Changelog for 'lsmeans' package
2.18
In DESCRIPTION, moved all Enhances packages to Suggests;
Enhancements can't be tested and cause headaches
Fixed bug in lstrends - 'data' argument was not used correctly
Fixed bug in cld where fatal error occurs when type = "response"
Added temporary workaround for 'maov' and 'manova' objects
(error in stats coef.maov now fixed in R-devel)
Re-enabled existing code for 'mer' support (lme4.0) --
previously had trouble with > 1 Additional_repositories
Made "dunnettx"-adjusted critical values more robust
Coding improvements for adjusted p values and critical values
Added 'consec.lsmc' and 'mean_chg.lsmc' to available contrasts
Added support for the CARBayes package
2.17
Removed unneeded import of 'Matrix' (could have done this in 2.12
when I stopped using my own adaptation of 'pbkrtest' code)
Bug fix for gls, lme, nlme objects with 'weights' argument
Allows for character predictors in models as well as factors
Exported selected S3 methods for lsm.basis and recover.data
for use by other packages
Added 'post.beta' slot in 'ref.grid' and 'lsmobj' classes;
if not NA, holds sample from posterior of fixed effects.
Also added 'as.mcmc' function to return posterior sample
of lsmeans when 'post.beta' has data
Added support for 'MCMCglmm' and some 'mcmc' objects produced
by the 'MCMCpack' package
2.16
Added support for 'nlme' objects (for parameters in 'fixed')
(and associated additional vignette example)
Degrees of freedom now produced with lme and nlme objects
(uses containment-like method)
Addition of 'name' argument in 'contrast'
Now built with byte-compiler enabled
Bug fix in lstrends when there is a multivariate response
Corrected error in annotation for Tukey-adjusted P values
Other minor bug fixes and documentation improvements
2.15
Clarified annotations for Tukey and Scheffe-adjusted summaries
Moved estimability code to a separate 'estmability' package
Basic support for model objects in rms package
Explicit non-support for gam (previously ran due to
inheritance, but produced the wrong results!)
2.14
Model weights are now used instead of frequencies when weights
are not "equal"
Fixed error in 'lstrends' when 'specs' is two-sided formula
Added more/better references for LS means
Yet more enhancements for for clm, clmm, polr...
"mean.class" mode, uses response name for "prob" mode
"scale" mode does lsmeans for estimated log-scale
Enhancements to 'weights' argument in 'lsmeans':
- May now provide a matrix - it cycles through its rows
- weights = "show.levels" shows the factor comb's averaged
Added 'reverse' option to 'pairs'
Added 'type' argument in 'ref.grid' for convenience
Fixed some errors/omissions in documentation of 'update'
One-sided 'tail' spec now applies to CIs as well as tests
New adjustment methods added:
"mvt" provides exact one-step methods like Tukey, Dunnett
"dunnettx" is approximate and only available for 2-sided cases
Added contrast fcns "tukey" and "dunnett" - these are pseudonyms
for "pairwise" and "trt.vs.ctrl" resp.
More adjustments are available for confidence intervals
Tries harder to use only appropriate adjust methods
New 'estType' attribute for 'update' related to the above
'cld' accommodates when 'multcompView' isn't installed, thus
can still pass checks without that package
Removed .old.lsmeans and associated vignette
2.13
Provides for equivalence, noninferiority, etc. tests via
'side' and 'delta' arguments in 'summary' or 'test'. Also
for non-zero null values via 'null'
Added support for ordinal package objects 'clm', 'clmm'
Option 'mode' added for 'polr' objects, defaulting to "latent".
NOTE - NEED TO SET 'mode = "linear.predictor" TO REPRODUCE
PAST RESULTS FOR 'polr' OBJECTS.
nlme and lme4 moved to 'Enhances' field for consistency
### Added limited support for mer objects (lme4.0 package)
### I dropped this because it messes-up the CRAN checks
Added 'adjustSigma' option for 'lme' objects
(works like in 'summary.lme')
Fixed error in handling offsets for 'polr' objects
Fixed error in omitting modeled covariates when there was a
multivariate response.
Fixed bug in 'contrast' that failed to update 'pri.vars'
which, e.g., creates an error in a subsequent plot
Fixed bug in plot - it had ignored xlab when horizontal = FALSE
In lsmip with type = "response", the vertical axis is
now labeled with misc$inv.lbl when available
Removed frequencies and offsets from row labels in 'as.glht'
Fixed 'as.glht' so df may be omitted or set to NA for asymptotics
Renamed the 'parm' argument in 'test' to 'null'
Removed superfluous "P values are asymptotic" messages.
