From 4c09de23ceb738b262c2907fa329915ac79d9276 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Thu, 21 Nov 2024 21:53:36 +0100 Subject: [PATCH] rename parameters to `alpha_*` pattern --- R/plot.bayesfactor_parameters.R | 6 +++--- R/plot.check_homogeneity.R | 4 ++-- R/plot.check_model.R | 22 +++++++++---------- R/plot.check_normality.R | 26 +++++++++++------------ R/plot.check_outliers.R | 4 ++-- R/plot.check_outliers_new.R | 4 ++-- R/plot.check_predictions.R | 28 ++++++++++++------------- R/plot.describe_distribution.R | 18 ++++++++-------- R/plot.equivalence_test.R | 18 ++++++++-------- R/plot.estimate_density.R | 14 ++++++------- R/plot.p_direction.R | 4 ++-- R/plot.p_function.R | 10 ++++----- R/plot.p_significance.R | 4 ++-- R/plot.parameters_brms_meta.R | 8 +++---- R/plot.parameters_simulate.R | 4 ++-- R/plot.performance_simres.R | 4 ++-- R/plot.point_estimates.R | 22 +++++++++---------- R/plot.rope.R | 4 ++-- R/plot.si.R | 6 +++--- R/utils_add_prior_layer.R | 16 +++++++------- man/plot.see_bayesfactor_parameters.Rd | 4 ++-- man/plot.see_check_normality.Rd | 4 ++-- man/plot.see_check_outliers.Rd | 4 ++-- man/plot.see_equivalence_test.Rd | 6 +++--- man/plot.see_estimate_density.Rd | 8 +++---- man/plot.see_p_direction.Rd | 4 ++-- man/plot.see_p_function.Rd | 4 ++-- man/plot.see_p_significance.Rd | 4 ++-- man/plot.see_parameters_brms_meta.Rd | 8 +++---- man/plot.see_parameters_distribution.Rd | 4 ++-- man/plot.see_parameters_simulate.Rd | 4 ++-- man/plot.see_performance_simres.Rd | 4 ++-- man/plot.see_point_estimate.Rd | 4 ++-- man/plot.see_rope.Rd | 4 ++-- man/plot.see_si.Rd | 4 ++-- man/print.see_performance_pp_check.Rd | 6 +++--- 36 files changed, 151 insertions(+), 151 deletions(-) diff --git a/R/plot.bayesfactor_parameters.R b/R/plot.bayesfactor_parameters.R index a3eae8ae7..26fad6f0f 100644 --- a/R/plot.bayesfactor_parameters.R +++ b/R/plot.bayesfactor_parameters.R @@ -3,7 +3,7 @@ #' The `plot()` method for the `bayestestR::bayesfactor_parameters()` function. #' #' @param size_point Numeric specifying size of point-geoms. -#' @param rope_alpha Numeric specifying transparency level of ROPE ribbon. +#' @param alpha_rope Numeric specifying transparency level of ROPE ribbon. #' @param color_rope Character specifying color of ROPE ribbon. #' @param show_intercept Logical, if `TRUE`, the intercept-parameter is included #' in the plot. By default, it is hidden because in many cases the @@ -20,7 +20,7 @@ plot.see_bayesfactor_parameters <- function(x, size_point = 2, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, show_intercept = FALSE, ...) { if ("log_BF" %in% names(x) && !"BF" %in% names(x)) { @@ -81,7 +81,7 @@ plot.see_bayesfactor_parameters <- function(x, ymin = 0, ymax = Inf, fill = color_rope, - alpha = rope_alpha + alpha = alpha_rope ) } else { p <- p + diff --git a/R/plot.check_homogeneity.R b/R/plot.check_homogeneity.R index bb5c6bec4..ea7a4b2a1 100644 --- a/R/plot.check_homogeneity.R +++ b/R/plot.check_homogeneity.R @@ -140,7 +140,7 @@ plot.see_check_homogeneity <- function(x, data = NULL, ...) { size_axis_title = 10, base_size = 10, colors = unname(social_colors(c("green", "blue", "red"))), - dot_alpha_level = 0.8, + alpha_dot = 0.8, show_dots = TRUE) { p <- ggplot2::ggplot(x, ggplot2::aes(x = .data$x, .data$y)) @@ -149,7 +149,7 @@ plot.see_check_homogeneity <- function(x, data = NULL, ...) { geom_point2( colour = colors[2], size = size_point, - alpha = dot_alpha_level + alpha = alpha_dot ) } diff --git a/R/plot.check_model.R b/R/plot.check_model.R index 0039acc5c..065a8f636 100644 --- a/R/plot.check_model.R +++ b/R/plot.check_model.R @@ -38,7 +38,7 @@ plot.see_check_model <- function(x, size_axis_title <- attr(x, "axis_title_size") size_title <- attr(x, "title_size") alpha_level <- attr(x, "alpha") - dot_alpha_level <- attr(x, "dot_alpha") + alpha_dot <- attr(x, "alpha_dot") show_dots <- attr(x, "show_dots") detrend <- attr(x, "detrend") model_info <- attr(x, "model_info") @@ -73,8 +73,8 @@ plot.see_check_model <- function(x, alpha_level <- 0.2 } - if (is.null(dot_alpha_level)) { - dot_alpha_level <- 0.8 + if (is.null(alpha_dot)) { + alpha_dot <- 0.8 } if (is.null(base_size)) { @@ -124,7 +124,7 @@ plot.see_check_model <- function(x, size_axis_title = size_axis_title, size_title = size_title, colors = colors, - dot_alpha_level = dot_alpha_level, + alpha_dot = alpha_dot, show_dots = show_dots ) } @@ -168,7 +168,7 @@ plot.see_check_model <- function(x, size_axis_title = size_axis_title, size_title = size_title, colors = colors, - dot_alpha_level = dot_alpha_level, + alpha_dot = alpha_dot, show_dots = show_dots ) } @@ -185,7 +185,7 @@ plot.see_check_model <- function(x, size_title = size_title, base_size = base_size, colors = colors, - dot_alpha_level = dot_alpha_level, + alpha_dot = alpha_dot, show_dots = show_dots ) } @@ -212,7 +212,7 @@ plot.see_check_model <- function(x, linewidth = linewidth, size_point = 0.9 * size_point, alpha = alpha_level, - dot_alpha = dot_alpha_level, + alpha_dot = alpha_dot, colors = colors, detrend = detrend, style = style, @@ -232,7 +232,7 @@ plot.see_check_model <- function(x, theme_style = style, base_size = base_size, colors = colors, - dot_alpha_level = dot_alpha_level, + alpha_dot = alpha_dot, show_dots = TRUE, # qq-plots w/o dots makes no sense model_info = model_info, model_class = model_class @@ -264,7 +264,7 @@ plot.see_check_model <- function(x, theme_style = style, base_size = base_size, colors = colors, - dot_alpha_level = dot_alpha_level, + alpha_dot = alpha_dot, show_dots = TRUE # qq-plots w/o dots makes no sense ) @@ -292,7 +292,7 @@ plot.see_check_model <- function(x, theme_style = theme_lucid, base_size = 10, colors = unname(social_colors(c("green", "blue", "red"))), - dot_alpha_level = 0.8, + alpha_dot = 0.8, show_dots = TRUE) { p <- ggplot2::ggplot(x, ggplot2::aes(x = .data$x, y = .data$y)) @@ -301,7 +301,7 @@ plot.see_check_model <- function(x, geom_point2( colour = colors[2], size = size_point, - alpha = dot_alpha_level + alpha = alpha_dot ) } diff --git a/R/plot.check_normality.R b/R/plot.check_normality.R index 1e40b530e..bfbee7aba 100644 --- a/R/plot.check_normality.R +++ b/R/plot.check_normality.R @@ -8,7 +8,7 @@ #' `"pp"` for probability-probability (P-P) plots, or #' `"density"` for density overlay plots. #' @param linewidth Numeric value specifying size of line geoms. -#' @param dot_alpha Numeric value specifying alpha level of the point geoms. +#' @param alpha_dot Numeric value specifying alpha level of the point geoms. #' @param alpha Numeric value specifying alpha level of the confidence bands. #' @param colors Character vector of length two, indicating the colors (in #' hex-format) for points and line. @@ -48,7 +48,7 @@ plot.see_check_normality <- function(x, size_axis_title = base_size, base_size = 10, alpha = 0.2, - dot_alpha = 0.8, + alpha_dot = 0.8, colors = c("#3aaf85", "#1b6ca8"), detrend = TRUE, method = "ell", @@ -96,7 +96,7 @@ plot.see_check_normality <- function(x, linewidth = linewidth, size_point = size_point, alpha = alpha, - dot_alpha = dot_alpha, + alpha_dot = alpha_dot, colors = colors, detrend = detrend, base_size = base_size, @@ -120,7 +120,7 @@ plot.see_check_normality <- function(x, base_size = base_size, alpha_level = alpha, detrend = detrend, - dot_alpha_level = dot_alpha, + alpha_dot = alpha_dot, model_info = model_info, method = method, model_class = class(model)[1] @@ -160,7 +160,7 @@ plot.see_check_normality <- function(x, size_title = size_title, alpha_level = alpha, detrend = detrend, - dot_alpha_level = dot_alpha, + alpha_dot = alpha_dot, method = method ) } @@ -222,7 +222,7 @@ plot.see_check_normality <- function(x, theme_style = theme_lucid, base_size = 10, colors = unname(social_colors(c("green", "blue", "red"))), - dot_alpha_level = 0.8, + alpha_dot = 0.8, show_dots = TRUE, model_info = NULL, model_class = NULL) { @@ -259,7 +259,7 @@ plot.see_check_normality <- function(x, stroke = 0, size = size_point, colour = colors[2], - alpha = dot_alpha_level, + alpha = alpha_dot, detrend = detrend ), qqplotr::stat_qq_line( @@ -358,7 +358,7 @@ plot.see_check_normality <- function(x, theme_style = theme_lucid, base_size = 10, colors = unname(social_colors(c("green", "blue", "red"))), - dot_alpha_level = 0.8) { + alpha_dot = 0.8) { if (requireNamespace("qqplotr", quietly = TRUE)) { p_plot <- ggplot2::ggplot(x, ggplot2::aes(sample = .data$res)) + qqplotr::stat_pp_band(alpha = alpha_level, detrend = detrend, bandType = method) + @@ -371,7 +371,7 @@ plot.see_check_normality <- function(x, shape = 16, stroke = 0, size = size_point, colour = colors[2], - alpha = dot_alpha_level, + alpha = alpha_dot, detrend = detrend ) } else if (requireNamespace("MASS", quietly = TRUE)) { @@ -391,7 +391,7 @@ plot.see_check_normality <- function(x, mapping = if (detrend) ggplot2::aes(y = .data$y - .data$probs), colour = colors[2], size = size_point, - alpha = dot_alpha_level + alpha = alpha_dot ) } else { insight::format_error("Package 'qqplotr' OR 'MASS' required for P-P plots. Please install one of them.") @@ -430,7 +430,7 @@ plot.see_check_normality <- function(x, theme_style = theme_lucid, base_size = 10, colors = unname(social_colors(c("green", "blue", "red"))), - dot_alpha_level = 0.8, + alpha_dot = 0.8, show_dots = TRUE) { lapply(names(x), function(i) { dat <- x[[i]] @@ -452,7 +452,7 @@ plot.see_check_normality <- function(x, ggplot2::aes(ymin = .data$conf.low, ymax = .data$conf.high), width = 0, colour = colors[2], - alpha = dot_alpha_level + alpha = alpha_dot ) + theme_style( base_size = base_size, @@ -467,7 +467,7 @@ plot.see_check_normality <- function(x, geom_point2( colour = colors[2], size = size_point, - alpha = dot_alpha_level + alpha = alpha_dot ) } diff --git a/R/plot.check_outliers.R b/R/plot.check_outliers.R index 5732ce30f..8bd259578 100644 --- a/R/plot.check_outliers.R +++ b/R/plot.check_outliers.R @@ -36,7 +36,7 @@ plot.see_check_outliers <- function(x, size_title = 12, size_axis_title = base_size, base_size = 10, - dot_alpha = 0.8, + alpha_dot = 0.8, colors = c("#3aaf85", "#1b6ca8", "#cd201f"), rescale_distance = TRUE, type = c("dots", "bars"), @@ -55,7 +55,7 @@ plot.see_check_outliers <- function(x, size_axis_title = size_axis_title, size_title = size_title, base_size = base_size, - dot_alpha_level = dot_alpha, + alpha_dot = alpha_dot, colors = colors ) } else if (length(outlier_methods) == 1) { diff --git a/R/plot.check_outliers_new.R b/R/plot.check_outliers_new.R index 544c61c4c..acbf5ea49 100644 --- a/R/plot.check_outliers_new.R +++ b/R/plot.check_outliers_new.R @@ -11,7 +11,7 @@ theme_style = theme_lucid, base_size = 10, colors = unname(social_colors(c("green", "blue grey", "red"))), - dot_alpha_level = 0.8, + alpha_dot = 0.8, show_dots = TRUE) { linewidth <- linewidth %||% 0.7 size_text <- size_text %||% 3 @@ -30,7 +30,7 @@ p <- p + geom_point2( aes(colour = .data$Influential), na.rm = na.rm, - alpha = dot_alpha_level, + alpha = alpha_dot, size = size_point ) } diff --git a/R/plot.check_predictions.R