NEWS

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LMERConvenienceFunctions 3.0 (2020-10-06)

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

LMERConvenienceFunctions 2.12

• Fixed warning in “pamer.fnc” with glmer models.
• Updated “pamer.fnc” help page, more specifically, removed the note about glmer models.

LMERConvenienceFunctions 2.8

• 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)”.

LMERConvenienceFunctions 2.5 (2013-12-14)

• Fixed a bug win “bfFixefLMER_F.fnc” and “bfFixefLMER_t.fnc” when backfitting on AIC, BIC, llrt, relLik.AIC, and relLik.BIC.
• Added option "z" to argument “method”.
• Added examples to test backfitting on all methods for lmer and glmer models.

LMERConvenienceFunctions 2.4 (2013-11-30)

• Updated package to work with post-version 1.0 of package lme4.
• Revived, so to speak, function “plotLMER.fnc” from archived package “languageR” and revised everything to be compatible with lme4 version > 1.0.
• Removed any mention of “pvals.fnc” and associated functions from archived package “languageR” from any function that used it.
• In functions “ffRanefLMER.fnc” and “fitLMER.fnc”, argument “data” is depricated.

LMERConvenienceFunctions 2.1 (2013-09-24)

• Updated the percentage of deviance explained in function “pamer.fnc”.
• 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

LMERConvenienceFunctions 2.0 (2013-04-10)

• 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).
• Added backfitting on AIC, BIC, relLik.AIC, or relLik.BIC capabilities to functions “bfFixefLMER_F.fnc”, “bfFixefLMER_t.fnc”, and “fitLMER.fnc”.
• Also added functions “bfFixefLMER_F.fnc”,“bfFixefLMER_t.fnc”, and “fitLMER.fnc” an option to not test (and thus not remove) main effects.
• Updated the arguments in function “fitLMER.fnc” accordingly.
• In function “ffRanefLMER.fnc”, changed the default of argument “log.file” to “NULL”.
• Fixed a bug in fucntion “bfFixefLMER_t.fnc” when backfitting glmer models.
• Function “ffRanefLMER.fnc” can now be used with glmer models.
• Fixed a bug in function “fitLMER.fnc” regarding the forward fitting of random effects.
• WISH LIST: AIC, BIC, relLik.AIC, and relLik.BIC for random effect forward fitting (for function “ffRanefLMER.fnc”).

LMERConvenienceFunctions 1.7.0

• Fixed little bug in functions “bfFixefLMER_t.fnc” and “bfFixefLMER_F.fnc” regarding the pruning of random effects.
• Put back a piece of code that was mistakingly removed in previous version in “bfFixefLMER_t.fnc”.
• When the model is a GLMER, “z-value” instead of “t-value” is printed.
• Added function “relLik”.
• Added argument “verbosity” to function “mcposthoc.fnc”.
• Added function “summary.mcposthoc”.
• In “plotLMER3d.fnc”, “plotDensity3d.fnc”, and “plotRaw3d.fnc”, for 3d perspective plots (“persp3d”) changed the edges of the color matrix from 0 to 1.
• Re-vamped examples to make them run faster.
• Added comments to code.
• Function “posthoc.fnc” now depends on package “parallel”.
• In “plotDensity3d.fnc”, “plotLMER3d.fnc”, and “plotRaw3d.fnc”, removed argument “ret”. now invisibly returns potting information.
• Added plot.type = “image.plot” to functions “plotLMER3d.fnc” and “plotRaw3d.fnc”.

LMERConvenienceFunctions 1.6.8.3 (2012-05-28)

• 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.
• 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".
• Added glmer capabilites for function “mcposthoc.fnc”.

LMERConvenienceFunctions 1.6.8.2 (2012-04-12)

• 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 <[email protected]> for this one.
• Function “posthoc.fnc” is now depricated and replaced by “mcposthoc.fnc”;
• Added MCMC p-values functionality to function “mcposthoc.fnc”;
• Shortened example run time;
• Removed argument “data” from functions “bfFixefLMER_F.fnc”, “bfFixefLMER_t.fnc”, and “fitLMER.fnc”.

