shortened startup message, changed line endigs to LF

.gitignore

@@ -11,3 +11,4 @@
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
+.Rproj.user

DESCRIPTION

@@ -1,25 +1,25 @@
-Package: afex
-Type: Package
-Title: Analysis of Factorial Experiments
-Depends: R (>= 3.0.0), lme4 (>= 1.0.5), reshape2, lsmeans (>= 2.17)
-Suggests: ascii, xtable, parallel, plyr, optimx, nloptr, knitr, lattice, multcomp, testthat, mlmRev
-Imports: stringr, coin, Matrix, pbkrtest (>= 0.3-6), car, stats, utils
-Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models.
-            aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures),
-            or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per
-            row), potentially aggregating multiple observations per individual and cell of the design. mixed()
-            fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either
-            Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and
-            GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default
-            (imitating commercial statistical software).
-URL: https://github.com/singmann/afex
-License: GPL (>=3)
-Encoding: UTF-8
-VignetteBuilder: knitr
-Authors@R: c(person(given="Henrik", family="Singmann", role=c("aut", "cre"), email="singmann+afex@gmail.com"),
-            person(given="Ben", family="Bolker", role=c("aut")), person(given="Jake", family="Westfall",
-            role=c("aut")), person(given="Søren", family="Højsgaard", role=c("ctb")), person(given="John",
-            family="Fox", role=c("ctb")), person(given="Michael A.", family="Lawrence", role=c("ctb")),
-            person(given="Ulf", family="Mertens", role=c("ctb")) )
-Version: 0.14-1
-Date: 2015-08-13
+Package: afex
+Type: Package
+Title: Analysis of Factorial Experiments
+Depends: R (>= 3.0.0), lme4 (>= 1.0.5), reshape2, lsmeans (>= 2.17)
+Suggests: ascii, xtable, parallel, plyr, optimx, nloptr, knitr, lattice, multcomp, testthat, mlmRev
+Imports: stringr, coin, Matrix, pbkrtest (>= 0.3-6), car, stats, utils
+Description: Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(),
+             aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed
+             between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row),
+             potentially aggregating multiple observations per individual and cell of the design. mixed() fits mixed
+             models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger
+             approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio
+             tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical
+             software).
+URL: https://github.com/singmann/afex
+License: GPL (>=3)
+Encoding: UTF-8
+VignetteBuilder: knitr
+Authors@R: c(person(given="Henrik", family="Singmann", role=c("aut", "cre"), email="singmann+afex@gmail.com"),
+             person(given="Ben", family="Bolker", role=c("aut")), person(given="Jake", family="Westfall", role=c("aut")),
+             person(given="Søren", family="Højsgaard", role=c("ctb")), person(given="John", family="Fox", role=c("ctb")),
+             person(given="Michael A.", family="Lawrence", role=c("ctb")), person(given="Ulf", family="Mertens",
+             role=c("ctb")) )
+Version: 0.14-1
+Date: 2015-08-16

