Package 'ggmice'

Title: Visualizations for 'mice' with 'ggplot2'
Description: Enhance a 'mice' imputation workflow with visualizations for incomplete and/or imputed data. The plotting functions produce 'ggplot' objects which may be easily manipulated or extended. Use 'ggmice' to inspect missing data, develop imputation models, evaluate algorithmic convergence, or compare observed versus imputed data.
Authors: Hanne Oberman [aut, cre] , Utrecht University [fnd], University Medical Centre Utrecht [fnd], Thom Volker [ctb] , Gerko Vink [ctb] , Pepijn Vink [ctb] , Jamie Wallis [ctb]
Maintainer: Hanne Oberman <[email protected]>
License: GPL (>= 3)
Version: 0.1.0.9000
Built: 2024-03-20 05:11:09 UTC
Source: https://github.com/amices/ggmice

Help Index


Box-and-whisker plot of observed and imputed data

Description

Box-and-whisker plot of observed and imputed data

Usage

bwplot(...)

Arguments

...

Any arguments passed to the function.

Value

The output of mice::bwplot and a message about the ggmice equivalent.

Examples

imp <- mice::mice(mice::nhanes, maxit = 1, printFlag = FALSE)
bwplot(imp)

Densityplot of observed and imputed data

Description

Densityplot of observed and imputed data

Usage

densityplot(...)

Arguments

...

Any arguments passed to the function.

Value

The output of mice::densityplot and a message about the ggmice equivalent.

Examples

imp <- mice::mice(mice::nhanes, maxit = 1, printFlag = FALSE)
densityplot(imp)

Plot incomplete or imputed data

Description

Plot incomplete or imputed data

Usage

ggmice(data = NULL, mapping = ggplot2::aes())

Arguments

data

An incomplete dataset (of class data.frame), or an object of class mice::mids.

mapping

A list of aesthetic mappings created with ggplot2::aes().

Value

An object of class ggplot2::ggplot. The ggmice function returns output equivalent to ggplot2::ggplot output, with a few important exceptions:

See Also

See the ggmice vignette to use the ggmice() function on incomplete data or imputed data.

Examples

dat <- mice::nhanes
ggmice(dat, ggplot2::aes(x = age, y = bmi)) + ggplot2::geom_point()
imp <- mice::mice(dat, print = FALSE)
ggmice(imp, ggplot2::aes(x = age, y = bmi)) + ggplot2::geom_point()

Plot correlations between (incomplete) variables

Description

Plot correlations between (incomplete) variables

Usage

plot_corr(
  data,
  vrb = "all",
  label = FALSE,
  square = TRUE,
  diagonal = FALSE,
  rotate = FALSE,
  caption = TRUE
)

Arguments

data

A dataset of class data.frame, tibble, or matrix.

vrb

String, vector, or unquoted expression with variable name(s), default is "all".

label

Logical indicating whether correlation values should be displayed.

square

Logical indicating whether the plot tiles should be squares.

diagonal

Logical indicating whether the correlation of each variable with itself should be displayed.

rotate

Logical indicating whether the variable name labels should be rotated 90 degrees.

caption

Logical indicating whether the figure caption should be displayed.

Value

An object of class ggplot2::ggplot.

Examples

plot_corr(mice::nhanes, label = TRUE)

Plot the influx and outflux of a multivariate missing data pattern

Description

Plot the influx and outflux of a multivariate missing data pattern

Usage

plot_flux(data, vrb = "all", label = TRUE, caption = TRUE)

Arguments

data

An incomplete dataset of class data.frame or matrix.

vrb

String, vector, or unquoted expression with variable name(s), default is "all".

label

Logical indicating whether variable names should be displayed within the plot (the default) or with colors in the legend.

caption

Logical indicating whether the figure caption should be displayed.

Value

An object of class ggplot2::ggplot.

Examples

plot_flux(mice::nhanes)

Plot the missing data pattern of an incomplete dataset

Description

Plot the missing data pattern of an incomplete dataset

Usage

plot_pattern(
  data,
  vrb = "all",
  square = TRUE,
  rotate = FALSE,
  cluster = NULL,
  npat = NULL,
  caption = TRUE
)

Arguments

data

An incomplete dataset of class data.frame or matrix.

vrb

String, vector, or unquoted expression with variable name(s), default is "all".

square

Logical indicating whether the plot tiles should be squares, defaults to squares to mimick mice::md.pattern().

rotate

Logical indicating whether the variable name labels should be rotated 90 degrees.

cluster

Optional character string specifying which variable should be used for clustering (e.g., for multilevel data).

npat

Optional numeric input specifying the number of missing data patterns to be visualized, defaults to all patterns.

caption

Logical indicating whether the figure caption should be displayed.

Value

An object of class ggplot2::ggplot.

Examples

plot_pattern(mice::nhanes)

Plot the predictor matrix of an imputation model

Description

Plot the predictor matrix of an imputation model

Usage

plot_pred(
  data,
  vrb = "all",
  method = NULL,
  label = TRUE,
  square = TRUE,
  rotate = FALSE
)

Arguments

data

A predictor matrix for mice, typically generated with mice::make.predictorMatrix or mice::quickpred.

vrb

String, vector, or unquoted expression with variable name(s), default is "all".

method

Character string or vector with imputation methods.

label

Logical indicating whether predictor matrix values should be displayed.

square

Logical indicating whether the plot tiles should be squares.

rotate

Logical indicating whether the variable name labels should be rotated 90 degrees.

Value

An object of class ggplot2::ggplot.

Examples

pred <- mice::quickpred(mice::nhanes)
plot_pred(pred)

Plot the trace lines of the imputation algorithm

Description

Plot the trace lines of the imputation algorithm

Usage

plot_trace(data, vrb = "all")

Arguments

data

An object of class mice::mids.

vrb

String, vector, or unquoted expression with variable name(s), default is "all".

Value

An object of class ggplot2::ggplot.

Examples

imp <- mice::mice(mice::nhanes, print = FALSE)
plot_trace(imp)

Stripplot of observed and imputed data

Description

Stripplot of observed and imputed data

Usage

stripplot(...)

Arguments

...

Any arguments passed to the function.

Value

The output of mice::stripplot and a message about the ggmice equivalent.

Examples

imp <- mice::mice(mice::nhanes, maxit = 1, printFlag = FALSE)
stripplot(imp)

Theme for mice style ggplot2::ggplot objects

Description

Theme for mice style ggplot2::ggplot objects

Usage

theme_mice()

Value

A ggplot2 theme.


Minimal theme for mice style ggplot2::ggplot objects

Description

Minimal theme for mice style ggplot2::ggplot objects

Usage

theme_minimice()

Value

A ggplot2 theme.


Scatterplot of observed and imputed data

Description

Scatterplot of observed and imputed data

Usage

xyplot(...)

Arguments

...

Any arguments passed to the function.

Value

The output of mice::xyplot and a message about the ggmice equivalent.

Examples

imp <- mice::mice(mice::nhanes, maxit = 1, printFlag = FALSE)
xyplot(imp, bmi ~ age)