prepare minor CRAN submission

DESCRIPTION

@@ -77,5 +77,5 @@ Authors@R: c(person(given="Henrik", family="Singmann", role=c("aut", "cre"),
          person(given="Russell", family="Lenth", role=c("ctb")), 
          person(given="Rune", family="Haubo Bojesen Christensen", role=c("ctb")))
 Version: 1.4-1
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyData: true

R/mixed.R

@@ -35,8 +35,8 @@
 #'   tests, taken from \code{\link{afex_options}}.
 #' @param method character vector indicating which methods for obtaining
 #'   p-values should be used: \code{"S"} corresponds to the Satterthwaite
-#'   approximation for degrees of freedom (via \code{\link{lmerTest}}, only
-#'   LMMs), \code{"KR"} corresponds to the Kenward-Roger approximation for
+#'   approximation for degrees of freedom (via \code{\link[lmerTest]{lmerTest}},
+#'   only LMMs), \code{"KR"} corresponds to the Kenward-Roger approximation for
 #'   degrees of freedom (only LMMs), \code{"PB"} calculates p-values based on
 #'   parametric bootstrap, \code{"LRT"} calculates p-values via the likelihood
 #'   ratio tests implemented in the \code{anova} method for \code{merMod}
@@ -102,8 +102,9 @@
 #'   the \code{+}, \code{sig_symbols = rep("", 4)} will display no symbols. The
 #'   default is given by \code{afex_options("sig_symbols")}.
 #' @param ... further arguments (such as \code{weights}, \code{family}, or
-#'   \code{control}) passed to \code{\link{lmer}}/\code{\link{glmer}}. Note that
-#'   additional data (e.g., \code{weights}) need to be passed fully and not only
+#'   \code{control}) passed to
+#'   \code{\link[lme4]{lmer}}/\code{\link[lme4]{glmer}}. Note that additional
+#'   data (e.g., \code{weights}) need to be passed fully and not only
 #'   by name (e.g., \code{weights = df$weights} and not \code{weights =
 #'   weights}).
 #'
@@ -190,7 +191,7 @@
 #' of \code{anova.merMod}) which produces the known LRT tables.
 #'
 #' The \code{summary} method for objects of class \code{mixed} simply calls
-#' \code{\link{summary.merMod}} on the full model.
+#' \code{\link[lme4]{summary.merMod}} on the full model.
 #'
 #' If \code{return = "merMod"} (or when invoking \code{lmer_alt}), an object of
 #' class \code{"lmerModLmerTest"} or of class \code{"merMod"} (depending on the

dev.R

@@ -7,10 +7,11 @@ options(error = NULL)
 devtools::test()
 ## before building, consider recreating the glmmTMB object for the vignette
 devtools::build(args = "--compact-vignettes=both", 
+                manual = TRUE,
                 path = "development/") # R CMD build afex --compact-vignettes="gs+qpdf"
 document()
 check()
-check_built(path = "development/afex_1.3-1.tar.gz")
+check_built(path = "development/afex_1.4-1.tar.gz")
 
 ## works better on windows:
 devtools::test(filter = "plot", invert = TRUE)

vignettes/afex_analysing_accuracy_data.Rmd

@@ -4,7 +4,7 @@ author: "Henrik Singmann"
 date: "`r Sys.Date()`"
 show_toc: true
 output:
-  knitr:::html_vignette:
+  rmarkdown:::html_vignette:
     toc: yes
 vignette: >
   %\VignetteIndexEntry{Analysis of Accuracy Data using ANOVA and binomial GLMMs}

vignettes/afex_anova_example.Rmd

@@ -4,7 +4,7 @@ author: "Henrik Singmann"
 date: "`r Sys.Date()`"
 show_toc: true
 output:
-  knitr:::html_vignette:
+  rmarkdown:::html_vignette:
     toc: yes
 vignette: >
   %\VignetteIndexEntry{ANOVA and Post-Hoc Contrasts: Reanalysis of Singmann and Klauer (2011)}

vignettes/afex_mixed_example.Rmd

@@ -4,7 +4,7 @@ author: "Henrik Singmann"
 date: "`r Sys.Date()`"
 show_toc: true
 output:
-  knitr:::html_vignette:
+  rmarkdown:::html_vignette:
     toc: yes
 vignette: >
   %\VignetteIndexEntry{Mixed Model Example Analysis: Reanalysis of Freeman et al. (2010)}

vignettes/afex_plot_introduction.Rmd

@@ -4,7 +4,7 @@ author: "Henrik Singmann"
 date: "`r Sys.Date()`"
 show_toc: true
 output:
-  knitr:::html_vignette:
+  rmarkdown:::html_vignette:
     toc: yes
 vignette: >
   %\VignetteIndexEntry{afex_plot: Publication Ready Plots for Experimental Designs}

vignettes/afex_plot_supported_models.Rmd

@@ -4,7 +4,7 @@ author: "Henrik Singmann"
 date: "`r Sys.Date()`"
 show_toc: true
 output:
-  knitr:::html_vignette:
+  rmarkdown:::html_vignette:
     toc: yes
 vignette: >
   %\VignetteIndexEntry{afex_plot: Supported Models}

vignettes/assumptions_of_ANOVAs.Rmd

@@ -4,7 +4,7 @@ author: "Mattan S. Ben-Shachar"
 date: "`r Sys.Date()`"
 show_toc: true
 output:
-  knitr:::html_vignette:
+  rmarkdown:::html_vignette:
     toc: yes
 vignette: >
   %\VignetteIndexEntry{Testing the Assumptions of ANOVAs}