NAMESPACE

@@ -1,86 +1,86 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
-
-S3method(anova,afex_aov)
-S3method(anova,mixed)
-S3method(lsm.basis,afex_aov)
-S3method(lsm.basis,mixed)
-S3method(nice,afex_aov)
-S3method(nice,anova)
-S3method(nice,mixed)
-S3method(print,afex_aov)
-S3method(print,mixed)
-S3method(recover.data,afex_aov)
-S3method(recover.data,mixed)
-S3method(summary,afex_aov)
-S3method(summary,mixed)
-export(afex_options)
-export(allFit)
-export(aov.car)
-export(aov4)
-export(aov_4)
-export(aov_car)
-export(aov_ez)
-export(compare.2.vectors)
-export(ems)
-export(ez.glm)
-export(mixed)
-export(nice)
-export(round_ps)
-export(set_default_contrasts)
-export(set_deviation_contrasts)
-export(set_effects_contrasts)
-export(set_sum_contrasts)
-export(set_treatment_contrasts)
-import(pbkrtest)
-importClassesFrom(Matrix,Matrix)
-importFrom(Matrix,Matrix)
-importFrom(Matrix,rankMatrix)
-importFrom(Matrix,sparseMatrix)
-importFrom(car,Anova)
-importFrom(coin,approximate)
-importFrom(coin,median_test)
-importFrom(coin,oneway_test)
-importFrom(coin,pvalue)
-importFrom(coin,statistic)
-importFrom(coin,wilcox_test)
-importFrom(lme4,findbars)
-importFrom(lme4,fixef)
-importFrom(lme4,getME)
-importFrom(lme4,glmer)
-importFrom(lme4,glmerControl)
-importFrom(lme4,isGLMM)
-importFrom(lme4,isREML)
-importFrom(lme4,lmer)
-importFrom(lme4,lmerControl)
-importFrom(lme4,nobars)
-importFrom(lsmeans,lsm.basis)
-importFrom(lsmeans,recover.data)
-importFrom(parallel,clusterApplyLB)
-importFrom(parallel,clusterCall)
-importFrom(parallel,clusterEvalQ)
-importFrom(parallel,clusterExport)
-importFrom(reshape2,dcast)
-importFrom(stats,"contrasts<-")
-importFrom(stats,anova)
-importFrom(stats,as.formula)
-importFrom(stats,coef)
-importFrom(stats,logLik)
-importFrom(stats,model.frame)
-importFrom(stats,model.matrix)
-importFrom(stats,setNames)
-importFrom(stats,t.test)
-importFrom(stats,terms)
-importFrom(stats,update)
-importFrom(stats,vcov)
-importFrom(stats,wilcox.test)
-importFrom(stats,xtabs)
-importFrom(stringr,str_c)
-importFrom(stringr,str_detect)
-importFrom(stringr,str_extract)
-importFrom(stringr,str_replace_all)
-importFrom(utils,ls.str)
-importMethodsFrom(Matrix,"%*%")
-importMethodsFrom(Matrix,diag)
-importMethodsFrom(Matrix,isSymmetric)
-importMethodsFrom(Matrix,solve)
-importMethodsFrom(Matrix,t)
+# Generated by roxygen2 (4.1.1): do not edit by hand
+
+S3method(anova,afex_aov)
+S3method(anova,mixed)
+S3method(lsm.basis,afex_aov)
+S3method(lsm.basis,mixed)
+S3method(nice,afex_aov)
+S3method(nice,anova)
+S3method(nice,mixed)
+S3method(print,afex_aov)
+S3method(print,mixed)
+S3method(recover.data,afex_aov)
+S3method(recover.data,mixed)
+S3method(summary,afex_aov)
+S3method(summary,mixed)
+export(afex_options)
+export(allFit)
+export(aov.car)
+export(aov4)
+export(aov_4)
+export(aov_car)
+export(aov_ez)
+export(compare.2.vectors)
+export(ems)
+export(ez.glm)
+export(mixed)
+export(nice)
+export(round_ps)
+export(set_default_contrasts)
+export(set_deviation_contrasts)
+export(set_effects_contrasts)
+export(set_sum_contrasts)
+export(set_treatment_contrasts)
+import(pbkrtest)
+importClassesFrom(Matrix,Matrix)
+importFrom(Matrix,Matrix)
+importFrom(Matrix,rankMatrix)
+importFrom(Matrix,sparseMatrix)
+importFrom(car,Anova)
+importFrom(coin,approximate)
+importFrom(coin,median_test)
+importFrom(coin,oneway_test)
+importFrom(coin,pvalue)
+importFrom(coin,statistic)
+importFrom(coin,wilcox_test)
+importFrom(lme4,findbars)
+importFrom(lme4,fixef)
+importFrom(lme4,getME)
+importFrom(lme4,glmer)
+importFrom(lme4,glmerControl)
+importFrom(lme4,isGLMM)
+importFrom(lme4,isREML)
+importFrom(lme4,lmer)
+importFrom(lme4,lmerControl)
+importFrom(lme4,nobars)
+importFrom(lsmeans,lsm.basis)
+importFrom(lsmeans,recover.data)
+importFrom(parallel,clusterApplyLB)
+importFrom(parallel,clusterCall)
+importFrom(parallel,clusterEvalQ)
+importFrom(parallel,clusterExport)
+importFrom(reshape2,dcast)
+importFrom(stats,"contrasts<-")
+importFrom(stats,anova)
+importFrom(stats,as.formula)
+importFrom(stats,coef)
+importFrom(stats,logLik)
+importFrom(stats,model.frame)
+importFrom(stats,model.matrix)
+importFrom(stats,setNames)
+importFrom(stats,t.test)
+importFrom(stats,terms)
+importFrom(stats,update)
+importFrom(stats,vcov)
+importFrom(stats,wilcox.test)
+importFrom(stats,xtabs)
+importFrom(stringr,str_c)
+importFrom(stringr,str_detect)
+importFrom(stringr,str_extract)
+importFrom(stringr,str_replace_all)
+importFrom(utils,ls.str)
+importMethodsFrom(Matrix,"%*%")
+importMethodsFrom(Matrix,diag)
+importMethodsFrom(Matrix,isSymmetric)
+importMethodsFrom(Matrix,solve)
+importMethodsFrom(Matrix,t)

