rename error to sem

NAMESPACE

@@ -28,8 +28,6 @@ export(add_data_points_jitter)
 export(add_density_curve)
 export(add_density_histogram)
 export(add_donut)
-export(add_error_bar)
-export(add_error_ribbon)
 export(add_heatmap)
 export(add_histogram)
 export(add_line)
@@ -51,6 +49,8 @@ export(add_range_ribbon)
 export(add_reference_lines)
 export(add_sd_bar)
 export(add_sd_ribbon)
+export(add_sem_bar)
+export(add_sem_ribbon)
 export(add_stats_asterisks)
 export(add_stats_pvalue)
 export(add_sum_area)

R/add-general.R

@@ -66,7 +66,7 @@ ff_errorbar <- function(.fun.data) {
 }
 #' Add error bar
 #'
-#' * `add_error_bar()` adds the standard error of mean.
+#' * `add_sem_bar()` adds the standard error of mean.
 #' * `add_range_bar()` adds the range from smallest to largest value.
 #' * `add_sd_bar()` adds the standard deviation.
 #' * `add_ci95_bar()` adds the 95% confidence interval.
@@ -77,7 +77,7 @@ ff_errorbar <- function(.fun.data) {
 #' study %>%
 #'   tidyplot(x = treatment, y = score, color = treatment) %>%
 #'   add_data_points() %>%
-#'   add_error_bar()
+#'   add_sem_bar()
 #' study %>%
 #'   tidyplot(x = treatment, y = score, color = treatment) %>%
 #'   add_data_points() %>%
@@ -92,14 +92,14 @@ ff_errorbar <- function(.fun.data) {
 #'   add_ci95_bar()
 #'
 #' @export
-add_error_bar <- ff_errorbar(.fun.data = ggplot2::mean_se)
-#' @rdname add_error_bar
+add_sem_bar <- ff_errorbar(.fun.data = ggplot2::mean_se)
+#' @rdname add_sem_bar
 #' @export
 add_range_bar <- ff_errorbar(.fun.data = min_max)
-#' @rdname add_error_bar
+#' @rdname add_sem_bar
 #' @export
 add_sd_bar <- ff_errorbar(.fun.data = mean_sdl)
-#' @rdname add_error_bar
+#' @rdname add_sem_bar
 #' @export
 add_ci95_bar <- ff_errorbar(.fun.data = mean_cl_boot)
 
@@ -118,7 +118,7 @@ ff_ribbon <- function(.fun.data) {
 }
 #' Add ribbon
 #'
-#' * `add_error_ribbon()` adds the standard error of mean.
+#' * `add_sem_ribbon()` adds the standard error of mean.
 #' * `add_range_ribbon()` adds the range from smallest to largest value.
 #' * `add_sd_ribbon()` adds the standard deviation.
 #' * `add_ci95_ribbon()` adds the 95% confidence interval.
@@ -129,7 +129,7 @@ ff_ribbon <- function(.fun.data) {
 #' time_course %>%
 #'   tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>%
 #'   add_mean_line() %>%
-#'   add_error_ribbon()
+#'   add_sem_ribbon()
 #' time_course %>%
 #'   tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>%
 #'   add_mean_line() %>%
@@ -144,14 +144,14 @@ ff_ribbon <- function(.fun.data) {
 #'   add_ci95_ribbon()
 #'
 #' @export
-add_error_ribbon <- ff_ribbon(.fun.data = ggplot2::mean_se)
-#' @rdname add_error_ribbon
+add_sem_ribbon <- ff_ribbon(.fun.data = ggplot2::mean_se)
+#' @rdname add_sem_ribbon
 #' @export
 add_range_ribbon <- ff_ribbon(.fun.data = min_max)
-#' @rdname add_error_ribbon
+#' @rdname add_sem_ribbon
 #' @export
 add_sd_ribbon <- ff_ribbon(.fun.data = ggplot2::mean_sdl)
-#' @rdname add_error_ribbon
+#' @rdname add_sem_ribbon
 #' @export
 add_ci95_ribbon <- ff_ribbon(.fun.data = ggplot2::mean_cl_boot)
 

