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xgxr - Exploratory Graphics R Package - README

The xgxr package supports a structured approach for exploring PKPD data, which is used by xGx website. The package contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot) and the package enables the modeler to follow best graphical practices (by providing an xgx theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, the package provides some data checking and summarizing functions for rapidly exploring a PKPD dataset.

Detailed documentation of xgxr is available here

The xgxr package is also available on CRAN.

A cheatsheet for the xGx website and xgxr package is available here

If you're interested in contributing to this package, we follow the tidyverse style guide.

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Version

Install

install.packages('xgxr')

Monthly Downloads

2,184

Version

1.1.6

License

MIT + file LICENSE

Maintainer

Andrew Stein

Last Published

August 3rd, 2026

Functions in xgxr (1.1.6)

xgx_scale_x_time_units

Convert time units for plotting

xgx_annotate_status

Create a status (e.g. DRAFT) annotation layer

xgx_scale_y_percentchangelog10

percentchangelog10 transform for the y scale.

Plot data with median and percent intervals

Create a new xgx plot

xgx_scale_y_log10

log10 scales the y axis with a "pretty" set of breaks

xgx_minor_breaks_log10

Sets the default minor_breaks for log10 scales

Saving plot, automatically annotating the status and denoting the filenames

xgx_scale_x_reverselog10

Reverse-log transform for the x scale.

xgx_labels_log10

Nice labels for log10.

Saving table as an image, also labeling the program that created the table and where the table is stored

xgx_summarize_covariates

Summarize Covariate information in a dataset

xgx_scale_x_log10

log10 scales the x axis with a "pretty" set of breaks

xgx_summarize_data

Check data for various issues

xgx_scale_y_reverselog10

Reverselog transform for the y scale.

Sets the standard theme for xGx graphics

Calls the standard theme for xGx graphics

xgx_stat_smooth

Wrapper for stat_smooth

Plot data with median and percent intervals

Plot data with mean and confidence intervals

edit_rmd_template_str

Edit a Rmd Template from xgx

StatSmoothOrdinal

Stat object for producing smooths through ordinal data

mad_missing_duplicates

Multiple Ascending Dose Data Set (Duplicates Removed)

StatSummaryBinQuant

Stat ggproto object for binning by quantile for xgx_stat_ci

StatSummaryOrdinal

Stat ggproto object for creating ggplot layers of binned confidence intervals for probabiliities of classes in ordinal data

get_rmd_str returns a Rmd template string, based on the desired PKPD parameters

Determine the name of a Rmd template

Calls the standard theme for xGx graphics

Prediction data frame for nls

Prediction data frame for polr

xgx_annotate_filenames

Append filenames to bottom of the plot

Multiple Ascending Dose Data Set

Objects exported from other packages

Multiple Ascending Dose Noncompartmental Analysis (NCA) dataset

Single Ascending Dose Data Set

nlmixr Theophylline SD Data Set

Case 1 PKPD Data Set

xgx_conf_int returns a dataframe with mean +/- confidence intervals

xgx_breaks_time

Sets the default breaks for a time axis

Prediction data frame from ggplot2 Get predictions with standard errors into data frame

Plot data with mean and confidence intervals

xgx_annotate_status_png

Annotate a png file or directory of png files

Check data for various issues

Append filenames to bottom of the plot

xgx_auto_explore

Produce an xgx-styled report the given dataset using xgx R markdown templates, or a user-provided R markdown template. (Note: The R markdown template provided must be formatted in a similar manner to that of the xgx R markdown templates to work.) The working directory will contain a new directory (`xgx_autoexplore_output`) after running this function, which will contain a directory for the dataset, and futher a directory for the type of analysis / R markdown template.

xgx_breaks_log10

Sets the default breaks for log10