Merge remote-tracking branch 'origin/master'

LudvigOlsen · Oct 25, 2020 · 98b6234 · 98b6234
2 parents 5064353 + 10c8793
commit 98b6234
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diff --git a/R/angle.R b/R/angle.R
@@ -1,6 +1,5 @@
 
 
-
 #   __________________ #< 1bae15c31fc98d40b9bd4b7b5434d7b3 ># __________________
 #   Angle                                                                   ####
 
@@ -36,7 +35,6 @@
 #' @inheritParams multi_mutator_
 #' @family measuring functions
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -78,7 +76,6 @@
 #'   y_col = "y",
 #'   origin_fn = centroid
 #' )
-#' }
 angle <- function(data,
                   x_col = NULL,
                   y_col = NULL,

diff --git a/R/apply_transformation_matrix.R b/R/apply_transformation_matrix.R
@@ -52,7 +52,6 @@
 #' @family mutate functions
 #' @inheritParams multi_mutator_
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -73,7 +72,7 @@
 #' )
 #'
 #' # Apply identity matrix
-#' mat <- matrix(c(1,0,0,0,1,0,0,0,1), nrow=3)
+#' mat <- matrix(c(1, 0, 0, 0, 1, 0, 0, 0, 1), nrow = 3)
 #' apply_transformation_matrix(
 #'   data = df,
 #'   mat = mat,
@@ -84,7 +83,7 @@
 #' # Apply rotation matrix
 #' # 90 degrees around z-axis
 #' # Origin is the most centered point
-#' mat <- matrix(c(0,1,0,-1,0,0,0,0,1), nrow=3)
+#' mat <- matrix(c(0, 1, 0, -1, 0, 0, 0, 0, 1), nrow = 3)
 #' res <- apply_transformation_matrix(
 #'   data = df,
 #'   mat = mat,
@@ -95,9 +94,9 @@
 #' # Plot the rotation
 #' # z wasn't changed so we plot x and y
 #' res %>%
-#'   ggplot(aes(x=x, y=y)) +
+#'   ggplot(aes(x = x, y = y)) +
 #'   geom_point() +
-#'   geom_point(aes(x=x_transformed, y=y_transformed)) +
+#'   geom_point(aes(x = x_transformed, y = y_transformed)) +
 #'   theme_minimal()
 #'
 #' # Apply rotation matrix to grouped data frame
@@ -112,12 +111,10 @@
 #'
 #' # Plot the rotation
 #' res %>%
-#'   ggplot(aes(x=x, y=y, color=g)) +
+#'   ggplot(aes(x = x, y = y, color = g)) +
 #'   geom_point() +
-#'   geom_point(aes(x=x_transformed, y=y_transformed)) +
+#'   geom_point(aes(x = x_transformed, y = y_transformed)) +
 #'   theme_minimal()
-#'
-#' }
 apply_transformation_matrix <- function(data,
                                         mat,
                                         cols,

diff --git a/R/by_distance.R b/R/by_distance.R
@@ -43,7 +43,6 @@
 #' @return
 #'  The sorted \code{data.frame} (\code{tibble}) / \code{vector}.
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -98,7 +97,8 @@
 #'     cols = "B",
 #'     origin_fn = create_origin_fn(median)
 #'   )$B,
-#'   xlab = "Position", ylab = "B"
+#'   xlab = "Position",
+#'   ylab = "B"
 #' )
 #' plot(
 #'   x = 1:10,
@@ -107,13 +107,13 @@
 #'     origin_fn = create_origin_fn(median),
 #'     shuffle_ties = TRUE
 #'   )$A,
-#'   xlab = "Position", ylab = "A"
+#'   xlab = "Position",
+#'   ylab = "A"
 #' )
 #'
 #' # In multiple dimensions
 #' df %>%
 #'   closest_to(cols = c("A", "B"), origin_fn = most_centered)
-#' }
 closest_to <- function(data,
                        cols = NULL,
                        origin = NULL,

diff --git a/R/centering.R b/R/centering.R
@@ -31,7 +31,6 @@
 #' @return
 #'  The sorted \code{data.frame} (\code{tibble}) / \code{vector}.
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -72,7 +71,6 @@
 #' # Plot the centered values
 #' plot(x = 1:10, y = center_max(df, col = "B")$B)
 #' plot(x = 1:10, y = center_max(df, col = "B", shuffle_sides = TRUE)$B)
-#' }
 center_max <- function(data,
                        col = NULL,
                        shuffle_sides = FALSE) {
@@ -112,7 +110,6 @@ center_max <- function(data,
 #' @return
 #'  The sorted \code{data.frame} (\code{tibble}) / \code{vector}.
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -153,7 +150,6 @@ center_max <- function(data,
 #' # Plot the centered values
 #' plot(x = 1:10, y = center_min(df, col = "B")$B)
 #' plot(x = 1:10, y = center_min(df, col = "B", shuffle_sides = TRUE)$B)
-#' }
 center_min <- function(data,
                        col = NULL,
                        shuffle_sides = FALSE) {

diff --git a/R/centroid.R b/R/centroid.R
@@ -16,7 +16,6 @@
 #' @export
 #' @return Means of the supplied \code{vectors}/\code{columns}. Either as a \code{vector} or a \code{data.frame}.
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -53,7 +52,6 @@
 #' df %>%
 #'   dplyr::group_by(g) %>%
 #'   centroid(cols = c("x", "y", "z"))
-#' }
 centroid <- function(..., cols = NULL, na.rm = FALSE) {
   # Apply centroid function
   apply_coord_fn_(