R/feature_requests.R

@@ -12,7 +12,7 @@
 #   animals %>%
 #   tidyplot(family, size, color = family) %>%
 #   add_mean_bar(alpha = 0.3) %>%
-#   add_error_bar() %>%
+#   add_sem_bar() %>%
 #   adjust_data_labels(family, sort_by = size)
 #
 # # default random jitter

README.Rmd

@@ -50,7 +50,7 @@ library(tidyplots)
 study %>% 
   tidyplot(x = treatment, y = score, color = treatment) %>% 
   add_mean_bar(alpha = 0.3) %>% 
-  add_error_bar() %>% 
+  add_sem_bar() %>% 
   add_data_points_beeswarm()
 
 ```
@@ -99,7 +99,7 @@ time_course %>%
   tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>%
   add_mean_line() %>%
   add_mean_dot() %>%
-  add_error_ribbon()
+  add_sem_ribbon()
 
 ```
 
@@ -116,7 +116,7 @@ gene_expression %>%
   dplyr::filter(external_gene_name %in% c("Apol6", "Col5a3", "Vgf", "Bsn")) %>% 
   tidyplot(x = condition, y = expression, color = sample_type) %>% 
   add_mean_dash() %>% 
-  add_error_bar() %>% 
+  add_sem_bar() %>% 
   add_data_points_beeswarm() %>% 
   add_stats_asterisks(include_info = FALSE) %>% 
   remove_x_axis_title() %>% 
@@ -128,7 +128,7 @@ gene_expression %>%
 study %>% 
   tidyplot(x = treatment, y = score, color = treatment) %>% 
   add_mean_bar(alpha = 0.3) %>% 
-  add_error_bar() %>% 
+  add_sem_bar() %>% 
   add_data_points_beeswarm() %>% 
   view_plot(title = "Default color scheme: metro") %>% 
   adjust_colors(colors_discrete_seaside) %>% 

README.md

@@ -41,7 +41,7 @@ library(tidyplots)
 study %>% 
   tidyplot(x = treatment, y = score, color = treatment) %>% 
   add_mean_bar(alpha = 0.3) %>% 
-  add_error_bar() %>% 
+  add_sem_bar() %>% 
   add_data_points_beeswarm()
 ```
 
@@ -96,7 +96,7 @@ time_course %>%
   tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>%
   add_mean_line() %>%
   add_mean_dot() %>%
-  add_error_ribbon()
+  add_sem_ribbon()
 ```
 
 <img src="man/figures/README-unnamed-chunk-8-1.png" style="display: block; margin: auto;" />
@@ -115,7 +115,7 @@ gene_expression %>%
   dplyr::filter(external_gene_name %in% c("Apol6", "Col5a3", "Vgf", "Bsn")) %>% 
   tidyplot(x = condition, y = expression, color = sample_type) %>% 
   add_mean_dash() %>% 
-  add_error_bar() %>% 
+  add_sem_bar() %>% 
   add_data_points_beeswarm() %>% 
   add_stats_asterisks(include_info = FALSE) %>% 
   remove_x_axis_title() %>% 
@@ -128,7 +128,7 @@ gene_expression %>%
 study %>% 
   tidyplot(x = treatment, y = score, color = treatment) %>% 
   add_mean_bar(alpha = 0.3) %>% 
-  add_error_bar() %>% 
+  add_sem_bar() %>% 
   add_data_points_beeswarm() %>% 
   view_plot(title = "Default color scheme: metro") %>% 
   adjust_colors(colors_discrete_seaside) %>% 

