Upgrades to documentation, ttest can now compare variance of fits onl…

…y, some outputs now look better.

R/b_color.R

@@ -15,7 +15,7 @@
 #' @return An object of class `color_class`
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors for rgb
 #' mu_prior <- b_prior(family="uniform", pars=c(0, 255))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 100))

R/b_linear.R

@@ -16,7 +16,7 @@
 #' @return An object of class `linear_class`.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors
 #' mu_prior <- b_prior(family="normal", pars=c(0, 100))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 500))

R/b_reaction_time.R

@@ -15,7 +15,7 @@
 #' @return An object of class `reaction_time_class`
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors
 #' mu_prior <- b_prior(family="normal", pars=c(0, 100))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 500))

R/b_success_rate.R

@@ -15,7 +15,7 @@
 #' @return An object of class `success_rate_class`.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors
 #' p_prior <- b_prior(family="beta", pars=c(1, 1))
 #' tau_prior <- b_prior(family="uniform", pars=c(0, 500))

R/b_ttest.R

@@ -14,7 +14,7 @@
 #' @return An object of class `ttest_class`.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors
 #' mu_prior <- b_prior(family="normal", pars=c(0, 1000))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 500))
@@ -46,11 +46,11 @@ b_ttest <- function(data,
   n <- length(data)
 
   # prior ids and values
-  p_ids <- rep(0, 3)
-  p_values <- rep(0, 6)
+  p_ids <- rep(0, 2)
+  p_values <- rep(0, 4)
 
   # parameter mapping
-  df_pars <- data.frame(par=c("mu", "sigma", "nu"), index=c(1, 2, 3))
+  df_pars <- data.frame(par=c("mu", "sigma"), index=c(1, 2))
 
   # priors
   if (!is.null(priors)) {
@@ -64,7 +64,7 @@ b_ttest <- function(data,
       if (nrow(par_id) > 0) {
         id <- par_id$index
       } else {
-        wrong_prior <- "Provided an unknown parameter for prior, use \"mu\" \"sigma\" or \"nu\"."
+        wrong_prior <- "Provided an unknown parameter for prior, use \"mu\" or \"sigma\"."
         warning(wrong_prior)
         return()
       }

R/color_class.R

@@ -67,7 +67,7 @@
 #' @slot data Data on which the fit is based.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors for rgb
 #' mu_prior <- b_prior(family="uniform", pars=c(0, 255))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 100))

R/linear_class.R

@@ -41,7 +41,7 @@
 #' @slot data Raw data for the tested group.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors
 #' mu_prior <- b_prior(family="normal", pars=c(0, 100))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 500))
@@ -177,9 +177,9 @@ setMethod(f="summary", signature(object="linear_class"), definition=function(obj
   sigma_hdi <- mcmc_hdi(object@extract$mu_s)
 
   # print
-  cat(sprintf("intercept (alpha):\t%.2f +/- %.5f,, 95%% HDI: [%.2f, %.2f]\n",
+  cat(sprintf("intercept (alpha):\t%.2f +/- %.5f, 95%% HDI: [%.2f, %.2f]\n",
               alpha, mcmcse::mcse(object@extract$mu_a)$se, alpha_hdi[1], alpha_hdi[2]))
-  cat(sprintf("slope (beta):\t\t%.2f +/- %.5f,, 95%% HDI: [%.2f, %.2f]\n",
+  cat(sprintf("slope (beta):\t\t%.2f +/- %.5f, 95%% HDI: [%.2f, %.2f]\n",
               beta, mcmcse::mcse(object@extract$mu_b)$se, beta_hdi[1], beta_hdi[2]))
   cat(sprintf("sigma:\t\t\t%.2f +/- %.5f, 95%% HDI: [%.2f, %.2f]\n",
               sigma, mcmcse::mcse(object@extract$mu_s)$se, sigma_hdi[1], sigma_hdi[2]))
@@ -426,7 +426,7 @@ setMethod(f="plot_means_difference", signature(object="linear_class"), definitio
 #' @title plot_means
 #' @description \code{plot_means} plots means or the first and the second group means.
 #' @param object linear_class object.
-#' @param ... fit2 - a second linear_class object, par - specific parameter of comparison (slope or intercept).
+#' @param ... fit2 - a second linear_class object, par - plot a specific parameter (slope or intercept).
 #' @rdname linear_class-plot_means
 #' @aliases plot_means_linear
 #' @return A ggplot visualization or a warning if something went wrong.

