version 0.5.0

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: ggcorset
 Type: Package
 Title: The Corset Plot
-Version: 0.4.5
+Version: 0.5.0
 Author: Kyla Belisario
 Maintainer: Kyla Belisario <kyla_belisario@protonmail.com>
 Description: Corset plots are a visualization technique used strictly to visualize repeat measures 
@@ -13,14 +13,17 @@ Description: Corset plots are a visualization technique used strictly to visuali
   integration so that users can customize their visualizations as required. Users can create corset 
   plots using data in either wide or long format using the functions gg_corset() or gg_corset_elongated(), respectively.
 License: MIT + file LICENSE
+URL: https://cran.r-project.org/package=ggcorset,
+        https://github.com/kbelisar/ggcorset
+BugReports: https://github.com/kbelisar/ggcorset/issues
 Depends: R (>= 3.5.0)
-Imports: ggplot2, dplyr, gghalves, ggstance
+Imports: ggplot2, gghalves
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Suggests: rmarkdown, knitr, viridis, MetBrewer
 VignetteBuilder: knitr
 NeedsCompilation: no
-Packaged: 2022-12-11 20:03:15 UTC; kyla
+Packaged: 2024-04-07 12:39:39 UTC; kyla
 Repository: CRAN
-Date/Publication: 2022-12-11 22:20:03 UTC
+Date/Publication: 2024-04-07 13:33:01 UTC

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
+YEAR: 2024
 COPYRIGHT HOLDER: Kyla Belisario

MD5

@@ -1,17 +1,24 @@
-8f8f8b0a1cd561a653281a103406f374 *DESCRIPTION
-1fcfae4844cb568b775335b275609d11 *LICENSE
-a406bc588db87dfbba630968849ab089 *NAMESPACE
+8cb469a466b45d9f7e1b6580e0488579 *DESCRIPTION
+672f685c5daca7f6746577c64bc13f5c *LICENSE
+489b593d868009d26a569651eed4048f *NAMESPACE
 9753e382e198a937b1f0e8bff825edbd *R/drinkdays.R
-096ca5ef36c67c3251311a49a54d18af *R/gg_corset.R
-8240cf1377d16caf9463be81763509db *R/gg_corset_elongated.R
-a97921e44510b1d57ce85d292ffb09ed *R/utils.R
-dc68d114330f4a706ba9a93b44f5d7ce *build/vignette.rds
+cd6f40e5ba3beefc4533d08ca4c83c80 *R/gg_corset.R
+3c8868d82d93df553606d9a97700e118 *R/gg_corset_elongated.R
+4f98e6786aa23461491d09d250bf8993 *R/position_dodgev.R
+7b4e2dcc8d465e92a33eeb2fba87894a *R/utils.R
+ef47a0f3c02fc091f3c418aef6370d96 *build/vignette.rds
 7203565e8cdf031b0129f2ab67255c27 *data/drinkdays.RData
+3e976817af1a71729b893234d2a9d7dd *inst/CITATION
 79e7dd20ecd6bd22e10d592d87ebc73b *inst/doc/corset_plot_intro.R
 be9049924c48578256ff4184d715046c *inst/doc/corset_plot_intro.Rmd
-799dd20c16b5caca68fc622a2ec4c5c5 *inst/doc/corset_plot_intro.html
+81353cf77999c6b16b529677195d936e *inst/doc/corset_plot_intro.html
 026e24a42ca777d27938d48aba91a424 *man/drinkdays.Rd
-811316312af04ce91a78735f271b6d73 *man/gg_corset.Rd
-4fc75a80a25e8e4803926f05037bbae3 *man/gg_corset_elongated.Rd
+02e66264842faf6ae5f77eb1559d5af3 *man/gg_corset.Rd
+aa9f3f2bc3ea54884478d48ddd341ecf *man/gg_corset_elongated.Rd
 4c23ad4bf155fea3c3f1cc268fd9abd7 *man/theme_ggcorset.Rd
 be9049924c48578256ff4184d715046c *vignettes/corset_plot_intro.Rmd
+6bf4ef1932e9bc7f838a534f80d31c6a *vignettes/img/example_corset_plot_age.png
+374cef61cc0c6a4687f0cebe310d98cf *vignettes/img/example_corset_plot_anatomy.png
+cf31710c21e2d18d8201c8ba57733d11 *vignettes/img/example_corset_plot_github_eyelets.png
+60edaf15bb75116badbe2685e26e4938 *vignettes/img/example_corset_plot_github_faceted.png
+0e8adbff3db6eefb6938532c4e6a9305 *vignettes/img/example_corset_plot_latentclass.png

NAMESPACE

@@ -3,11 +3,6 @@
 export(gg_corset)
 export(gg_corset_elongated)
 export(theme_ggcorset)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,filter)
-importFrom(dplyr,group_by)
-importFrom(dplyr,select)
-importFrom(dplyr,summarize)
 importFrom(gghalves,geom_half_violin)
 importFrom(ggplot2,"%+replace%")
 importFrom(ggplot2,aes)
@@ -26,6 +21,6 @@ importFrom(ggplot2,position_nudge)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_classic)
 importFrom(ggplot2,unit)
-importFrom(ggstance,position_dodgev)
 importFrom(stats,reshape)
+importFrom(stats,sd)
 importFrom(stats,var)