_pkgdown.yml

@@ -48,7 +48,7 @@ reference:
 - contents:
   - starts_with("add_boxplot")
   - starts_with("add_violin")
-  - starts_with("add_error")
+  - starts_with("add_sem")
 - subtitle: Proportion
 - contents:
   - starts_with("add_areastack")

data-raw/distributions.R

@@ -19,13 +19,13 @@ distributions %>%
   add_violin() %>%
   add_data_points_beeswarm() %>%
   add_mean_dash(color = "red") %>%
-  add_error_bar(color = "red") %>%
+  add_sem_bar(color = "red") %>%
   add_reference_lines(y = c(7, 8.25, 5.75))
 
 distributions %>%
   tidyplot(x = group, y = value, color = group) %>%
   add_mean_bar(alpha = 0.3) %>%
-  add_error_bar()
+  add_sem_bar()
 
 distributions %>%
   tidyplot(x = group, y = value, color = group) %>%

data-raw/study.R

@@ -14,33 +14,33 @@ study <-
 study %>%
   tidyplot(treatment, score, color = treatment) %>%
   add_mean_bar(alpha = 0.3) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points_beeswarm()
 
 study %>%
   tidyplot(treatment, score) %>%
   add_mean_bar(alpha = 0.3) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points() %>%
   add_line()
 
 study %>%
   tidyplot(treatment, score) %>%
   add_mean_bar(alpha = 0.3) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points() %>%
   add_line(group = participant)
 
 study %>%
   tidyplot(dose, score, color = group) %>%
   add_mean_bar(alpha = 0.3) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points_beeswarm()
 
 study %>%
   tidyplot(treatment, score, color = group) %>%
   add_mean_bar(alpha = 0.3) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points() %>%
   add_line(group = participant) %>%
   adjust_data_labels(treatment, sort_by = dose)

data-raw/testing.R

@@ -73,13 +73,13 @@ study %>%
 study %>%
   tidyplot(treatment, score, color = treatment) %>%
   add(geom_col(alpha = 0.4, color = NA, width = 0.6)) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points(jitter_width = 0.2)
 
 study %>%
   tidyplot(treatment, score, color = treatment) %>%
   add_mean_bar(alpha = 0.2) %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points(jitter_width = 0.2)
 
 mapping <- ggplot2::aes(color = dose, fill = ggplot2::after_scale(apply_saturation(colour, saturation)))
@@ -291,7 +291,7 @@ p <-
 
 p %>% add_boxplot() %>% add_data_points()
 p %>% add_violin() %>% add_data_points() # preserve = "single" destroys violins, therefore not implemented here
-p %>% add_error_bar() %>% add_data_points()
+p %>% add_sem_bar() %>% add_data_points()
 p %>% add_mean_dash() %>% add_data_points()
 p %>% add_mean_bar() %>% add_data_points()
 
@@ -401,7 +401,7 @@ ggplot(data, aes(x = category, y = value)) +
 gene_expression %>%
   tidyplot(x = sample_type, y = expression, color = condition) %>%
   add_mean_dash() %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points() %>%
   add_stats_asterisks(include_info = FALSE) %>%
   split_plot(by = external_gene_name, ncol = 3, nrow = 3) %>%
@@ -410,7 +410,7 @@ gene_expression %>%
 gene_expression %>%
   tidyplot(x = sample_type, y = expression, color = condition) %>%
   add_mean_dash() %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   add_data_points() %>%
   add_stats_asterisks() %>%
   split_plot(by = external_gene_name, ncol = 3, nrow = 3) %>%
@@ -419,6 +419,6 @@ gene_expression %>%
 gene_expression %>%
   tidyplot(x = sample_type, y = expression, color = condition) %>%
   add_mean_dash() %>%
-  add_error_bar() %>%
+  add_sem_bar() %>%
   split_plot(by = external_gene_name, ncol = 3, nrow = 3) %>%
   save_plot("multipage4.pdf", units = "in")

data-raw/time_course.R

@@ -11,7 +11,7 @@ time_course %>%
   tidyplot(x = day, y = score, color = treatment, dodge_width = 0) %>%
   add_mean_line() %>%
   add_mean_dot() %>%
-  add_error_ribbon()
+  add_sem_ribbon()
 
 library(tidyverse)