Revision to function producing estimates, SEs, and df
Added provision to specify 'estHook' and 'vcovHook' in 'misc' slot
to allow for custom routines for estimates and covariances.
'.is.estble' is renamed 'is.estble' -- exported and documented.
The 'by' variable for 'test' now also works when 'joint = TRUE'
2.12
*** Developers supporting lsmeans please note: ***
*** Change to lsm.basis prototype: Added a "..." argument ***
Removed own patch for df from pbkrtest in favor of its Lb_ddf.
This means you must have pbkrtest 0.4-1 or newer
Added 'plot.lsmobj' method to display confidence intervals
These plots also optionally can display comparison arrows
that attempt to display significance of pairwise comparisons
according to their degree of overlap
Added 'joint' argument to 'test'
Fixed a bug in vcov
Modified 'auto.noise' so 'side' has levels 'L' and 'R'
rather than 'R' and 'L' (so not in reverse position in plots!)
Added support for:
gee, geeglm, and geese objects (gee, geepack);
glmmadmb objects (glmmADMB);
mixed objects (afex)
Added 'lsmobj' function to construct an lsmobj from
summary statistics
Overhauled 'lsmeans-package' help page to provide an overview
with links to key functions, and integrated details of
model-specific implementation in a new 'models' help page
2.11
Added vcov method for ref.grid
Added 'weights' argument for lsmeans - may be numeric, or
the string "equal", "proportional", "outer", or "cells"
Enhanced 'cov.reduce' argument in 'ref.grid' to allow formulas,
useful when you think covariates depend on other variables.
Also, when cov.reduce is a list, it may now include
anything -- function, logical, or formula
Additional dataset 'feedlot'
Now 'cld' does not break when there are non-estimable lsmeans
Fixed situation where one error message masks another more
informative one
Added possibility of 'summary=' spec for lsm.options, which
sets defaults for summary, predict, and lsmip
Improvements/updates to vignettes
Minor coding/efficiency improvements
Removed 'df' arg for ref.grid, stupidly added in 2.10
(we can set df as part of 'options' arg)
2.10
Support for 'aovlist' objects (does intra-block analysis)
To use, avoid contr.treatment; use contr.sum or other that sums to 0
Added 'contrast', 'test', 'pairs', 'confint', 'cld' methods for
lsmlist, with 'which' argument defaulting to 1
Added 'disable.pbkrtest' option (via lsm.options) if you don't want
bias correction and K-R degrees of freedom with lmerMod objects
Added 'df' argument to 'ref.grid' constructor, also 'summary' and
'update'.
2.05
Corrected error in Tukey-adjusted confidence intervals
New dataset 'oranges'
Completely revised, improved vignette 'using-lsmeans'
New vignette 'extending lsmeans'
New 'mult.name' argument in 'ref.grid'
New 'lsm.options' function and associated support for
setting display defaults for various objects
Improved estimability checking and ability to set the
tolerance via lsmeans.options(estble.tol = ...)
Added estimability support for merMod, now that lme4
supports rank-deficient models
Miscellaneous small improvements to code and datasets
2.00-5
Additional message showing what factors have been averaged over
Now adds offsets to predictions when model contains
offset() terms (but not for an 'offset' argument)
New 'update' method for "ref.grid" objects
Broader support for transformations (see ?update.ref.grid)
Changed all S3 methods for "lsmobj", except 'show', to S3
methods for the "ref.grid" class, since they all work
just fine for this class as well.
Added an example for 'lstrends'
Removed unneeded misc$ylevs element in ref.grid objects
New way to bypass unneeded package-loading from pbkrtest
Added an example for lstrends as there wasn't one
Fixed minor bug in summary() - a try() call should have been
with silent=TRUE
2.00-4
Reverted to code that just loads pbkrtest and its required
(but unneeded) packages when pbkrtest is needed
2.00-3
Slight change in use of attach() in lsm.basis.merMod
2.00-2
Added some support for adjusted confidence limits
Minor bug fix to make recover.data work with more gls models
Fewer unneeded packages are loaded
2.00-1
Fixed a minor formatting issue in a vignette
2.00-0
This is a major redesign of the package. Single function 'lsmeans'
is replaced by methods for different types of models and
specifications, and returns an 'lsmobj' rather than a 'data.frame'.
New functions 'ref.grid', 'contrast', 'lstrends', and new 'summary',
'confint', 'test', 'glht', 'cld' methods for 'ref.grid' and 'lsmobj'
objects. See the vignette "lsmeans-changes" for more details.
This version is easily extensible to various types of model objects,
and several more are supported such as survreg, coxph, polr.
There is also full support for na.actions, and for back-transforming
results when a response is transformed or a link function is used.
