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xgxr

Exploratory Graphics for Pharmacometrics

Supports a structured approach for exploring PKPD data <https://opensource.nibr.com/xgx/>. It also 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). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.

Functions (48)

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

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

pipe

Pipe operator

predict.nls

predict.nls

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

reexports

Objects exported from other packages

sad

Single Ascending Dose Data Set

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_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_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_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

xgxr

Exploratory Graphics for Pharmacometrics

v1.1.1

MIT + file LICENSE

Authors

Andrew Stein [aut, cre], Alison Margolskee [aut], Fariba Khanshan [aut], Konstantin Krismer [aut] (<https://orcid.org/0000-0001-8994-3416>), Matthew Fidler [ctb] (<https://orcid.org/0000-0001-8538-6691>), Novartis Pharma AG [cph, fnd]

Initial release

xgxr

Functions (48)

xgxr

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