R/reaction_time_class.R

@@ -53,7 +53,7 @@
 #' @slot data Data on which the fit is based.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' # priors
 #' mu_prior <- b_prior(family="normal", pars=c(0, 100))
 #' sigma_prior <- b_prior(family="uniform", pars=c(0, 500))
@@ -290,7 +290,7 @@ setMethod(f="get_subject_parameters", signature(object="reaction_time_class"), d
 #' @title compare_means
 #' @description \code{compare_means} prints difference in reaction times between two groups or multiple groups.
 #' @param object reaction_time_class object.
-#' @param ... fit2 - a second reaction_time_class object, fits - a list of reaction_time_class objects, rope - region of practical equivalence, par - specific parameter of comparison - mu or lambda.
+#' @param ... fit2 - a second reaction_time_class object, fits - a list of reaction_time_class objects, rope - region of practical equivalence, par - specific parameter of comparison (mu or lambda).
 #' @rdname reaction_time_class-compare_means
 #' @aliases compare_means_reaction_time
 #' @return Comparison results or a warning if something went wrong.
@@ -396,7 +396,7 @@ setMethod(f="compare_means", signature(object="reaction_time_class"), definition
 
   # largest/smallest probabilities
   if (n > 2) {
-    cat("\nProbabilities that a certain group is smallest/largest or equal to all others:\n\n")
+    cat("\nProbabilities that a certain group is\nsmallest/largest or equal to all others:\n\n")
     smallest_largest <- is_smallest_or_largest(data=y, rope=rope)
     print(smallest_largest)
     cat("\n\n")
@@ -410,7 +410,7 @@ setMethod(f="compare_means", signature(object="reaction_time_class"), definition
 #' @title plot_means_difference
 #' @description \code{plot_means_difference} a visualization of the difference between two groups or multiple groups.
 #' @param object reaction_time_class object.
-#' @param ... fit2 - a second reaction_time_class object, fits - a list of reaction_time_class objects, rope - region of practical equivalence, bins - number of bins in the histogram, par - specific parameter of comparison - mu or lambda.
+#' @param ... fit2 - a second reaction_time_class object, fits - a list of reaction_time_class objects, rope - region of practical equivalence, bins - number of bins in the histogram, par - specific parameter of comparison (mu or lambda).
 #' @rdname reaction_time_class-plot_means_difference
 #' @aliases plot_means_difference_reaction_time
 #' @return A ggplot visualization or a warning if something went wrong.
@@ -556,7 +556,7 @@ setMethod(f="plot_means_difference", signature(object="reaction_time_class"), de
 #' @title plot_means
 #' @description \code{plot_means} plots density of means for one, two or multiple groups.
 #' @param object reaction_time_class object.
-#' @param ... fit2 - a second reaction_time_class object, fits - a list of reaction_time_class objects, par - specific parameter of comparison - mu or lambda.
+#' @param ... fit2 - a second reaction_time_class object, fits - a list of reaction_time_class objects, par - plot a specific parameter (mu or lambda).
 #' @rdname reaction_time_class-plot_means
 #' @aliases plot_means_reaction_time
 #' @return A ggplot visualization or a warning if something went wrong.
@@ -750,7 +750,7 @@ setMethod(f="compare_distributions", signature(object="reaction_time_class"), de
 
   # largest/smallest probabilities
   if (n > 2) {
-    cat("\nProbabilities that a certain group is smallest/largest or equal to all others:\n\n")
+    cat("\nProbabilities that a certain group is\nsmallest/largest or equal to all others:\n\n")
     smallest_largest <- is_smallest_or_largest(data=y, rope=rope)
     print(smallest_largest)
     cat("\n\n")

R/success_rate_class.R

@@ -53,7 +53,7 @@
 #' @slot data Data on which the fit is based.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' #priors
 #' p_prior <- b_prior(family="beta", pars=c(1, 1))
 #' tau_prior <- b_prior(family="uniform", pars=c(0, 500))
@@ -328,7 +328,7 @@ setMethod(f="compare_means", signature(object="success_rate_class"), definition=
 
   # largest/smallest probabilities
   if (n > 2) {
-    cat("\nProbabilities that a certain group is smallest/largest or equal to all others:\n\n")
+    cat("\nProbabilities that a certain group is\nsmallest/largest or equal to all others:\n\n")
     smallest_largest <- is_smallest_or_largest(data=y, rope=rope)
     print(smallest_largest)
     cat("\n\n")
@@ -593,7 +593,7 @@ setMethod(f="compare_distributions", signature(object="success_rate_class"), def
 
   # largest/smallest probabilities
   if (n > 2) {
-    cat("\nProbabilities that a certain group is smallest/largest or equal to all others:\n\n")
+    cat("\nProbabilities that a certain group is\nsmallest/largest or equal to all others:\n\n")
     smallest_largest <- is_smallest_or_largest(data=y, rope=rope)
     print(smallest_largest)
     cat("\n\n")