or not they are registered (#220)
  • Patches to gamlss support. Smoothers are not supported but other aspects are more reliable. See CV posting
  • Improvement to auto-detection of transformations (#223)
  • Added aes argument in pwpp() for more control over rendering (#178)
  • Fix to a situation in plot.emmGrid() where ordering of factor levels could change depending on CIs and PIs (#225)

Changes in version 1.5.0

• Changed help page for joint_tests() to reflect cov.keep (ver. 1.4.2)
  • emm_options() gains a disable argument to use for setting aside any existing options. Useful for reproducible bug reporting.
  • In emmeans() with a contr argument or two-sided formula, we now suppress several particular ... arguments from being passed on to contrast() when they should apply only to the construction of the EMMs (#214)
  • More control of what ... arguments are passed to methods
  • CLD() was deprecated in version 1.3.4. THIS IS THE LAST VERSION where it will continue to be available. Users should use multcomp::cld() instead, for which an emmGrid method will continue to exist.
  • Experimental submodel option
    • Bug fix therein (#217)
  • Enhancements to mgcv::gam support (#216)
  • New ubds dataset for testing with messy situations
  • Added minimal support for lqm and lqmm models (#213)
  • Interim support for user-supplied contrasts for stanreg models (#212)

Changes in version 1.4.8

• Bug fix and smoother support for stanreg objects (#202)
  • Fix to emmip() to be consistent between one curve and several, in whether points are displayed (style option)
  • Added "scale" option to make.tran()
  • Auto-detection of standardized response transformation
  • Fix to a scoping issue in emtrends() (#201)
  • Bug fix for #197 created a new issue #206. Both now fixed.
  • Non-existent reference levels in trt.vs.ctrl.emmc() now throws an error (#208)
  • Added a default for linfct (the identity) to emmobj
  • Provisions for more flexible and consistent labeling/naming of results. This includes added emm_options "sep" and "parens", and a parens argument in contrast(). sep controls how factor levels are combined when ploted or contrasted, and parens sets whether, what, and how labels are parenthesized in contrast(). In constructing contrasts of contrasts, for example, labels like A - B - C - D are now (A - B) - (C - D), by default. To reproduce old labeling, do `emm_options(sep = ",", parens = "a^")

Changes in version 1.4.7

• Repairs to pwpp() so it plays nice with nonestimable cases
  • Added "xplanations" vignette with additional documentation on methods used. (comparison arrows, for starters)
  • Touch-ups to plot(), especially regarding comparison arrows
  • Bug fix for stanreg models (#196)
  • Fixed error in emmeans(obj, "1", by = "something") (#197)
  • eff_size() now supports emm_list objects with a $contrasts component, using those contrasts. This helps those who specify pairwise ~ treatment.
  • Labels in contrast() for factor combinations with by groups were wacky (#199)
  • emtrends() screwed up with multivariate models (#200).
  • Added a new argument calc to summary(). For example, calc = c(n = ~.wgt.) will add a column of sample sizes to the summary.

Changes in version 1.4.6

• Improvements to coxph support for models with strata
  • emmeans() with specs of class list now passes any offset and trend arguments (#179)
  • Added plim argument to pwpp() to allow controlling the scale
  • More documentation on using params (#180)
  • Robustified support for gls objects when data are incomplete (#181)
  • Fixed bug in joint_tests() and test(..., joint = TRUE) that can occur with nontrivial @dffun() slots (#184)
  • Improved support for Satterthwaite-based methods in gls (#185) and renamed boot-satterthwaite to appx-satterthwaite (#176)
  • Further repairs to nesting-related code (#186)
  • Fix transform argument in ref_grid() so it is same as in regrid() (#188)
  • Added pwpm() function for displaying estimates, pairwise comparisons, and P values in matrix form

Changes in version 1.4.5

• Change to .all.vars() that addresses #170
  • Addition of hidden argument scheffe.rank in summary.emmGrid() to manually specify the desired dimensionality of a Scheffe adjustment (#171)
  • Provided for ... to be included in options in calls to emmeans() and contrast(). This allows passing any summary() argument more easily, e.g., emmeans(..., type = "response", bias.adjust = TRUE, infer = c(TRUE, TRUE)) (Before, we would have had to wrap this in summary())
  • Added a plotit argument to plot.emmGrid() that works similarly to that in emmip().
  • Removed startup message for behavior change in 1.4.2; it's been long enough.
  • Fixed bug with character predictors in at` (#175)

