old_friends.R
In ggmice: Visualizations for 'mice' with 'ggplot2'

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 7.2,
  fig.height = 4,
  warning = FALSE,
  message = FALSE
)
options(rmarkdown.html_vignette.check_title = FALSE)

## ----setup, warning = FALSE, message = FALSE----------------------------------
# load packages
library(ggmice)
library(mice)
library(ggplot2)
# load incomplete dataset from mice
dat <- boys
# generate imputations
imp <- mice(dat, method = "pmm", printFlag = FALSE)

## ----bwplot-------------------------------------------------------------------
# original plot
mice::bwplot(imp, hgt ~ .imp)
# ggmice equivalent
ggmice(imp, aes(x = .imp, y = hgt)) +
  geom_boxplot() +
  labs(x = "Imputation number")
# extended reproduction with ggmice
ggmice(imp, aes(x = .imp, y = hgt)) +
  stat_boxplot(geom = "errorbar", linetype = "dashed") +
  geom_boxplot(outlier.colour = "grey", outlier.shape = 1) +
  labs(x = "Imputation number") +
  theme(legend.position = "none")

## ----densityplot--------------------------------------------------------------
# original plot
mice::densityplot(imp, ~hgt)
# ggmice equivalent
ggmice(imp, aes(x = hgt, group = .imp)) +
  geom_density()
# extended reproduction with ggmice
ggmice(imp, aes(x = hgt, group = .imp, size = .where)) +
  geom_density() +
  scale_size_manual(
    values = c("observed" = 1, "imputed" = 0.5),
    guide = "none"
  ) +
  theme(legend.position = "none")

## ----flux---------------------------------------------------------------------
# original plot
fluxplot(dat)
# ggmice equivalent
plot_flux(dat)

## ----md.pattern---------------------------------------------------------------
# original plot
md <- md.pattern(dat)
# ggmice equivalent
plot_pattern(dat)
# extended reproduction with ggmice
plot_pattern(dat, square = TRUE) +
  theme(
    legend.position = "none",
    axis.title = element_blank(),
    axis.title.x.top = element_blank(),
    axis.title.y.right = element_blank()
  )

## ----plot.mids----------------------------------------------------------------
# original plot
plot(imp, hgt ~ .it | .ms)
# ggmice equivalent
plot_trace(imp, "hgt")

## ----stripplot----------------------------------------------------------------
# original plot
mice::stripplot(imp, hgt ~ .imp)
# ggmice equivalent
ggmice(imp, aes(x = .imp, y = hgt)) +
  geom_jitter(width = 0.25) +
  labs(x = "Imputation number")
# extended reproduction with ggmice (not recommended)
ggmice(imp, aes(x = .imp, y = hgt)) +
  geom_jitter(
    shape = 1,
    width = 0.1,
    na.rm = TRUE,
    data = data.frame(
      hgt = dat$hgt,
      .imp = factor(rep(1:imp$m, each = nrow(dat))),
      .where = "observed"
    )
  ) +
  geom_jitter(shape = 1, width = 0.1) +
  labs(x = "Imputation number") +
  theme(legend.position = "none")

## -----------------------------------------------------------------------------
# original plot
mice::xyplot(imp, hgt ~ age)
# ggmice equivalent
ggmice(imp, aes(age, hgt)) +
  geom_point()
# extended reproduction with ggmice
ggmice(imp, aes(age, hgt)) +
  geom_point(size = 2, shape = 1) +
  theme(legend.position = "none")

## ----plotly-------------------------------------------------------------------
# load packages
library(plotly)
# influx and outflux plot
p <- plot_flux(dat)
ggplotly(p)

## ----mapping------------------------------------------------------------------
# load packages
library(purrr)
library(patchwork)
# create vector with variable names
vrb <- names(dat)

## ----bwplots------------------------------------------------------------------
# original plot
mice::bwplot(imp)
# ggmice equivalent
p <- map(vrb, ~ {
  ggmice(imp, aes(x = .imp, y = .data[[.x]])) +
    geom_boxplot() +
    scale_x_discrete(drop = FALSE) +
    labs(x = "Imputation number")
})
wrap_plots(p, guides = "collect") &
  theme(legend.position = "bottom")

## ----densityplots, message=FALSE, warning=FALSE-------------------------------
# original plot
mice::densityplot(imp)
# ggmice equivalent
p <- map(vrb, ~ {
  ggmice(imp, aes(x = .data[[.x]], group = .imp)) +
    geom_density()
})
wrap_plots(p, guides = "collect") &
  theme(legend.position = "bottom")

## ----stripplots---------------------------------------------------------------
# original plot
mice::stripplot(imp)
# ggmice equivalent
p <- map(vrb, ~ {
  ggmice(imp, aes(x = .imp, y = .data[[.x]])) +
    geom_jitter() +
    labs(x = "Imputation number")
})
wrap_plots(p, guides = "collect") &
  theme(legend.position = "bottom")

## ----session, class.source = 'fold-hide'--------------------------------------
sessionInfo()