                  Changes in version 3.0 (2020-10-06)                   

    o   A recent change to LME4 (commit 98d8c8a, released in

                        Changes in version 2.12                         

    o   Fixed warning in ``pamer.fnc'' with glmer models.

    o   Updated ``pamer.fnc'' help page, more specifically, 
	removed the note about glmer models.

                         Changes in version 2.8                         

    o   In functions ``ffRanefLMER.fnc'', disabled the blocking
	of random effects that are not in the fixed effect structure.
	This was done so as to enable the addition of random effects
	such as ``(1+VAR1*VAR2|VAR3)''.

                  Changes in version 2.5 (2013-12-14)                   

    o   Fixed a bug win ``bfFixefLMER_F.fnc'' and
	``bfFixefLMER_t.fnc'' when backfitting on AIC,
	BIC, llrt, relLik.AIC, and relLik.BIC.

    o   Added option "z" to argument ``method''.

    o   Added examples to test backfitting on all methods for
	lmer and glmer models.

                  Changes in version 2.4 (2013-11-30)                   

    o   Updated package to work with post-version 1.0 of 
	package lme4.

    o   Revived, so to speak, function ``plotLMER.fnc'' from 
	archived package ``languageR'' and revised everything to 
	be compatible with lme4 version > 1.0.

    o   Removed any mention of ``pvals.fnc'' and associated 
	functions from archived package ``languageR'' from any 
	function that used it.

    o   In functions ``ffRanefLMER.fnc'' and ``fitLMER.fnc'', 
	argument ``data'' is depricated.

                  Changes in version 2.1 (2013-09-24)                   

    o   Updated the percentage of deviance explained in function 
	``pamer.fnc''.

    o   Revised the random effects backfitting algorithm: 
	If you have the model
	    lmm.1<-lmer(abundance~year+(year|site))
	where year is not significant, then
	-- old backfit:
	   - year is removed from fixed effects
	   - random effect is completely removed (which can actually 
	     be problematic (statistically), if it is part of your 
	     experimental set up, leading to pseudoreplicates).
	   - problems with lmer because no random effect in formula
	-- new backkfit:
	   - year is removed from fixed effects
	   - random effect is adjusted. new formula: abundance~(1|year)
	   - no problems with lmer because no random effect in formula

                  Changes in version 2.0 (2013-04-10)                   

    o   In functions ``bfFixefLMER_t.fnc'', backfitting when the
	model has factor variables with levels greater than 2 will
	issue a warning (instead of stopping the process).

    o   Added backfitting on AIC, BIC, relLik.AIC, or relLik.BIC
	capabilities to functions ``bfFixefLMER_F.fnc'',
	``bfFixefLMER_t.fnc'', and ``fitLMER.fnc''.

    o   Also added functions ``bfFixefLMER_F.fnc'',``bfFixefLMER_t.fnc'', 
	and ``fitLMER.fnc'' an option to not test (and thus not remove) 
	main effects.

    o   Updated the arguments in function ``fitLMER.fnc'' accordingly.

    o   In function ``ffRanefLMER.fnc'', changed the default of argument 
	``log.file'' to ``NULL''.

    o   Fixed a bug in fucntion ``bfFixefLMER_t.fnc'' when 
	backfitting glmer models.

    o   Function ``ffRanefLMER.fnc'' can now be used with glmer models.

    o   Fixed a bug in function ``fitLMER.fnc'' regarding the forward
	fitting of random effects.

    o   WISH LIST: AIC, BIC, relLik.AIC, and relLik.BIC for 
	random effect forward fitting (for function 
	``ffRanefLMER.fnc'').

                        Changes in version 1.7.0                        

    o   Fixed little bug in functions ``bfFixefLMER_t.fnc'' and 
	``bfFixefLMER_F.fnc'' regarding the pruning of random effects.

    o   Put back a piece of code that was mistakingly removed in 
	previous version in ``bfFixefLMER_t.fnc''.

    o   When the model is a GLMER, ``z-value'' instead of
	``t-value'' is printed.

    o   Added function ``relLik''.

    o   Added argument ``verbosity'' to function ``mcposthoc.fnc''.

    o   Added function ``summary.mcposthoc''.

    o   In ``plotLMER3d.fnc'', ``plotDensity3d.fnc'', and ``plotRaw3d.fnc'', 
	for 3d perspective plots (``persp3d'') changed the edges of the color 
	matrix from 0 to 1.

    o   Re-vamped examples to make them run faster.

    o   Added comments to code. 

    o   Function ``posthoc.fnc'' now depends on package ``parallel''. 

    o   In ``plotDensity3d.fnc'', ``plotLMER3d.fnc'', and ``plotRaw3d.fnc'', 
	removed argument ``ret''. now invisibly returns potting information.

    o   Added plot.type = ``image.plot'' to functions ``plotLMER3d.fnc'' and 
	``plotRaw3d.fnc''.