diff --git a/R/circularize.R b/R/circularize.R
@@ -25,7 +25,6 @@
 #' @family forming functions
 #' @inheritParams multi_mutator_
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -122,7 +121,6 @@
 #'   )) +
 #'   geom_point() +
 #'   theme_minimal()
-#' }
 circularize <- function(data,
                         y_col = NULL,
                         .min = NULL,

diff --git a/R/cluster_groups.R b/R/cluster_groups.R
@@ -39,7 +39,6 @@
 #' @family mutate functions
 #' @family clustering functions
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -131,7 +130,6 @@
 #'   group_col = "g"
 #' )
 #'
-#' }
 #' \dontrun{
 #' # Plot 3d with plotly
 #' plotly::plot_ly(

diff --git a/R/conversion.R b/R/conversion.R
@@ -13,7 +13,6 @@
 #'
 #'  Missing values (\code{NA}s) are returned as they are.
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -26,7 +25,6 @@
 #'
 #' # Get back the original degrees
 #' radians_to_degrees(degrees_to_radians(c(90, 180, 270)))
-#' }
 degrees_to_radians <- function(degrees) {
   checkmate::assert_numeric(degrees)
   degrees * (pi / 180)

diff --git a/R/create_dimming_fn.R b/R/create_dimming_fn.R
@@ -38,7 +38,6 @@
 #'
 #'  \code{\}}
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(ggplot2)
@@ -73,7 +72,6 @@
 #'   geom_point() +
 #'   geom_line() +
 #'   theme_minimal()
-#' }
 create_dimming_fn <- function(numerator = 1, exponent = 2, add_to_distance = 1) {
 
   # Check arguments ####

diff --git a/R/create_n_fn.R b/R/create_n_fn.R
@@ -39,7 +39,6 @@
 #'  Note: The dots argument in the generated function should not to be confused with the dots
 #'  argument in \code{create_n_fn()}).
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #'
@@ -83,7 +82,6 @@
 #'   mean(y, na.rm = TRUE),
 #'   mean(z, na.rm = TRUE)
 #' ))
-#' }
 create_n_fn <- function(fn,
                         use_index = FALSE,
                         negate = FALSE,

diff --git a/R/create_origin_fn.R b/R/create_origin_fn.R
@@ -17,7 +17,6 @@
 #' @return Function with the dots (\code{...}) argument that applies the \code{`fn`} function to
 #'  each element in \code{...} (usually one vector per dimension).
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #'
@@ -53,7 +52,6 @@
 #'   mean(y, na.rm = TRUE),
 #'   mean(z, na.rm = TRUE)
 #' )
-#' }
 create_origin_fn <- function(fn, ...) {
   args <- list(...)
   function(...) {

diff --git a/R/dim_values.R b/R/dim_values.R
@@ -74,7 +74,6 @@
 #' @family distance functions
 #' @inheritParams multi_mutator_
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -145,7 +144,6 @@
 #'   geom_point() +
 #'   theme_minimal() +
 #'   labs(x = "x", y = "y", color = "Cluster", alpha = "o_dimmed")
-#' }
 dim_values <- function(data,
                        cols,
                        dimming_fn = create_dimming_fn(

diff --git a/R/distance.R b/R/distance.R
@@ -31,7 +31,6 @@
 #' @family measuring functions
 #' @family distance functions
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -60,7 +59,6 @@
 #'   cols = c("x", "y"),
 #'   origin_fn = centroid
 #' )
-#' }
 distance <- function(data,
                      cols = NULL,
                      origin = NULL,

diff --git a/R/expand_distances.R b/R/expand_distances.R
@@ -84,7 +84,6 @@
 #' @family distance functions
 #' @inheritParams multi_mutator_
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -220,7 +219,6 @@
 #'   geom_point() +
 #'   theme_minimal() +
 #'   labs(x = "x", y = "y", color = "g")
-#' }
 expand_distances <- function(data,
                              cols = NULL,
                              multiplier = NULL,

diff --git a/R/expand_distances_each.R b/R/expand_distances_each.R
@@ -90,7 +90,6 @@
 #' @family distance functions
 #' @inheritParams multi_mutator_
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -251,7 +250,6 @@
 #'   geom_point() +
 #'   theme_minimal() +
 #'   labs(x = "x", y = "y", color = "g")
-#' }
 expand_distances_each <- function(data,
                                   cols = NULL,
                                   multipliers = NULL,

diff --git a/R/flip_values.R b/R/flip_values.R
@@ -41,7 +41,6 @@
 #' @family mutate functions
 #' @inheritParams multi_mutator_
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -106,7 +105,6 @@
 #'   geom_line(aes(y = A_flip_3, color = "Flipped A (3)")) +
 #'   geom_hline(aes(color = "3", yintercept = 3)) +
 #'   theme_minimal()
-#' }
 flip_values <- function(data,
                         cols = NULL,
                         origin = NULL,

diff --git a/R/generate_clusters.R b/R/generate_clusters.R
@@ -35,7 +35,6 @@
 #'  }
 #' @family clustering functions
 #' @examples
-#' \donttest{
 #' # Attach packages
 #' library(rearrr)
 #' library(dplyr)
@@ -73,7 +72,6 @@
 #'   num_clusters = 5, compactness = 1.6
 #' )
 #'
-#' }
 #' \dontrun{
 #' # Plot 3d with plotly
 #' plotly::plot_ly(