b/R/plot.check_predictions.R index 1fc87a213..e619fb60c 100644 --- a/R/plot.check_predictions.R +++ b/R/plot.check_predictions.R @@ -53,7 +53,7 @@ data_plot.performance_pp_check <- function(x, type = "density", ...) { #' #' The `plot()` method for the `performance::check_predictions()` function. #' -#' @param line_alpha Numeric value specifying alpha of lines indicating `yrep`. +#' @param alpha_line Numeric value specifying alpha of lines indicating `yrep`. #' @param style A ggplot2-theme. #' @param type Plot type for the posterior predictive checks plot. Can be `"density"` #' (default), `"discrete_dots"`, `"discrete_interval"` or `"discrete_both"` (the @@ -93,7 +93,7 @@ print.see_performance_pp_check <- function(x, size_axis_title = base_size, size_title = 12, base_size = 10, - line_alpha = 0.15, + alpha_line = 0.15, style = theme_lucid, colors = unname(social_colors(c("green", "blue"))), type = c("density", "discrete_dots", "discrete_interval", "discrete_both"), @@ -118,7 +118,7 @@ print.see_performance_pp_check <- function(x, x, linewidth = linewidth, size_point = size_point, - line_alpha = line_alpha, + alpha_line = alpha_line, theme_style = style, colors = colors, base_size = base_size, @@ -150,7 +150,7 @@ plot.see_performance_pp_check <- function(x, size_axis_title = base_size, size_title = 12, base_size = 10, - line_alpha = 0.15, + alpha_line = 0.15, style = theme_lucid, colors = unname(social_colors(c("green", "blue"))), type = c("density", "discrete_dots", "discrete_interval", "discrete_both"), @@ -175,7 +175,7 @@ plot.see_performance_pp_check <- function(x, x, linewidth = linewidth, size_point = size_point, - line_alpha = line_alpha, + alpha_line = alpha_line, theme_style = style, base_size = base_size, size_axis_title = size_axis_title, @@ -200,7 +200,7 @@ plot.see_performance_pp_check <- function(x, .plot_pp_check <- function(x, linewidth, size_point, - line_alpha, + alpha_line, theme_style, base_size = 10, size_axis_title = 10, @@ -215,7 +215,7 @@ plot.see_performance_pp_check <- function(x, # discrete plot type from "bayesplot::pp_check()" returns a different data # structure, so we need to handle it differently if (isTRUE(is_stan) && type != "density") { - return(.plot_check_predictions_stan_dots(x, colors, info, linewidth, size_point, line_alpha, ...)) + return(.plot_check_predictions_stan_dots(x, colors, info, linewidth, size_point, alpha_line, ...)) } # default bandwidth, for smooting @@ -228,7 +228,7 @@ plot.see_performance_pp_check <- function(x, suggest_dots <- (minfo$is_bernoulli || minfo$is_count || minfo$is_ordinal || minfo$is_categorical) if (!is.null(type) && type %in% c("discrete_dots", "discrete_interval", "discrete_both") && suggest_dots) { - out <- .plot_check_predictions_dots(x, colors, info, linewidth, size_point, line_alpha, type, ...) + out <- .plot_check_predictions_dots(x, colors, info, linewidth, size_point, alpha_line, type, ...) } else { if (suggest_dots) { insight::format_alert( @@ -237,7 +237,7 @@ plot.see_performance_pp_check <- function(x, ) } # denity plot - for models that have no binary or count/ordinal outcome - out <- .plot_check_predictions_density(x, colors, info, linewidth, line_alpha, bandwidth, ...) + out <- .plot_check_predictions_density(x, colors, info, linewidth, alpha_line, bandwidth, ...) } @@ -272,7 +272,7 @@ plot.see_performance_pp_check <- function(x, colors, info, linewidth, - line_alpha, + alpha_line, bandwidth, ...) { ggplot2::ggplot(x) + @@ -303,7 +303,7 @@ plot.see_performance_pp_check <- function(x, ggplot2::scale_alpha_manual( values = c( "Observed data" = 1, - "Model-predicted data" = line_alpha + "Model-predicted data" = alpha_line ), guide = "none" ) + @@ -328,7 +328,7 @@ plot.see_performance_pp_check <- function(x, info, linewidth, size_point, - line_alpha, + alpha_line, type = "discrete_dots", ...) { # make sure we have a factor, so "table()" generates frequencies for all levels @@ -409,7 +409,7 @@ plot.see_performance_pp_check <- function(x, group = .data$grp, color = .data$key ), - alpha = line_alpha, + alpha = alpha_line, position = ggplot2::position_jitter(width = 0.1, height = 0.02), size = 0.8 * size_point, stroke = 0, @@ -480,7 +480,7 @@ plot.see_performance_pp_check <- function(x, info, linewidth, size_point, - line_alpha, + alpha_line, ...) { # make sure we have a factor, so "table()" generates frequencies for all levels # for each group - we need tables of same size to bind data frames diff --git a/R/plot.describe_distribution.R b/R/plot.describe_distribution.R index 551cedf5a..dd0dcd43e 100644 --- a/R/plot.describe_distribution.R +++ b/R/plot.describe_distribution.R @@ -34,7 +34,7 @@ data_plot.parameters_distribution <- function(x, data = NULL, ...) { #' #' @param dispersion Logical. If `TRUE`, a range of dispersion for #' each variable to the plot will be added. -#' @param dispersion_alpha Numeric value specifying the transparency level of dispersion ribbon. +#' @param alpha_dispersion Numeric value specifying the transparency level of dispersion ribbon. #' @param color_dispersion Character specifying the color of dispersion ribbon. #' @param dispersion_style Character describing the style of dispersion area. #' `"ribbon"` for a ribbon, `"curve"` for a normal-curve. @@ -59,7 +59,7 @@ data_plot.parameters_distribution <- function(x, data = NULL, ...) { #' @export plot.see_parameters_distribution <- function(x, dispersion = FALSE, - dispersion_alpha = 0.3, + alpha_dispersion = 0.3, color_dispersion = "#3498db", dispersion_style = c("ribbon", "curve"), size_bar = 0.7, @@ -84,7 +84,7 @@ plot.see_parameters_distribution <- function(x, lapply( x, .plot_see_parameters_distribution, - dispersion_alpha, + alpha_dispersion, color_dispersion, dispersion_style, show_dispersion = dispersion, @@ -95,7 +95,7 @@ plot.see_parameters_distribution <- function(x, } else { .plot_see_parameters_distribution( x, - dispersion_alpha, + alpha_dispersion, color_dispersion, dispersion_style, show_dispersion = dispersion, @@ -109,7 +109,7 @@ plot.see_parameters_distribution <- function(x, .plot_see_parameters_distribution <- function(x, - dispersion_alpha, + alpha_dispersion, color_dispersion, dispersion_style, show_dispersion, @@ -159,7 +159,7 @@ plot.see_parameters_distribution <- function(x, p <- p + geom_vline( xintercept = centrality, colour = color_dispersion, - alpha = dispersion_alpha + alpha = alpha_dispersion ) } if (!is.null(dispersion)) { @@ -170,7 +170,7 @@ plot.see_parameters_distribution <- function(x, xintercept = .range, linetype = "dashed", colour = color_dispersion, - alpha = dispersion_alpha + alpha = alpha_dispersion ) + annotate( "rect", @@ -179,13 +179,13 @@ plot.see_parameters_distribution <- function(x, ymin = 0, ymax = Inf, fill = color_dispersion, - alpha = (dispersion_alpha / 3) + alpha = (alpha_dispersion / 3) ) } else { p <- p + geom_ribbon( aes(ymin = 0, ymax = .data$curve_y), - alpha = dispersion_alpha, + alpha = alpha_dispersion, fill = color_dispersion, colour = NA ) diff --git a/R/plot.equivalence_test.R b/R/plot.equivalence_test.R index 91294ced8..24d94b595 100644 --- a/R/plot.equivalence_test.R +++ b/R/plot.equivalence_test.R @@ -16,7 +16,7 @@ #' @export plot.see_equivalence_test <- function(x, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, show_intercept = FALSE, n_columns = 1, ...) { @@ -132,7 +132,7 @@ plot.see_equivalence_test <- function(x, if ("legend.title" %in% names(add.args)) legend.title <- eval(add.args[["legend.title"]]) if ("labels" %in% names(add.args)) axis_labels <- eval(add.args[["labels"]]) - rope.line.alpha <- 1.25 * rope_alpha + rope.line.alpha <- 1.25 * alpha_rope if (rope.line.alpha > 1) rope.line.alpha <- 1 insight::check_if_installed("ggridges") @@ -145,7 +145,7 @@ plot.see_equivalence_test <- function(x, ymin = 0, ymax = Inf, fill = color_rope, - alpha = (rope_alpha / 3), + alpha = (alpha_rope / 3), na.rm = TRUE ) + geom_vline( @@ -208,7 +208,7 @@ plot.see_equivalence_test <- function(x, #' @export plot.see_equivalence_test_df <- function(x, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, data = NULL, n_columns = 1, ...) { @@ -277,7 +277,7 @@ plot.see_equivalence_test_df <- function(x, if ("legend.title" %in% names(add.args)) legend.title <- eval(add.args[["legend.title"]]) if ("labels" %in% names(add.args)) axis_labels <- eval(add.args[["labels"]]) - rope.line.alpha <- 1.25 * rope_alpha + rope.line.alpha <- 1.25 * alpha_rope if (rope.line.alpha > 1) rope.line.alpha <- 1 @@ -291,7 +291,7 @@ plot.see_equivalence_test_df <- function(x, ymin = 0, ymax = Inf, fill = color_rope, - alpha = (rope_alpha / 3) + alpha = (alpha_rope / 3) ) + geom_vline( xintercept = .rope, @@ -334,7 +334,7 @@ plot.see_equivalence_test_df <- function(x, plot.see_equivalence_test_lm <- function(x, size_point = 0.7, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, show_intercept = FALSE, n_columns = 1, ...) { @@ -393,7 +393,7 @@ plot.see_equivalence_test_lm <- function(x, if ("x.title" %in% names(add.args)) x.title <- eval(add.args[["x.title"]]) if ("legend.title" %in% names(add.args)) legend.title <- eval(add.args[["legend.title"]]) - rope.line.alpha <- 1.25 * rope_alpha + rope.line.alpha <- 1.25 * alpha_rope if (rope.line.alpha > 1) rope.line.alpha <- 1 p <- ggplot( @@ -413,7 +413,7 @@ plot.see_equivalence_test_lm <- function(x, ymin = 0, ymax = Inf, fill = color_rope, - alpha = (rope_alpha / 3) + alpha = (alpha_rope / 3) ) + geom_vline( xintercept = .rope, diff --git a/R/plot.estimate_density.R b/R/plot.estimate_density.R index e63e62ca0..4371f383d 100644 --- a/R/plot.estimate_density.R +++ b/R/plot.estimate_density.R @@ -74,9 +74,9 @@ data_plot.estimate_density <- function(x, #' @param priors Logical. If `TRUE`, prior distributions are simulated #' (using [bayestestR::simulate_prior()]) and added #' to the plot. -#' @param priors_alpha Numeric value specifying alpha for the prior +#' @param alpha_priors Numeric value specifying alpha for the prior #' distributions. -#' @param posteriors_alpha Numeric value specifying alpha for the posterior +#' @param alpha_posteriors Numeric value specifying alpha for the posterior #' distributions. #' @param centrality Character specifying the point-estimate (centrality index) #' to compute. Can be `"median"`, `"mean"` or `"MAP"`. @@ -103,8 +103,8 @@ plot.see_estimate_density <- function(x, show_intercept = FALSE, n_columns = 1, priors = FALSE, - priors_alpha = 0.4, - posteriors_alpha = 0.7, + alpha_priors = 0.4, + alpha_posteriors = 0.7, linewidth = 0.9, size_point = 2, centrality = "median", @@ -159,11 +159,11 @@ plot.see_estimate_density <- function(x, model, parameter = params, show_intercept = show_intercept, - priors_alpha = priors_alpha, + alpha_priors = alpha_priors, show_ridge_line = FALSE ) + ggridges::geom_ridgeline(aes(fill = "Posterior"), - alpha = posteriors_alpha, + alpha = alpha_posteriors, color = NA ) + guides(color = "none") + @@ -174,7 +174,7 @@ plot.see_estimate_density <- function(x, p <- p + ggridges::geom_ridgeline(aes(fill = "Posterior"), - alpha = posteriors_alpha, + alpha = alpha_posteriors, color = NA ) + guides(fill = "none", color = "none") + diff --git a/R/plot.p_direction.R b/R/plot.p_direction.R index 56dc24f3a..48496e320 100644 --- a/R/plot.p_direction.R +++ b/R/plot.p_direction.R @@ -166,7 +166,7 @@ plot.see_p_direction <- function(x, data = NULL, show_intercept = FALSE, priors = FALSE, - priors_alpha = 0.4, + alpha_priors = 0.4, n_columns = 1, ...) { # save model for later use @@ -209,7 +209,7 @@ plot.see_p_direction <- function(x, model, parameter = params, show_intercept = show_intercept, - priors_alpha = priors_alpha + alpha_priors = alpha_priors ) } diff --git a/R/plot.p_function.R b/R/plot.p_function.R index 533671d49..8fddd6277 100644 --- a/R/plot.p_function.R +++ b/R/plot.p_function.R @@ -6,7 +6,7 @@ #' @param colors Character vector of length two, indicating the colors (in #' hex-format) used when only one parameter is plotted, resp. when panels #' are plotted as facets. -#' @param line_alpha Numeric value specifying alpha of lines indicating the +#' @param alpha_line Numeric value specifying alpha of lines indicating the #' emphasized compatibility interval levels (see `?parameters::p_function`). #' #' @inheritParams data_plot @@ -31,7 +31,7 @@ plot.see_p_function <- function(x, size_point = 1.2, linewidth = c(0.7, 0.9), size_text = 3, - line_alpha = 0.15, + alpha_line = 0.15, show_labels = TRUE, n_columns = NULL, show_intercept = FALSE, @@ -103,7 +103,7 @@ plot.see_p_function <- function(x, ), colour = colors[1], size = size_point, - alpha = line_alpha, + alpha = alpha_line, show.legend = FALSE ) + # points for vertical CI bars @@ -116,7 +116,7 @@ plot.see_p_function <- function(x, ), colour = colors[1], size = size_point, - alpha = line_alpha, + alpha = alpha_line, show.legend = FALSE ) + # lines for vertical CI bars @@ -131,7 +131,7 @@ plot.see_p_function <- function(x, linewidth = .data$group ), colour = colors[1], - alpha = line_alpha, + alpha = alpha_line, show.legend = FALSE ) diff --git a/R/plot.p_significance.R b/R/plot.p_significance.R index e8a62e791..1348c1333 100644 --- a/R/plot.p_significance.R +++ b/R/plot.p_significance.R @@ -191,7 +191,7 @@ plot.see_p_significance <- function(x, data = NULL, show_intercept = FALSE, priors = FALSE, - priors_alpha = 0.4, + alpha_priors = 0.4, n_columns = 1, ...) { # save model for later use @@ -235,7 +235,7 @@ plot.see_p_significance <- function(x, model, parameter = params, show_intercept = show_intercept, - priors_alpha = priors_alpha + alpha_priors = alpha_priors ) + scale_fill_manual(values = c("white", "#FFFC00", "#cd201f", "#0077B5")) } else { diff --git a/R/plot.parameters_brms_meta.R b/R/plot.parameters_brms_meta.R index 10293ab61..ea194f296 100644 --- a/R/plot.parameters_brms_meta.R +++ b/R/plot.parameters_brms_meta.R @@ -142,8 +142,8 @@ plot.see_parameters_brms_meta <- function(x, size_point = 2, linewidth = 0.8, size_text = 3.5, - posteriors_alpha = 0.7, - rope_alpha = 0.15, + alpha_posteriors = 0.7, + alpha_rope = 0.15, color_rope = "cadetblue", normalize_height = TRUE, show_labels = TRUE, @@ -176,7 +176,7 @@ plot.see_parameters_brms_meta <- function(x, ymin = 0, ymax = Inf, fill = color_rope, - alpha = rope_alpha + alpha = alpha_rope ) } @@ -187,7 +187,7 @@ plot.see_parameters_brms_meta <- function(x, mapping = ggplot2::aes(fill = .data$Group), color = NA, scale = 1, - alpha = posteriors_alpha + alpha = alpha_posteriors ) + ggplot2::geom_errorbarh( data = datasummary, diff --git a/R/plot.parameters_simulate.R b/R/plot.parameters_simulate.R index 0bb2ee267..a99edcc92 100644 --- a/R/plot.parameters_simulate.R +++ b/R/plot.parameters_simulate.R @@ -91,7 +91,7 @@ plot.see_parameters_simulate <- function(x, n_columns = NULL, normalize_height = FALSE, linewidth = 0.9, - posteriors_alpha = 0.7, + alpha_posteriors = 0.7, centrality = "median", ci = 0.95, ...) { @@ -115,7 +115,7 @@ plot.see_parameters_simulate <- function(x, show_intercept = show_intercept, n_columns = n_columns, linewidth = linewidth, - posteriors_alpha = posteriors_alpha, + alpha_posteriors = alpha_posteriors, centrality = centrality, ci = ci, ... diff --git a/R/plot.performance_simres.R b/R/plot.performance_simres.R index a4ec097c6..1dc95307e 100644 --- a/R/plot.performance_simres.R +++ b/R/plot.performance_simres.R @@ -37,7 +37,7 @@ plot.see_performance_simres <- function(x, size_axis_title = base_size, base_size = 10, alpha = 0.2, - dot_alpha = 0.8, + alpha_dot = 0.8, colors = c("#3aaf85", "#1b6ca8"), detrend = FALSE, transform = NULL, @@ -105,7 +105,7 @@ plot.see_performance_simres <- function(x, distribution = dfun, dparams = dp, size = size_point, - alpha = dot_alpha, + alpha = alpha_dot, colour = colors[2], detrend = detrend ) diff --git a/R/plot.point_estimates.R b/R/plot.point_estimates.R index 466cf3356..bf1af45f4 100644 --- a/R/plot.point_estimates.R +++ b/R/plot.point_estimates.R @@ -106,7 +106,7 @@ plot.see_point_estimate <- function(x, show_labels = TRUE, show_intercept = FALSE, priors = FALSE, - priors_alpha = 0.4, + alpha_priors = 0.4, ...) { # save model for later use model <- .retrieve_data(x) @@ -149,18 +149,18 @@ plot.see_point_estimate <- function(x, model, parameter = x_lab, show_intercept = show_intercept, - priors_alpha = priors_alpha, + alpha_priors = alpha_priors, fill_color = "#FF9800" ) - posterior_alpha <- 0.7 + alpha_posteriors <- 0.7 } else { - posterior_alpha <- 1 + alpha_posteriors <- 1 } p_object <- p_object + geom_ribbon(aes(ymin = 0, ymax = .data$y), fill = "#FFC107", - alpha = posterior_alpha + alpha = alpha_posteriors ) if (!is.null(mean_x) && !is.null(mean_y)) { @@ -172,14 +172,14 @@ plot.see_point_estimate <- function(x, yend = mean_y, color = "#E91E63", linewidth = 1, - alpha = posterior_alpha + alpha = alpha_posteriors ) + geom_point( x = mean_x, y = mean_y, color = "#E91E63", size = size_point, - alpha = posterior_alpha + alpha = alpha_posteriors ) if (show_labels) { p_object <- p_object + @@ -202,14 +202,14 @@ plot.see_point_estimate <- function(x, yend = median_y, color = "#2196F3", linewidth = 1, - alpha = posterior_alpha + alpha = alpha_posteriors ) + geom_point( x = median_x, y = median_y, color = "#2196F3", size = size_point, - alpha = posterior_alpha + alpha = alpha_posteriors ) if (show_labels) { p_object <- p_object + @@ -232,14 +232,14 @@ plot.see_point_estimate <- function(x, yend = map_y, color = "#4CAF50", linewidth = 1, - alpha = posterior_alpha + alpha = alpha_posteriors ) + geom_point( x = map_x, y = map_y, color = "#4CAF50", size = size_point, - alpha = posterior_alpha + alpha = alpha_posteriors ) if (show_labels) { p_object <- p_object + diff --git a/R/plot.rope.R b/R/plot.rope.R index a069e2c97..5bc7ec81f 100644 --- a/R/plot.rope.R +++ b/R/plot.rope.R @@ -87,7 +87,7 @@ data_plot.rope <- function(x, data = NULL, show_intercept = FALSE, ...) { #' @export plot.see_rope <- function(x, data = NULL, - rope_alpha = 0.5, + alpha_rope = 0.5, color_rope = "cadetblue", show_intercept = FALSE, n_columns = 1, @@ -123,7 +123,7 @@ plot.see_rope <- function(x, ymin = 0, ymax = Inf, fill = color_rope, - alpha = rope_alpha + alpha = alpha_rope ) + add_plot_attributes(x) diff --git a/R/plot.si.R b/R/plot.si.R index 6ae784952..1289dc571 100644 --- a/R/plot.si.R +++ b/R/plot.si.R @@ -2,7 +2,7 @@ #' #' The `plot()` method for the `bayestestR::si()`. #' -#' @param si_alpha Numeric value specifying Transparency level of SI ribbon. +#' @param alpha_si Numeric value specifying Transparency level of SI ribbon. #' @param color_si Character specifying color of SI ribbon. #' @param support_only Logical. Decides whether to plot only the support data, #' or show the "raw" prior and posterior distributions? Only applies when @@ -24,7 +24,7 @@ #' @export plot.see_si <- function(x, color_si = "#0171D3", - si_alpha = 0.2, + alpha_si = 0.2, show_intercept = FALSE, support_only = FALSE, ...) { @@ -65,7 +65,7 @@ plot.see_si <- function(x, aes(xmin = .data$CI_low, xmax = .data$CI_high), ymin = 0, ymax = Inf, data = x, - fill = color_si, alpha = si_alpha, + fill = color_si, alpha = alpha_si, linetype = "dashed", colour = "grey50", inherit.aes = FALSE ) + diff --git a/R/utils_add_prior_layer.R b/R/utils_add_prior_layer.R index 90b0dbbac..3ac51a32e 100644 --- a/R/utils_add_prior_layer.R +++ b/R/utils_add_prior_layer.R @@ -1,7 +1,7 @@ .add_prior_layer_ridgeline <- function(model, parameter = NULL, show_intercept = FALSE, - priors_alpha = 0.5, + alpha_priors = 0.5, fill_color = NULL, show_ridge_line = TRUE) { dat <- tryCatch( @@ -42,7 +42,7 @@ group = as.factor(.data$Parameter) ), fill = fill_color, - alpha = priors_alpha, + alpha = alpha_priors, na.rm = TRUE ) } else { @@ -55,7 +55,7 @@ group = as.factor(.data$Parameter) ), fill = fill_color, - alpha = priors_alpha, + alpha = alpha_priors, color = NA, na.rm = TRUE ) @@ -70,7 +70,7 @@ group = as.factor(.data$Parameter), fill = "Priors" ), - alpha = priors_alpha, + alpha = alpha_priors, na.rm = TRUE ) } else { @@ -83,7 +83,7 @@ group = as.factor(.data$Parameter), fill = "Priors" ), - alpha = priors_alpha, + alpha = alpha_priors, color = NA, na.rm = TRUE ) @@ -98,7 +98,7 @@ .add_prior_layer_ribbon <- function(model, parameter = NULL, show_intercept = FALSE, - priors_alpha = 0.5, + alpha_priors = 0.5, fill_color = NULL) { dat <- tryCatch( { @@ -135,7 +135,7 @@ group = as.factor(.data$Parameter) ), fill = fill_color, - alpha = priors_alpha + alpha = alpha_priors ) } else { geom_ribbon( @@ -147,7 +147,7 @@ group = as.factor(.data$Parameter), fill = "Prior" ), - alpha = priors_alpha + alpha = alpha_priors ) } } diff --git a/man/plot.see_bayesfactor_parameters.Rd b/man/plot.see_bayesfactor_parameters.Rd index 37ede6bbc..01fe5aa4a 100644 --- a/man/plot.see_bayesfactor_parameters.Rd +++ b/man/plot.see_bayesfactor_parameters.Rd @@ -8,7 +8,7 @@ x, size_point = 2, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, show_intercept = FALSE, ... ) @@ -20,7 +20,7 @@ \item{color_rope}{Character specifying color of ROPE ribbon.} -\item{rope_alpha}{Numeric specifying transparency level of ROPE ribbon.} +\item{alpha_rope}{Numeric specifying transparency level of ROPE ribbon.} \item{show_intercept}{Logical, if \code{TRUE}, the intercept-parameter is included in the plot. By default, it is hidden because in many cases the diff --git a/man/plot.see_check_normality.Rd b/man/plot.see_check_normality.Rd index 81cade257..137a9bcf0 100644 --- a/man/plot.see_check_normality.Rd +++ b/man/plot.see_check_normality.Rd @@ -14,7 +14,7 @@ size_axis_title = base_size, base_size = 10, alpha = 0.2, - dot_alpha = 0.8, + alpha_dot = 0.8, colors = c("#3aaf85", "#1b6ca8"), detrend = TRUE, method = "ell", @@ -41,7 +41,7 @@ axis and plot titles.} \item{alpha}{Numeric value specifying alpha level of the confidence bands.} -\item{dot_alpha}{Numeric value specifying alpha level of the point geoms.} +\item{alpha_dot}{Numeric value specifying alpha level of the point geoms.} \item{colors}{Character vector of length two, indicating the colors (in hex-format) for points and line.