1.10-4
Fixed bug in cld spec that caused multiple letter columns
1.10-3
Added cld capability
Fix to lsmip so factor levels are not re-ordered
Added new dataset: 'auto.noise'
Fixed problem in documentation link to another package
1.10-2
Added simple support for models with a multivariate response
Bug fix for case when only one contrast is specified
Examples that use lme4 package are made conditional per CRAN requirements
since lme4 version 1.0-4 and later depend on a non-portable package
Dependency modifications to meet CRAN requirements. Includes adding
multcomp as required package, since we enhance glht
1.10-01
Now works again for 'gls' objects
1.10-00
Added contrast families for effects and "deleted effects"
Added "scheffe" option for 'adjust' argument
Added lsmip function (interaction plots)
Fixed Tukey-adjusted P values for d.f. near 2.
(Note: ptukey does not work when there are less than 2 d.f.)
Allow covariates in 'specs' formula (also allows covariates to
have multiple levels and be part of the reference grid that
is averaged over in determining LS means)
Allow cov.reduce to be logical - mostly to implement a 'unique' option
No d.f. or adjusted covariance matrix for GLMMs (questionable validity,
plus pbkrtest won't play along)
Now checks lengths of contrast coef's for conformity
Fixed a bug in estimability checking (occurred when qr.R does not
return a square matrix)
Efficiency improvements. Now requires 'plyr' package
1.06-06 - June 13, 2013
Added support for lmerMod objects (gitHub version of lme4)
1.06-05 - February 13, 2013
Fixed a bug whereby unused levels of factors can create havoc.
1.06-00 - January 14, 2013
Added a 'trend' argument for estimating and contrasting fitted trends
rather than lsmeans
1.05-01 - December 5, 2012
Fixed a bug that occurs when model contains expressions like (a + b + c)^2
or other expressions that expand to interaction terms
1.05-00 - November 2, 2012
Added an 'lf' boolean argument to return the matrices of linear functions
without evaluating them
Added a function 'lsm' and corresponding method for 'glht'; thus, now we
can use lsm() much like mcp()
Changed examples with glht to integer df -- due to a recent change in mvtnorm
glhargs$df is coerced to an integer before passing, but in lsm() it is
up to the user to pass appropriate arguments to glht
1.00-00 - October 19, 2012
Added support for factors in 'at' argument (can use it to restrict results)
Added columns with factor levels to lsmeans table - for possible use in plots
Extended trt.vs.ctrl.lsmc to accommodate more than one reference level
(Thanks to Florent Duyme, ARVALIS - Institut du v?g?tal, for suggesting this)
Refinements to print methods, including new class 'data.frame.lsm' to display
results the way I want them
If 'glhargs' is used, those elements are now of class 'summary.glht'.
We can still use those results in the same ways as before
Added support for adjustment methods in 'p.adjust' (stats)
Included a couple of sample datasets
Various small bug fixes (e.g. subsets bug)
0.99-80 - September 19, 2012
Now finds degrees of freedom when appropriate for all but lme objects
(For mer objects, get df only if 'pbkrtest' installed)
lsmeans tables now show confidence intervals instead of t tests
and contrast output shows p values (both assuming df are available)
Added a 'conf' argument for confidence level in lsmean intervals
Added a 'glhargs' argument; if provided, lsmeans passes its contrasts
to the 'glht' function in the 'multcomp' package
Added an 'adjust' argument for popular single-step multiplicity corrections
(uncorrected, Tukey, Bonferroni, and Sidak)
Contrast-generating functions now produce an 'adjust' attribute which
provides a default multiplicity-adjustment method
The 'check.cells' argument is now deprecated. Instead, we do an actual
check of estimability in rank-deficient cases (currently can happen
only with 'lm' objects). This check is not optional
Renamed the vignette to avoid confusion with the regular documentation
Returned object is now assigned class "lsm" which has its own print method.
0.99 - August 27, 2012
Now can handle predictors coerced to 'factor' or 'ordered'
Now can handle predictors deleted due to rank deficiency
Now can handle models with matrices among the predictors
(uses 'cov.reduce' on each column; 'at' not supported for matrix covariate)
Added support for gls objects (and documented that it works also for glm and glmer)
Added a check for empty cells in the design (relative to the model). This (by default)
forces a NA to be outputted for any lsmeans that are corrupted by rank deficiencies
Generates a warning if specified factor(s) interact with other predictors
Better and more comprehensive vignette
Added a whole lot of comments to the code (you won't see these, but be glad,
as it greatly aids maintainability)
Added error messages for anticipatable user errors
Numerous bug fixes and corrections to documentation
Still no d.f. or P values. Those could take awhile.
0.90 - August 14, 2012
First release, still needs some refinements and bullet-proofing