Changes in version 1.4.4

• Fixed bug in emmeans() associated with non-factors such as Date (#162)
  • Added nesting.order option to emmip() (#163)
  • New style argument for emmip() allows plotting on a numeric scale
  • More robust detection of response transformations (#166)
  • Ensure pwpp() has tick marks on P-value axis (#167)
  • Bug fix for regrid() for error when estimates exceed bounds
  • Bug fix in auto-detecting nesting (#169) to make it less "enthusiastic"
  • Fixes to formula operations needed because formula.tools:::as.character.formula messes me up (thanks to Berwin Turloch, UWA, for alerting me)
  • Making dqrg() more visible in the documentation (because it's often useful)
  • Added more methods for emm_list objects, e.g. rbind() and as.data.frame(), as.list(), and as.emm_list()

Changes in version 1.4.3.01

• Fixed bug in post-grid support that affects, e.g., the ggeffects package (#161)

Changes in version 1.4.3

• Added "bcnPower" option to make.tran() (per car::bcnPower())
  • Scoping correction for emmtrends() (#153)
  • Allow passing ... to hook functions (need exposed by #154)
  • Addition to regrid() whereby we can fake any response transformation -- not just "log" (again inspired by #154)
  • Informative message when pbkrtest or lmerTest is not found (affects merMod objects) (#157)
  • Change in pwpp() to make extremely small P values more distinguishable

Changes in version 1.4.2

• First argument of emtrends() is now object, not model, to avoid potential mis-matching of the latter with optional mode argument
  • emtrends() now uses more robust and efficient code whereby a single reference grid is constructed containing all needed values of var. The old version could fail, e.g., in cases where the reference grid involves post-processing. (#145)
  • Added scale argument to contrast()
  • Added new "identity" contrast method
  • New eff_size() function for Cohen effect sizes
  • Expanded capabilities for interaction contrasts (#146)
  • New cov.keep argument in ref_grid() for specifying covariates to be treated just like factors (#148). A side effect is that the system default for indicator variables as covariates is to treat them like 2-level factors. This could change the results obtained from some analyses using earlier versions. To replicate old analyses, set emm_options(cov.keep = character(0)).
  • Added merMod-related options as convenience arguments (#150)
  • Bug fixes: regrid ignored offsets with Bayesian models; emtrends() did not supply options and misc arguments to emm_basis() (#143)

Changes in version 1.4.1

• Added non-estimability infrastructure for Bayesian models, stanreg in particular (#114)
  • Added max.degree argument in emtrends() making it possible to obtain higher-order trends (#133). Plus minor tuneups, e.g., smaller default increment for difference quotients
  • Made emmeans() more forgiving with 'byvariables; e.g.,emmeans(model, ~ dose | treat, by = "route")will find bothbyvariables whereas previously"route"` would be ignored.
  • Temporary fix for glitch in gls support where Satterthwaite isn't always right.
  • Attempt to make annotations clearer and more consistent regarding degrees-of-freedom methods.
  • Provisions whereby externally provided emm_basis() and recover_data() methods are used in preference to internal ones - so package developers can provide improvements over what I've cobbled together.
  • Tried to produce more informative message when recover_data() fails
  • Fixed bug in contrast() in identifying true contrasts (#134)
  • Fixed a bug in plot.summary_emm() regarding CIs and intervals (#137)
  • Improved support for response transformations. Models with formulas like like log(y + 1) ~ ... and 2*sqrt(y + 0.5) ~ ... are now auto-detected. [This may cause discrepancies with examples in past usages, but if so, that would be because the response transformation was previously incorrectly interpreted.]
  • Added a ratios argument to contrast() to decide how to handle log and logit
  • Added message/annotation when contrasts are summarized with type = "response" but there is no way to back-transform them (or we opted out with ratios = FALSE)

Changes in version 1.4

• Added a courtesy function .emm_register() to make it easier for other packages to register their emmeans support methods
  • Clarified the "confidence intervals" vignette discussion of infer, explaining that Bayesian models are handled differently (#128)
  • Added PIs option to plot.emmGrid() and emmip() (#131). Also, in plot.emmGrid(), the intervals argument has been changed to CIs for sake of consistency and less confusion; intervals is still supported for backaward compatibility.
  • plot.emmGrid gains a colors argument so we can customize colors used.
  • Bug fix for glht support (#132 contributed by Balsz Banfai)
  • regrid gains sim and N.sim arguments whereby we can generate a fake posterior sample from a frequentist model.

Changes in version 1.3.5.1

• Bug fix for gls objects with non-matrix apVar member (#119)
  • Repairs faulty links in 1.3.5 vignettes

Changes in version 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

Changes in version 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.

Changes in version 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

Changes in version 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)

Changes in version 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

Changes in version 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

Changes in version 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

Changes in version 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

Changes in version 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)

Changes in version 1.2.1

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

Changes in version 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

Changes in version 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)

Changes in version 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

Changes in version 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

Changes in version 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

Changes in version 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

Changes in version 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.