LMERConvenienceFunctions 1.6.7 (2011-12-13)

• Added arguments “add.raw”, “color.raw”, and “alpha.raw” to function “plotLMER3d.fnc”, and fixed a little bug in that function.
• Removed argument “ret” from function “plotLMER3d.fnc”. The plotting data is now invisibly returned.
• Removed dependency on package “languageR”.
• Fixed a little bug in function “ffRanefLMER.fnc”.
• Removed all data sets and put them in a new package called “LCFdata”, which is now suggested.
• Added argument “scale” to function “plotRaw3d.fnc” and “plotLMER3d.fnc”.
• Added argument “shift” to function “plotLMER3d.fnc”.
• Changed default value of argument “shift” in function “plotRaw3d.fnc” from NULL to 0.

LMERConvenienceFunctions 1.6.6 (2011-11-17)

• Removed suggestion to package “Design” and changed examples accordingly.

LMERConvenienceFunctions 1.6.4

• Fixed little bug in function “ffRanefLMER.fnc”.
• Added argument “if.warn.not.add” to functions “ffRanefLMER.fnc” and “fitLMER.fnc”.
• Added arguments “plot.dat” and “path” to function “plotLMER3d.fnc”.
• Added arguments “add”, “alpha”, and “xy” to function “plotRaw3d.fnc”.
• 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 ...”.
• Added model “z” to run a new example in function “plotRaw3d.fnc”.
• Added function “mcposthoc.fnc”.

LMERConvenienceFunctions 1.6.3 (2011-07-23)

• In function “plotLMER3d.fnc”, added the possibility to add a tittle to "persp" plots, in addition to
• the option of having a flat miror image underneath the main 3d surface of "persp3d" plots,
• rug plots for the three types of plots and for the flat miror image underneath the main 3d surface of "persp3d" plots,
• transparency control for the main 3d surface, reference level, and flat miror image for "persp3d" plots, and
• the option to return the z and color matrices used for plotting.
• Added function “plotDensity3d.fnc”.
• Added function “plotRaw3d.fnc”.
• Added data “erpFz”.

LMERConvenienceFunctions 1.6.2 (2011-06-29)

• Added argument “data” to function “posthoc.fnc”.
• Added argument “prior.releveling” to function “posthoc.fnc”.

LMERConvenienceFunctions 1.6 (2011-06-22)

• Added function “plotLMER3d.fnc” to create (dyanmic) 3d plots of models fitted with LMER.
• Added sub-argument “corr” to argument “ran.effects” in functions “ffRanefLMER.fnc” and “fitLMER.fnc”.
• 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.
• Fixed a little bug in function “ffRanefLMER.fnc” regarding the testing of random effects of the form “(Condition|Subject)”.
• 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.
• Added argument “prune.ranefs” to functions “bfFixefLMER_F.fnc”, “bfFixefLMER_t.fnc”, and “fitLMER.fnc”.

LMERConvenienceFunctions 1.5.3 (2011-06-15)

• Function “pamer.fnc” now accepts models with interactions in the ranef structure (e.g., (1|X:Y).
• 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).
• 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.

LMERConvenienceFunctions 1.5.2 (2011-05-23)

• In function “fitLMER.fnc”, changed argument “file.name” to “log.file.name” to make it more transparent.
• 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”.
• 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).
• Column “expl.dev.” in function “pamer.fnc” now lists the percentage explained (which is simply the value returned in version

LMERConvenienceFunctions 1.5 (2011-05-17)

• Function “pamer.fnc” additioanlly returns the deviance explained, R-squared, for each model term.
• Fixed a little bug with the fitting logs. The user can now change the path to where the log will be saved.
• Added argument “col = "red"” to function “mcp.fnc”.

LMERConvenienceFunctions 1.4 (2011-04-30)

• Removed dependency on package “Design”, and consequently removed any example that uses “rcs” or “poly”.

LMERConvenienceFunctions 1.3 (2011-04-28)

• Added argument “trim” to functions “mcp.fnc” and “romr.fnc”;
• 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”).
• Added values “Upper Den. Df”, “Lower Den. DF”, and “Lower p value” to function “pamer.fnc”.
• Added argument “llrt” (log-likelihood ratio testing) to functions “bfFixefLMER_F.fnc”, “bfFixefLMER.fnc_t”, and “fitLMER.fnc”.
• 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.
• Added function “posthoc.fnc”.
• Added function “perSubjectTrim.fnc”.

LMERConvenienceFunctions 1.1-23

• 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.