# Exploratory Graphics for Pharmacometrics

## Documentation for package ‘xgxr’ version 1.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

case1_pkpd | Case 1 PKPD Data Set
edit_rmd_template_str | Edit a Rmd Template from xgx
get_rmd_name | Determine the name of a Rmd template
get_rmd_str | 'get_rmd_str' returns a Rmd template string, based on the desired PKPD parameters
mad | Multiple Ascending Dose Data Set
mad_missing_duplicates | Multiple Ascending Dose Data Set (Duplicates Removed)
mad_nca | Multiple Ascending Dose Noncompartmental Analysis (NCA) dataset
nlmixr_theo_sd | nlmixr Theophylline SD Data Set
predictdf | Prediction data frame from ggplot2 Get predictions with standard errors into data frame
predictdf.nls | Prediction data frame for nls
predictdf.polr | Prediction data frame for polr
sad | Single Ascending Dose Data Set
StatSmoothOrdinal | Stat object for producing smooths through ordinal data
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
theme_xgx | Calls the standard theme for xGx graphics
xgx_annotate_filenames | Append filenames to bottom of the plot
xgx_annotate_status | Create a status (e.g. DRAFT) annotation layer
xgx_annotate_status_png | Annotate a png file or directory of png files

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
xgx_breaks_time | Sets the default breaks for a time axis
xgx_check_data | Check data for various issues
xgx_conf_int | 'xgx_conf_int' returns a dataframe with mean +/- confidence intervals
xgx_dirs2char | Append filenames to bottom of the plot
xgx_geom_ci | Plot data with mean and confidence intervals
xgx_geom_pi | Plot data with median and percent intervals
xgx_geom_smooth | Wrapper for stat_smooth
xgx_geom_smooth_emax | Wrapper for stat_smooth
xgx_labels_log10 | Nice labels for log10.
xgx_minor_breaks_log10 | Sets the default minor_breaks for log10 scales
xgx_plot | Create a new xgx plot
xgx_save | Saving plot, automatically annotating the status and denoting the filenames
xgx_save_table | Saving table as an image, also labeling the program that created the table and where the table is stored
xgx_scale_x_log10 | log10 scales the x axis with a "pretty" set of breaks
xgx_scale_x_percentchangelog10 | percentchangelog10 transform for the y scale.
xgx_scale_x_reverselog10 | Reverse-log transform for the x scale.
xgx_scale_x_time_units | Convert time units for plotting
xgx_scale_y_log10 | log10 scales the y axis with a "pretty" set of breaks
xgx_scale_y_percentchangelog10 | percentchangelog10 transform for the y scale.
xgx_scale_y_reverselog10 | Reverselog transform for the y scale.
xgx_scale_y_time_units | Convert time units for plotting
xgx_stat_ci | Plot data with mean and confidence intervals
xgx_stat_pi | Plot data with median and percent intervals
xgx_stat_smooth | Wrapper for stat_smooth
xgx_summarize_covariates | Summarize Covariate information in a dataset
xgx_summarize_data | Check data for various issues
xgx_theme | Calls the standard theme for xGx graphics
xgx_theme_set | Sets the standard theme for xGx graphics