} diff --git a/man/plot.see_check_outliers.Rd b/man/plot.see_check_outliers.Rd index c7cd9cce3..f1b47e2ba 100644 --- a/man/plot.see_check_outliers.Rd +++ b/man/plot.see_check_outliers.Rd @@ -11,7 +11,7 @@ size_title = 12, size_axis_title = base_size, base_size = 10, - dot_alpha = 0.8, + alpha_dot = 0.8, colors = c("#3aaf85", "#1b6ca8", "#cd201f"), rescale_distance = TRUE, type = c("dots", "bars"), @@ -29,7 +29,7 @@ \item{base_size, size_axis_title, size_title}{Numeric value specifying size of axis and plot titles.} -\item{dot_alpha}{Numeric value specifying alpha level of the point geoms.} +\item{alpha_dot}{Numeric value specifying alpha level of the point geoms.} \item{colors}{Character vector of length two, indicating the colors (in hex-format) for points and line.} diff --git a/man/plot.see_equivalence_test.Rd b/man/plot.see_equivalence_test.Rd index baa26d176..528abdd70 100644 --- a/man/plot.see_equivalence_test.Rd +++ b/man/plot.see_equivalence_test.Rd @@ -12,7 +12,7 @@ \method{plot}{see_equivalence_test}( x, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, show_intercept = FALSE, n_columns = 1, ... @@ -22,7 +22,7 @@ x, size_point = 0.7, color_rope = "#0171D3", - rope_alpha = 0.2, + alpha_rope = 0.2, show_intercept = FALSE, n_columns = 1, ... @@ -35,7 +35,7 @@ \item{color_rope}{Character specifying color of ROPE ribbon.} -\item{rope_alpha}{Numeric specifying transparency level of ROPE ribbon.} +\item{alpha_rope}{Numeric specifying transparency level of ROPE ribbon.} \item{show_intercept}{Logical, if \code{TRUE}, the intercept-parameter is included in the plot. By default, it is hidden because in many cases the diff --git a/man/plot.see_estimate_density.Rd b/man/plot.see_estimate_density.Rd index e19771712..e33857d08 100644 --- a/man/plot.see_estimate_density.Rd +++ b/man/plot.see_estimate_density.Rd @@ -10,8 +10,8 @@ show_intercept = FALSE, n_columns = 1, priors = FALSE, - priors_alpha = 0.4, - posteriors_alpha = 0.7, + alpha_priors = 0.4, + alpha_posteriors = 0.7, linewidth = 0.9, size_point = 2, centrality = "median", @@ -39,10 +39,10 @@ panel-layout. If \code{NULL}, a single, integrated plot is shown.} (using \code{\link[bayestestR:simulate_prior]{bayestestR::simulate_prior()}}) and added to the plot.} -\item{priors_alpha}{Numeric value specifying alpha for the prior +\item{alpha_priors}{Numeric value specifying alpha for the prior distributions.} -\item{posteriors_alpha}{Numeric value specifying alpha for the posterior +\item{alpha_posteriors}{Numeric value specifying alpha for the posterior distributions.} \item{linewidth}{Numeric value specifying size of line geoms.} diff --git a/man/plot.see_p_direction.Rd b/man/plot.see_p_direction.Rd index 58c360cdc..044b9c290 100644 --- a/man/plot.see_p_direction.Rd +++ b/man/plot.see_p_direction.Rd @@ -9,7 +9,7 @@ data = NULL, show_intercept = FALSE, priors = FALSE, - priors_alpha = 0.4, + alpha_priors = 0.4, n_columns = 1, ... ) @@ -30,7 +30,7 @@ are hardly visible.} (using \code{\link[bayestestR:simulate_prior]{bayestestR::simulate_prior()}}) and added to the plot.} -\item{priors_alpha}{Numeric value specifying alpha for the prior +\item{alpha_priors}{Numeric value specifying alpha for the prior distributions.} \item{n_columns}{For models with multiple components (like fixed and random, diff --git a/man/plot.see_p_function.Rd b/man/plot.see_p_function.Rd index ea6318693..b4592d77a 100644 --- a/man/plot.see_p_function.Rd +++ b/man/plot.see_p_function.Rd @@ -10,7 +10,7 @@ size_point = 1.2, linewidth = c(0.7, 0.9), size_text = 3, - line_alpha = 0.15, + alpha_line = 0.15, show_labels = TRUE, n_columns = NULL, show_intercept = FALSE, @@ -30,7 +30,7 @@ are plotted as facets.} \item{size_text}{Numeric value specifying size of text labels.} -\item{line_alpha}{Numeric value specifying alpha of lines indicating the +\item{alpha_line}{Numeric value specifying alpha of lines indicating the emphasized compatibility interval levels (see \code{?parameters::p_function}).} \item{show_labels}{Logical. If \code{TRUE}, text labels are displayed.} diff --git a/man/plot.see_p_significance.Rd b/man/plot.see_p_significance.Rd index d9bb4440d..67e9d654b 100644 --- a/man/plot.see_p_significance.Rd +++ b/man/plot.see_p_significance.Rd @@ -9,7 +9,7 @@ data = NULL, show_intercept = FALSE, priors = FALSE, - priors_alpha = 0.4, + alpha_priors = 0.4, n_columns = 1, ... ) @@ -30,7 +30,7 @@ are hardly visible.} (using \code{\link[bayestestR:simulate_prior]{bayestestR::simulate_prior()}}) and added to the plot.} -\item{priors_alpha}{Numeric value specifying alpha for the prior +\item{alpha_priors}{Numeric value specifying alpha for the prior distributions.} \item{n_columns}{For models with multiple components (like fixed and random, diff --git a/man/plot.see_parameters_brms_meta.Rd b/man/plot.see_parameters_brms_meta.Rd index 0572330b5..15da5cb49 100644 --- a/man/plot.see_parameters_brms_meta.Rd +++ b/man/plot.see_parameters_brms_meta.Rd @@ -9,8 +9,8 @@ size_point = 2, linewidth = 0.8, size_text = 3.5, - posteriors_alpha = 0.7, - rope_alpha = 0.15, + alpha_posteriors = 0.7, + alpha_rope = 0.15, color_rope = "cadetblue", normalize_height = TRUE, show_labels = TRUE, @@ -26,10 +26,10 @@ \item{size_text}{Numeric value specifying size of text labels.} -\item{posteriors_alpha}{Numeric value specifying alpha for the posterior +\item{alpha_posteriors}{Numeric value specifying alpha for the posterior distributions.} -\item{rope_alpha}{Numeric specifying transparency level of ROPE ribbon.