R/position_dodgev.R

@@ -0,0 +1,119 @@
+### The following code for vertical dodging in ggplot (position_dodgev) is adapted from Lionel Henry's ggstance package
+### as it will be archived on CRAN in 2024 [https://github.com/lionel-/ggstance]
+### Edits include removing unused arguments; combining functions; and removing the use of the plyr::ddply function
+
+pos_dodgev <- function(df, height) {
+
+  n <- length(unique(df$group))
+
+  if (!all(c("ymin", "ymax") %in% names(df))) {
+    df$ymin <- df$y
+    df$ymax <- df$y
+  }
+
+  d_height <- max(df$ymax - df$ymin)
+
+  # Have a new group index from 1 to number of groups.
+  # This might be needed if the group numbers in this set don't include all of 1:n
+  groupidy <- match(df$group, sort(unique(df$group)))
+
+  # Find the center for each group, then use that to calculate ymin and ymax
+  df$y <- df$y + height * ((groupidy - 0.5) / n - .5)
+  df$ymin <- df$y - d_height / n / 2
+  df$ymax <- df$y + d_height / n / 2
+
+  return(df)
+}
+
+#' @inheritParams ggplot2::position_dodge
+
+collidev <- function(data, height = NULL, name, strategy) {
+
+  # Determine height
+  if (!is.null(height)) {
+    # Width set manually
+    if (!(all(c("ymin", "ymax") %in% names(data)))) {
+      data$ymin <- data$y - height / 2
+      data$ymax <- data$y + height / 2
+    }
+  } else {
+    if (!(all(c("ymin", "ymax") %in% names(data)))) {
+      data$ymin <- data$y
+      data$ymax <- data$y
+    }
+
+    # Width determined from data, must be floating point constant
+    heights <- unique(data$ymax - data$ymin)
+    heights <- heights[!is.na(heights)]
+    height <- heights[1]
+  }
+
+  # Reorder by x position, then on group
+  data <- data[order(data$ymin, data$group), ]
+
+  # Check for overlap
+  intervals <- as.numeric(t(unique(data[c("ymin", "ymax")])))
+  intervals <- intervals[!is.na(intervals)]
+
+  if (!is.null(data$xmax)) {
+    data <- pos_dodgev(data,height)
+  } else if (!is.null(data$x)) {
+    data$xmax <- data$x
+    data <- pos_dodgev(data,height)
+    data$x <- data$xmax
+    return(data)
+  } else {
+    stop("Neither x nor xmax defined")
+  }
+}
+
+#' @format NULL
+#' @usage NULL
+
+PositionDodgev <- ggplot2::ggproto("PositionDodgev", ggplot2::Position,
+                          height = NULL, preserve = "total",
+                          setup_params = function(self, data) {
+                            if (is.null(data$ymin) && is.null(data$ymax) && is.null(self$height)) {
+                              warning("Height not defined. Set with `position_dodge(height = ?)`",
+                                      call. = FALSE)
+                            }
+
+                            if (identical(self$preserve, "total")) {
+                              n <- NULL
+                            } else {
+                              panels <- unname(split(data, data$PANEL))
+                              ns <- vapply(panels, function(panel) max(table(panel$ymin)), double(1))
+                              n <- max(ns)
+                            }
+
+                            list(
+                              height = self$height,
+                              n = n
+                            )
+                          },
+
+                          setup_data = function(self, data, params) {
+                            if (!"y" %in% names(data) && all(c("ymin", "ymax") %in% names(data))) {
+                              data$y <- (data$ymin + data$ymax) / 2
+                            }
+                            data
+                          },
+
+                          compute_panel = function(data, params, scales) {
+                            collidev(
+                              data,
+                              params$height,
+                              name = "position_dodgev")
+                          }
+)
+
+
+#' POSITION DODGE-V
+#' @name position_dodgev
+#' @noRd
+
+position_dodgev <- function(height = NULL) {
+  ggplot2::ggproto(NULL, PositionDodgev,
+          height = height
+  )
+}

R/utils.R

@@ -38,3 +38,12 @@ theme_ggcorset <- function() {
           axis.ticks = element_line(size = 0.75),
           strip.text = element_text(size = 13, face = "bold", vjust = 0.5, margin = margin(t = 5, b = 5)))
 }
+
+#' `se()`
+#' This function calculates standard error.
+#' @name se
+#' @param x An R object.
+#' @noRd
+
+se <- function(x){sqrt(var(x[!is.na(x)])/length(x[!is.na(x)]))}
+

inst/CITATION

@@ -0,0 +1,9 @@
+bibentry(
+  bibtype = "Manual",
+  header = "To cite ggcorset in publications, please use the following:",
+  author = "Kyla Belisario",
+  title = "Corset Plots: Visualizing Heterogeneity in Change Outcomes Across Two Timepoints",
+  year = "2021",
+  doi = "10.5281/zenodo.4905031",
+  url = "https://cran.r-project.org/package=ggcorset"
+)