Create the ggmice
equivalent of mice
plots
How to re-create the output of the plotting functions from
mice
with ggmice
. In alphabetical order of the
mice
functions.
First load the ggmice
, mice
, and
ggplot2
packages, some incomplete data and a
mids
object into your workspace.
# 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
Box-and-whisker plot of observed and imputed data.
# 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
Density plot of observed and imputed data.
# 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")
md.pattern
Missing data pattern plot.
# 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
Plot the trace lines of the MICE algorithm.
# original plot
plot(imp, hgt ~ .it | .ms)
# ggmice equivalent
plot_trace(imp, "hgt")