} +\item{alpha_rope}{Numeric specifying transparency level of ROPE ribbon.} \item{color_rope}{Character specifying color of ROPE ribbon.} diff --git a/man/plot.see_parameters_distribution.Rd b/man/plot.see_parameters_distribution.Rd index aa001a2fc..693f944c9 100644 --- a/man/plot.see_parameters_distribution.Rd +++ b/man/plot.see_parameters_distribution.Rd @@ -7,7 +7,7 @@ \method{plot}{see_parameters_distribution}( x, dispersion = FALSE, - dispersion_alpha = 0.3, + alpha_dispersion = 0.3, color_dispersion = "#3498db", dispersion_style = c("ribbon", "curve"), size_bar = 0.7, @@ -22,7 +22,7 @@ \item{dispersion}{Logical. If \code{TRUE}, a range of dispersion for each variable to the plot will be added.} -\item{dispersion_alpha}{Numeric value specifying the transparency level of dispersion ribbon.} +\item{alpha_dispersion}{Numeric value specifying the transparency level of dispersion ribbon.} \item{color_dispersion}{Character specifying the color of dispersion ribbon.} diff --git a/man/plot.see_parameters_simulate.Rd b/man/plot.see_parameters_simulate.Rd index 3bd86000c..8c7b6ddc5 100644 --- a/man/plot.see_parameters_simulate.Rd +++ b/man/plot.see_parameters_simulate.Rd @@ -12,7 +12,7 @@ n_columns = NULL, normalize_height = FALSE, linewidth = 0.9, - posteriors_alpha = 0.7, + alpha_posteriors = 0.7, centrality = "median", ci = 0.95, ... @@ -45,7 +45,7 @@ result in very flat density-areas. In such cases, set \item{linewidth}{Numeric value specifying size of line geoms.} -\item{posteriors_alpha}{Numeric value specifying alpha for the posterior +\item{alpha_posteriors}{Numeric value specifying alpha for the posterior distributions.} \item{centrality}{Character specifying the point-estimate (centrality index) diff --git a/man/plot.see_performance_simres.Rd b/man/plot.see_performance_simres.Rd index 3d98eec86..b96e4e92e 100644 --- a/man/plot.see_performance_simres.Rd +++ b/man/plot.see_performance_simres.Rd @@ -12,7 +12,7 @@ size_axis_title = base_size, base_size = 10, alpha = 0.2, - dot_alpha = 0.8, + alpha_dot = 0.8, colors = c("#3aaf85", "#1b6ca8"), detrend = FALSE, transform = NULL, @@ -32,7 +32,7 @@ axis and plot titles.} \item{alpha}{Numeric value specifying alpha level of the confidence bands.} -\item{dot_alpha}{Numeric value specifying alpha level of the point geoms.} +\item{alpha_dot}{Numeric value specifying alpha level of the point geoms.} \item{colors}{Character vector of length two, indicating the colors (in hex-format) for points and line.} diff --git a/man/plot.see_point_estimate.Rd b/man/plot.see_point_estimate.Rd index d6ea11a64..c1d3204cf 100644 --- a/man/plot.see_point_estimate.Rd +++ b/man/plot.see_point_estimate.Rd @@ -13,7 +13,7 @@ show_labels = TRUE, show_intercept = FALSE, priors = FALSE, - priors_alpha = 0.4, + alpha_priors = 0.4, ... ) } @@ -45,7 +45,7 @@ are hardly visible.} (using \code{\link[bayestestR:simulate_prior]{bayestestR::simulate_prior()}}) and added to the plot.} -\item{priors_alpha}{Numeric value specifying alpha for the prior +\item{alpha_priors}{Numeric value specifying alpha for the prior distributions.} \item{...}{Arguments passed to or from other methods.} diff --git a/man/plot.see_rope.Rd b/man/plot.see_rope.Rd index 179e30d27..ff5c305ab 100644 --- a/man/plot.see_rope.Rd +++ b/man/plot.see_rope.Rd @@ -7,7 +7,7 @@ \method{plot}{see_rope}( x, data = NULL, - rope_alpha = 0.5, + alpha_rope = 0.5, color_rope = "cadetblue", show_intercept = FALSE, n_columns = 1, @@ -20,7 +20,7 @@ \item{data}{The original data used to create this object. Can be a statistical model.} -\item{rope_alpha}{Numeric specifying transparency level of ROPE ribbon.} +\item{alpha_rope}{Numeric specifying transparency level of ROPE ribbon.} \item{color_rope}{Character specifying color of ROPE ribbon.} diff --git a/man/plot.see_si.Rd b/man/plot.see_si.Rd index e51c7e976..fe95a25ea 100644 --- a/man/plot.see_si.Rd +++ b/man/plot.see_si.Rd @@ -7,7 +7,7 @@ \method{plot}{see_si}( x, color_si = "#0171D3", - si_alpha = 0.2, + alpha_si = 0.2, show_intercept = FALSE, support_only = FALSE, ... @@ -18,7 +18,7 @@ \item{color_si}{Character specifying color of SI ribbon.} -\item{si_alpha}{Numeric value specifying Transparency level of SI ribbon.} +\item{alpha_si}{Numeric value specifying Transparency level of SI ribbon.} \item{show_intercept}{Logical, if \code{TRUE}, the intercept-parameter is included in the plot. By default, it is hidden because in many cases the diff --git a/man/print.see_performance_pp_check.Rd b/man/print.see_performance_pp_check.Rd index 17eceb159..0d6fc9096 100644 --- a/man/print.see_performance_pp_check.Rd +++ b/man/print.see_performance_pp_check.Rd @@ -13,7 +13,7 @@ size_axis_title = base_size, size_title = 12, base_size = 10, - line_alpha = 0.15, + alpha_line = 0.15, style = theme_lucid, colors = unname(social_colors(c("green", "blue"))), type = c("density", "discrete_dots", "discrete_interval", "discrete_both"), @@ -29,7 +29,7 @@ size_axis_title = base_size, size_title = 12, base_size = 10, - line_alpha = 0.15, + alpha_line = 0.15, style = theme_lucid, colors = unname(social_colors(c("green", "blue"))), type = c("density", "discrete_dots", "discrete_interval", "discrete_both"), @@ -49,7 +49,7 @@ \item{base_size, size_axis_title, size_title}{Numeric value specifying size of axis and plot titles.} -\item{line_alpha}{Numeric value specifying alpha of lines indicating \code{yrep}.} +\item{alpha_line}{Numeric value specifying alpha of lines indicating \code{yrep}.} \item{style}{A ggplot2-theme.}