From 7b107d9441a46e3357478f574fab5c850545bed6 Mon Sep 17 00:00:00 2001
From: hanneoberman <h.i.oberman@uu.nl>
Date: Thu, 21 Dec 2023 15:40:00 +0100
Subject: [PATCH] Remove `plot_variance()` in line with `main`

---
 NAMESPACE            |  1 -
 R/plot_variance.R    | 71 --------------------------------------------
 man/plot_variance.Rd | 29 ------------------
 3 files changed, 101 deletions(-)
 delete mode 100644 R/plot_variance.R
 delete mode 100644 man/plot_variance.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 12244cea..8cf346e8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -10,7 +10,6 @@ export(plot_miss)
 export(plot_pattern)
 export(plot_pred)
 export(plot_trace)
-export(plot_variance)
 export(stripplot)
 export(xyplot)
 importFrom(magrittr,"%>%")
diff --git a/R/plot_variance.R b/R/plot_variance.R
deleted file mode 100644
index ff63b6ab..00000000
--- a/R/plot_variance.R
+++ /dev/null
@@ -1,71 +0,0 @@
-#' Plot the scaled between imputation variance for every cell as a heatmap
-#'
-#' This function plots the cell-level between imputation variance. The function
-#' scales the variances column-wise, without centering cf. `base::scale(center = FALSE)`
-#' and plots the data image as a heatmap. Darker red cells indicate more variance,
-#' lighter cells indicate less variance. White cells represent observed cells or unobserved cells with zero between
-#' imputation variance.
-#'
-#' @param data A package `mice` generated multiply imputed data set of class
-#' `mids`. Non-`mids` objects that have not been generated with `mice::mice()`
-#' can be converted through a pipeline with `mice::as.mids()`.
-#' @param grid Logical indicating whether grid lines should be displayed.
-#'
-#' @return An object of class `ggplot`.
-#' @examples
-#' imp <- mice::mice(mice::nhanes, printFlag = FALSE)
-#' plot_variance(imp)
-#' @export
-plot_variance <- function(data, grid = TRUE) {
-  verify_data(data, imp = TRUE)
-  if (data$m < 2) {
-    cli::cli_abort(
-      c(
-        "The between imputation variance cannot be computed if there are fewer than two imputations (m < 2).",
-        "i" = "Please provide an object with 2 or more imputations"
-      )
-    )
-  }
-  if (grid) {
-    gridcol <- "black"
-  } else {
-    gridcol <- NA
-  }
-
-  gg <- mice::complete(data, "long") %>%
-    dplyr::mutate(dplyr::across(where(is.factor), as.numeric)) %>%
-    dplyr::select(-.imp) %>%
-    dplyr::group_by(.id) %>%
-    dplyr::summarise(dplyr::across(dplyr::everything(), stats::var)) %>%
-    dplyr::ungroup() %>%
-    dplyr::mutate(dplyr::across(.cols = -.id, ~ scale_above_zero(.))) %>%
-    tidyr::pivot_longer(cols = -.id) %>%
-    ggplot2::ggplot(ggplot2::aes(name, .id, fill = value)) +
-    ggplot2::geom_tile(color = gridcol) +
-    ggplot2::scale_fill_gradient(low = "white", high = mice::mdc(2)) +
-    ggplot2::labs(
-      x = "Column name",
-      y = "Row number",
-      fill = "Imputation variability*
-      ",
-      caption = "*scaled cell-level between imputation variance"
-    ) + # "Cell-level between imputation\nvariance (scaled)\n\n"
-    ggplot2::scale_x_discrete(position = "top", expand = c(0, 0)) +
-    ggplot2::scale_y_continuous(trans = "reverse", expand = c(0, 0)) +
-    theme_minimice()
-
-  if (!grid) {
-    gg <-
-      gg + ggplot2::theme(panel.border = ggplot2::element_rect(fill = NA))
-  }
-
-  # return the ggplot object
-  return(gg)
-}
-
-# function to scale only non-zero values without centering
-scale_above_zero <- function(x) {
-  x <- as.matrix(x)
-  x[x != 0] <- scale(x[x != 0], center = FALSE)
-  return(x)
-}
diff --git a/man/plot_variance.Rd b/man/plot_variance.Rd
deleted file mode 100644
index ade26899..00000000
--- a/man/plot_variance.Rd
+++ /dev/null
@@ -1,29 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_variance.R
-\name{plot_variance}
-\alias{plot_variance}
-\title{Plot the scaled between imputation variance for every cell as a heatmap}
-\usage{
-plot_variance(data, grid = TRUE)
-}
-\arguments{
-\item{data}{A package \code{mice} generated multiply imputed data set of class
-\code{mids}. Non-\code{mids} objects that have not been generated with \code{mice::mice()}
-can be converted through a pipeline with \code{mice::as.mids()}.}
-
-\item{grid}{Logical indicating whether grid lines should be displayed.}
-}
-\value{
-An object of class \code{ggplot}.
-}
-\description{
-This function plots the cell-level between imputation variance. The function
-scales the variances column-wise, without centering cf. \code{base::scale(center = FALSE)}
-and plots the data image as a heatmap. Darker red cells indicate more variance,
-lighter cells indicate less variance. White cells represent observed cells or unobserved cells with zero between
-imputation variance.
-}
-\examples{
-imp <- mice::mice(mice::nhanes, printFlag = FALSE)
-plot_variance(imp)
-}