Package: xgxr 1.1.4

Andrew Stein

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.

Authors:Andrew Stein [aut, cre], Alison Margolskee [aut], Fariba Khanshan [aut], Konstantin Krismer [aut], Matthew Fidler [ctb], Novartis Pharma AG [cph, fnd]

xgxr_1.1.4.tar.gz
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xgxr.pdf |xgxr.html✨
xgxr/json (API)
NEWS

# Install 'xgxr' in R:
install.packages('xgxr', repos = c('https://novartis.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/novartis/xgxr/issues

Datasets:

On CRAN:

7.66 score 13 stars 4 packages 104 scripts 1.4k downloads 43 exports 107 dependencies

Last updated 1 years agofrom:c537fbf86d. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-winOKNov 05 2024
R-4.5-linuxOKNov 05 2024
R-4.4-winOKNov 05 2024
R-4.4-macOKNov 05 2024
R-4.3-winOKNov 05 2024
R-4.3-macOKNov 05 2024

Exports:%>%edit_rmd_template_strget_rmd_nameget_rmd_strgtablenlsLMStatSmoothOrdinalStatSummaryBinQuantStatSummaryOrdinaltheme_xgxxgx_annotate_filenamesxgx_annotate_statusxgx_annotate_status_pngxgx_auto_explorexgx_breaks_log10xgx_breaks_timexgx_check_dataxgx_conf_intxgx_dirs2charxgx_geom_cixgx_geom_pixgx_geom_smoothxgx_geom_smooth_emaxxgx_labels_log10xgx_minor_breaks_log10xgx_plotxgx_savexgx_save_tablexgx_scale_x_log10xgx_scale_x_percentchangelog10xgx_scale_x_reverselog10xgx_scale_x_time_unitsxgx_scale_y_log10xgx_scale_y_percentchangelog10xgx_scale_y_reverselog10xgx_scale_y_time_unitsxgx_stat_cixgx_stat_pixgx_stat_smoothxgx_summarize_covariatesxgx_summarize_dataxgx_themexgx_theme_set

Dependencies:askpassassertthatbackportsbase64encbinombitbit64bitopsbootbslibcachemcellrangercheckmateclassclicliprclustercolorspacecpp11crayoncurldata.tableDerivDescToolsdigestdplyre1071evaluateExactexpmfansifarverfastmapfontawesomeforeignFormulafsgenericsggplot2gldgluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobandjquerylibjsonliteknitrlabelinglatticelifecyclelmommagrittrMASSMatrixmemoisemgcvmimeminpack.lmmunsellmvtnormnlmennetopensslpanderpillarpkgconfigpngprettyunitsprogressproxyR6rappdirsRColorBrewerRcppRCurlreadrreadxlrematchrlangrmarkdownrootSolverpartrstudioapisassscalesstringistringrsystibbletidyselecttinytextzdbutf8vctrsviridisviridisLitevroomwithrxfunyaml

xgxr Overview

Andrew Stein, Fariba Khanshan, Alison Margolskee

Rendered fromxgxr_overview.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2023-08-18
Started: 2019-08-01

Readme and manuals

Help Manual

Help pageTopics
Case 1 PKPD Data Setcase1_pkpd
Edit a Rmd Template from xgxedit_rmd_template_str
Determine the name of a Rmd templateget_rmd_name
'get_rmd_str' returns a Rmd template string, based on the desired PKPD parametersget_rmd_str
Multiple Ascending Dose Data Setmad
Multiple Ascending Dose Data Set (Duplicates Removed)mad_missing_duplicates
Multiple Ascending Dose Noncompartmental Analysis (NCA) datasetmad_nca
nlmixr Theophylline SD Data Setnlmixr_theo_sd
predict.nlspredict.nls
Prediction data frame from ggplot2 Get predictions with standard errors into data framepredictdf
Prediction data frame for nlspredictdf.nls
Prediction data frame for polrpredictdf.polr
Single Ascending Dose Data Setsad
Stat object for producing smooths through ordinal dataStatSmoothOrdinal
Stat ggproto object for binning by quantile for xgx_stat_ciStatSummaryBinQuant
Stat ggproto object for creating ggplot layers of binned confidence intervals for probabiliities of classes in ordinal dataStatSummaryOrdinal
Calls the standard theme for xGx graphicstheme_xgx
Append filenames to bottom of the plotxgx_annotate_filenames
Create a status (e.g. DRAFT) annotation layerxgx_annotate_status
Annotate a png file or directory of png filesxgx_annotate_status_png
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_auto_explore
Sets the default breaks for log10xgx_breaks_log10
Sets the default breaks for a time axisxgx_breaks_time
Check data for various issuesxgx_check_data
'xgx_conf_int' returns a dataframe with mean +/- confidence intervalsxgx_conf_int
Append filenames to bottom of the plotxgx_dirs2char
Plot data with mean and confidence intervalsxgx_geom_ci
Plot data with median and percent intervalsxgx_geom_pi
Nice labels for log10.xgx_labels_log10
Sets the default minor_breaks for log10 scalesxgx_minor_breaks_log10
Create a new xgx plotxgx_plot
Saving plot, automatically annotating the status and denoting the filenamesxgx_save
Saving table as an image, also labeling the program that created the table and where the table is storedxgx_save_table
log10 scales the x axis with a "pretty" set of breaksxgx_scale_x_log10
Reverse-log transform for the x scale.xgx_scale_x_reverselog10
Convert time units for plottingxgx_scale_x_time_units xgx_scale_y_time_units
log10 scales the y axis with a "pretty" set of breaksxgx_scale_y_log10
percentchangelog10 transform for the y scale.xgx_scale_x_percentchangelog10 xgx_scale_y_percentchangelog10
Reverselog transform for the y scale.xgx_scale_y_reverselog10
Plot data with mean and confidence intervalsxgx_stat_ci
Plot data with median and percent intervalsxgx_stat_pi
Wrapper for stat_smoothxgx_geom_smooth xgx_geom_smooth_emax xgx_stat_smooth
Summarize Covariate information in a datasetxgx_summarize_covariates
Check data for various issuesxgx_summarize_data
Calls the standard theme for xGx graphicsxgx_theme
Sets the standard theme for xGx graphicsxgx_theme_set