R/afex-package.R

@@ -1,22 +1,22 @@
-#' Analysis of Factorial Experiments.
-#'
-#' \tabular{ll}{
-#' Package: \tab afex\cr
-#' Type: \tab Package\cr
-#' Version: \tab 0.14-1\cr
-#' Date: \tab 2015-08-13\cr
-#' Depends: \tab R (>= 3.0.0), lme4 (>= 1.0.5), reshape2, lsmeans (>= 2.17)\cr
-#' Encoding: \tab UTF-8\cr
-#' License: \tab GPL (>=3)\cr
-#' URL: \tab https://github.com/singmann/afex\cr
-#' }
-#'
-#' Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software).
-#'
-#' @aliases afex-package
-#' @name afex-package
-#' @docType package
-#' @title The afex Package
-#' @author Henrik Singmann, Ben Bolker, Jake Westfall, with contributions from Søren Højsgaard, John Fox, Michael A. Lawrence, Ulf Mertens
-#' @keywords package
-NULL
+#' Analysis of Factorial Experiments.
+#'
+#' \tabular{ll}{
+#' Package: \tab afex\cr
+#' Type: \tab Package\cr
+#' Version: \tab 0.14-1\cr
+#' Date: \tab 2015-08-16\cr
+#' Depends: \tab R (>= 3.0.0), lme4 (>= 1.0.5), reshape2, lsmeans (>= 2.17)\cr
+#' Encoding: \tab UTF-8\cr
+#' License: \tab GPL (>=3)\cr
+#' URL: \tab https://github.com/singmann/afex\cr
+#' }
+#'
+#' Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software).
+#'
+#' @aliases afex-package
+#' @name afex-package
+#' @docType package
+#' @title The afex Package
+#' @author Henrik Singmann, Ben Bolker, Jake Westfall, with contributions from Søren Højsgaard, John Fox, Michael A. Lawrence, Ulf Mertens
+#' @keywords package
+NULL