                Changes in version 1.6.8.3 (2012-05-28)                 

    o   Fixed a bug in ``bfFixefLMER_F.fnc'': The script did not 
	update the model after removing the last parameter within 
	a specific order. Now it does.

    o   In functions ``bfFixefLMER_t.fnc'' and ``bfFixefLMER_F.fnc'', 
	prior to this change, it was absolutely necessary that names of 
	factors should not occur as parts of other factor namess, e.g. "c"  
	and "cv". The script would recognise presence of "c" whereever "cv"
	is present. Now it looks for an exact string match, so factor "c" 
	will not be found in factor "cv".

    o   Added glmer capabilites for function ``mcposthoc.fnc''.

                Changes in version 1.6.8.2 (2012-04-12)                 

    o   Fixed an issues in ``bfFixefLMER_t.fnc'' with keeping 
	non-significant factors when they are present in higher 
	order interaction terms. For example: A non-significant 
	interaction term "c:d" will be excluded even though "c:t:d" 
	is significant. Thanks to Johannes Ransijn 
	<johannesransijn@gmail.com> for this one.

    o   Function ``posthoc.fnc'' is now depricated and replaced
	by ``mcposthoc.fnc'';

    o   Added MCMC p-values functionality to function ``mcposthoc.fnc'';

    o   Shortened example run time;

    o   Removed argument ``data'' from functions ``bfFixefLMER_F.fnc'',
	``bfFixefLMER_t.fnc'', and ``fitLMER.fnc''.

                 Changes in version 1.6.7 (2011-12-13)                  

    o   Added arguments ``add.raw'', ``color.raw'', and ``alpha.raw'' to 
	function ``plotLMER3d.fnc'', and fixed a little bug in that function.

    o   Removed argument ``ret'' from function ``plotLMER3d.fnc''. The plotting
	data is now invisibly returned.

    o   Removed dependency on package ``languageR''.

    o   Fixed a little bug in function ``ffRanefLMER.fnc''.

    o   Removed all data sets and put them in a new package called ``LCFdata'',
	which is now suggested. 

    o   Added argument ``scale'' to function ``plotRaw3d.fnc'' and 
	``plotLMER3d.fnc''. 

    o   Added argument ``shift'' to function ``plotLMER3d.fnc''.

    o   Changed default value of argument ``shift'' in function ``plotRaw3d.fnc''
	from NULL to 0.

                 Changes in version 1.6.6 (2011-11-17)                  

    o   Removed suggestion to package ``Design''
	and changed examples accordingly.

                        Changes in version 1.6.4                        

    o   Fixed little bug in function ``ffRanefLMER.fnc''.

    o   Added argument ``if.warn.not.add'' to functions ``ffRanefLMER.fnc'' and 
	``fitLMER.fnc''.

    o   Added arguments ``plot.dat'' and ``path'' to function 
	``plotLMER3d.fnc''.

    o   Added arguments ``add'', ``alpha'', and ``xy'' to function
	``plotRaw3d.fnc''. 

    o   In function ``plotLMER3d.fnc'', can now plot even if error message
	``Error in persp3d.default(x = as.numeric(rownames(z)), 
	y = as.numeric(colnames(z)),  : increasing 'x' and 'y' values expected''
	occurs. Issues the following warning: ``plotting anyways, but will not
	use supplied x- and y-values ...''.

    o   Added model ``z'' to run a new example in function 
	``plotRaw3d.fnc''.

    o   Added function ``mcposthoc.fnc''.

                 Changes in version 1.6.3 (2011-07-23)                  

    o   In function ``plotLMER3d.fnc'', added the possibility to 
	add a tittle to "persp" plots, in addition to

    o   the option of having a flat miror image underneath the main 3d 
	surface of "persp3d" plots,

    o   rug plots for the three types of plots and for the flat
	miror image underneath the main 3d surface of "persp3d" plots,

    o   transparency control for the main 3d surface, reference level, 
	and flat miror image for "persp3d" plots, and

    o   the option to return the z and color matrices used for 
	plotting.

    o   Added function ``plotDensity3d.fnc''.

    o   Added function ``plotRaw3d.fnc''.

    o   Added data ``erpFz''.

                 Changes in version 1.6.2 (2011-06-29)                  

    o   Added argument ``data'' to function ``posthoc.fnc''.

    o   Added argument ``prior.releveling'' to function ``posthoc.fnc''.

