Changelog for 'lsmeans' package

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