R/zzz.R

@@ -1,24 +1,24 @@
-
-
-## set default options for afex.options:
-.afexEnv <- new.env()
-assign("type", 3, envir = .afexEnv)
-assign("check.contrasts", TRUE, envir = .afexEnv)
-assign("method_mixed",  "KR", envir = .afexEnv)
-assign("return_aov",  "afex_aov", envir = .afexEnv)
-assign("es_aov",  "ges", envir = .afexEnv)
-assign("correction_aov",  "GG", envir = .afexEnv)
-assign("factorize", TRUE, envir = .afexEnv)
-
-.onAttach <- function(libname, pkgname) {
-	#assign(".oldContrasts", options("contrasts"), envir = .GlobalEnv)
-  packageStartupMessage("************\nWelcome to afex. Important changes in the current version:")
-  packageStartupMessage("- Functions for computing ANOVAs have been renamed to: aov_car(), aov_ez(), and aov_4().\n- ANOVA functions now return an object of class 'afex_aov' as default, see: ?aov_car\n- Objects of class 'afex_aov' can be directly passed to lsmeans for contrasts and follow-up tests.\n- As 'afex_aov' calculations can be costly reset previous behavior via: afex_options(return_aov='nice')\n- Many more arguments can now be set globally via options, see: afex_options()\n************")
-	#if (options("contrasts")[[1]][1] != "contr.sum") {
-		#packageStartupMessage("Setting contrasts to effects coding: options(contrasts=c('contr.sum', 'contr.poly'))\nThis affects all functions using contrasts (e.g., lmer, lm, aov, ...).\nTo reset default settings run: options(contrasts=c('contr.treatment', 'contr.poly')) (all afex functions should be unaffected by this)\n")
-    # \nPrevious contrasts saved in '.oldContrasts'.
-		#options(contrasts=c('contr.sum', 'contr.poly'))
-	#} else packageStartupMessage("Contrasts already set to effects coding: options(contrasts=c('contr.sum', '...'))\n")
-  #packageStartupMessage("afex loads the required packages (e.g., lme4, car, pbkrtest) in an order that should not lead to problems.\nLoading any of the packages (specifically lme4) beforehand can lead to problems (especially with older versions of either).\nLoading nlme in addition to afex (before or after loading it), may especially lead to problems.\n************")
-}
-
+
+
+## set default options for afex.options:
+.afexEnv <- new.env()
+assign("type", 3, envir = .afexEnv)
+assign("check.contrasts", TRUE, envir = .afexEnv)
+assign("method_mixed",  "KR", envir = .afexEnv)
+assign("return_aov",  "afex_aov", envir = .afexEnv)
+assign("es_aov",  "ges", envir = .afexEnv)
+assign("correction_aov",  "GG", envir = .afexEnv)
+assign("factorize", TRUE, envir = .afexEnv)
+
+.onAttach <- function(libname, pkgname) {
+	#assign(".oldContrasts", options("contrasts"), envir = .GlobalEnv)
+  packageStartupMessage("************\nWelcome to afex. Important changes in the current version:")
+  packageStartupMessage("- Functions for ANOVAs have been renamed to: aov_car(), aov_ez(), and aov_4().\n- ANOVA functions return an object of class 'afex_aov' as default, see: ?aov_car\n- 'afex_aov' objects can be passed to lsmeans for contrasts and follow-up tests.\n- Reset previous (faster) behavior via: afex_options(return_aov='nice')\n- Many more arguments can now be set globally via options, see: afex_options()\n************")
+	#if (options("contrasts")[[1]][1] != "contr.sum") {
+		#packageStartupMessage("Setting contrasts to effects coding: options(contrasts=c('contr.sum', 'contr.poly'))\nThis affects all functions using contrasts (e.g., lmer, lm, aov, ...).\nTo reset default settings run: options(contrasts=c('contr.treatment', 'contr.poly')) (all afex functions should be unaffected by this)\n")
+    # \nPrevious contrasts saved in '.oldContrasts'.
+		#options(contrasts=c('contr.sum', 'contr.poly'))
+	#} else packageStartupMessage("Contrasts already set to effects coding: options(contrasts=c('contr.sum', '...'))\n")
+  #packageStartupMessage("afex loads the required packages (e.g., lme4, car, pbkrtest) in an order that should not lead to problems.\nLoading any of the packages (specifically lme4) beforehand can lead to problems (especially with older versions of either).\nLoading nlme in addition to afex (before or after loading it), may especially lead to problems.\n************")
+}
+

man/afex-package.Rd

@@ -1,28 +1,28 @@
-% Generated by roxygen2 (4.1.1): do not edit by hand
-% Please edit documentation in R/afex-package.R
-\docType{package}
-\name{afex-package}
-\alias{afex-package}
-\title{The afex Package}
-\description{
-Analysis of Factorial Experiments.
-}
-\details{
-\tabular{ll}{
-Package: \tab afex\cr
-Type: \tab Package\cr
-Version: \tab 0.14-1\cr
-Date: \tab 2015-08-13\cr
-Depends: \tab R (>= 3.0.0), lme4 (>= 1.0.5), reshape2, lsmeans (>= 2.17)\cr
-Encoding: \tab UTF-8\cr
-License: \tab GPL (>=3)\cr
-URL: \tab https://github.com/singmann/afex\cr
-}
-
-Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software).
-}
-\author{
-Henrik Singmann, Ben Bolker, Jake Westfall, with contributions from Søren Højsgaard, John Fox, Michael A. Lawrence, Ulf Mertens
-}
-\keyword{package}
-
+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/afex-package.R
+\docType{package}
+\name{afex-package}
+\alias{afex-package}
+\title{The afex Package}
+\description{
+Analysis of Factorial Experiments.
+}
+\details{
+\tabular{ll}{
+Package: \tab afex\cr
+Type: \tab Package\cr
+Version: \tab 0.14-1\cr
+Date: \tab 2015-08-16\cr
+Depends: \tab R (>= 3.0.0), lme4 (>= 1.0.5), reshape2, lsmeans (>= 2.17)\cr
+Encoding: \tab UTF-8\cr
+License: \tab GPL (>=3)\cr
+URL: \tab https://github.com/singmann/afex\cr
+}
+
+Provides convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed between-within (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), potentially aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex uses type 3 sums of squares as default (imitating commercial statistical software).
+}
+\author{
+Henrik Singmann, Ben Bolker, Jake Westfall, with contributions from Søren Højsgaard, John Fox, Michael A. Lawrence, Ulf Mertens
+}
+\keyword{package}
+