                  Changes in version 1.6 (2011-06-22)                   

    o   Added function ``plotLMER3d.fnc'' to create (dyanmic) 3d
	plots of models fitted with LMER.

    o   Added sub-argument ``corr'' to argument ``ran.effects'' in 
	functions ``ffRanefLMER.fnc'' and ``fitLMER.fnc''.

    o   In function ``ffRanefLMER.fnc'', when ``ran.effects'' is a vector
	(e.g., c("(Condition | Subject)", "(0 + TrialNum | Subject)")), the 
	function now checks whether variables specified in ``ran.effects'' 
	are present in the fixed-effects structure. If the variable appearing 
	in a ranef is not present in model coefficients, it is skipped.

    o   Fixed a little bug in function ``ffRanefLMER.fnc'' regarding
	the testing of random effects of the form ``(Condition|Subject)''.

    o   Fixed a little bug in functions ``bfFixefLMER_F.fnc'' and 
	``bfFixefLMER_t.fnc'': When all model terms are removed, the 
	functions now return a model with only an intercept and whatever 
	random effects were in the model.

    o   Added argument ``prune.ranefs'' to functions ``bfFixefLMER_F.fnc'',
	``bfFixefLMER_t.fnc'', and ``fitLMER.fnc''.

                 Changes in version 1.5.3 (2011-06-15)                  

    o   Function ``pamer.fnc'' now accepts models with interactions
	in the ranef structure (e.g., (1|X:Y).

    o   Added lower- and upper-bound degrees of freedom to ``posthoc.fnc''
	results, as well as lower- and upper-bound unadjusted p-values
	and lower- and upper-bound adjusted p-values (Bonferroni corrected).

    o   fixed a bug in function ``fitLMER.fnc'': the function does not set
	the current working directory to ``tempdir()'' anymore and then leave 
	you there once the fitting is done.

                 Changes in version 1.5.2 (2011-05-23)                  

    o   In function ``fitLMER.fnc'', changed argument ``file.name'' to 
	``log.file.name'' to make it more transparent.

    o   Disabled the automatic changing of the current working directory
	to directory ``temp.dir'' in functions ``bfFixefLMER_F.fnc'', 
	``bfFixefLMER_t.fnc'', ``ffRanefLMER.fnc'', and ``fitLMER.fnc''.

    o   Argumants ``model'' and ``data'' now have no default value in
	functions ``bfFixefLMER_F.fnc'', ``bfFixefLMER_t.fnc'', 
	``ffRanefLMER.fnc'', and ``fitLMER.fnc'' (before version 1.5.2,
	these arguments had ``as.character()'' as a default).

    o   Column ``expl.dev.'' in function ``pamer.fnc'' now
	lists the percentage explained (which is simply the value
	returned in version 1.5 times 100). 

                  Changes in version 1.5 (2011-05-17)                   

    o   Function ``pamer.fnc'' additioanlly returns the deviance explained, 
	R-squared, for each model term.

    o   Fixed a little bug with the fitting logs. The user can now change the
	path to where the log will be saved.

    o   Added argument ``col = "red"'' to function ``mcp.fnc''.

                  Changes in version 1.4 (2011-04-30)                   

    o   Removed dependency on package ``Design'', and consequently removed 
	any example that uses ``rcs'' or ``poly''.

                  Changes in version 1.3 (2011-04-28)                   

    o   Added argument ``trim'' to functions ``mcp.fnc'' and ``romr.fnc'';

    o   Removed argument ``data'' in function ``mcp.fnc''. The data frame 
	on which the model was fitted is now automatically retrieved from the
	model object itself (``model@frame'').

    o   Added values ``Upper Den. Df'', ``Lower Den. DF'', and ``Lower p value'' 
	to function ``pamer.fnc''.

    o   Added argument ``llrt'' (log-likelihood ratio testing) to functions 
	``bfFixefLMER_F.fnc'', ``bfFixefLMER.fnc_t'', and ``fitLMER.fnc''.

    o   Added argument ``p.value'' to functions ``fitLMER.fnc'' and 
	``bfFixefLMER_F.fnc'' to allow the user to choose to backfit either 
	on upper-bound (anti-conservative) or lower-bound (consevative) 
	\emph{p''-values.

    o   Added function ``posthoc.fnc''.

    o   Added function ``perSubjectTrim.fnc''.

                       Changes in version 1.1-23                        

    o   of the table produced by anova(), breaking multiple
	functions within LMERConvenienceFunctions.
	* This was fixed.
	* Removed anything that had to do with RGL. It was too
	problematic.
