Package: xgxr 1.1.5

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_1.1.5.tar.gz
xgxr_1.1.5.zip(r-4.7)xgxr_1.1.5.zip(r-4.6)xgxr_1.1.5.zip(r-4.5)
xgxr_1.1.5.tgz(r-4.6-any)xgxr_1.1.5.tgz(r-4.5-any)
xgxr_1.1.5.tar.gz(r-4.7-any)xgxr_1.1.5.tar.gz(r-4.6-any)
xgxr_1.1.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
xgxr/json (API)

# Install 'xgxr' in R:

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

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

Datasets:

case1_pkpd - Case 1 PKPD Data Set
mad - Multiple Ascending Dose Data Set
mad_missing_duplicates - Multiple Ascending Dose Data Set
mad_nca - Multiple Ascending Dose Noncompartmental Analysis (NCA) dataset
nlmixr_theo_sd - Nlmixr Theophylline SD Data Set
sad - Single Ascending Dose Data Set

On CRAN:

8.34 score 16 stars 6 packages 126 scripts 2.4k downloads 43 exports 105 dependencies

Last updated from:2f8f687214. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	191
source / vignettes	OK	273
linux-release-x86_64	OK	190
macos-release-arm64	OK	123
macos-oldrel-arm64	OK	119
windows-devel	OK	161
windows-release	OK	147
windows-oldrel	OK	148
wasm-release	OK	139

Exports:%>%edit_rmd_template_str get_rmd_name get_rmd_str gtable nlsLM StatSmoothOrdinal StatSummaryBinQuant StatSummaryOrdinal theme_xgx xgx_annotate_filenames xgx_annotate_status xgx_annotate_status_png xgx_auto_explore xgx_breaks_log10 xgx_breaks_time xgx_check_data xgx_conf_int xgx_dirs2char xgx_geom_ci xgx_geom_pi xgx_geom_smooth xgx_geom_smooth_emax xgx_labels_log10 xgx_minor_breaks_log10 xgx_plot xgx_save xgx_save_table xgx_scale_x_log10 xgx_scale_x_percentchangelog10 xgx_scale_x_reverselog10 xgx_scale_x_time_units xgx_scale_y_log10 xgx_scale_y_percentchangelog10 xgx_scale_y_reverselog10 xgx_scale_y_time_units xgx_stat_ci xgx_stat_pi xgx_stat_smooth xgx_summarize_covariates xgx_summarize_data xgx_theme xgx_theme_set

Dependencies:askpass assertthat backports base64enc binom bit bit64 bitops boot bslib cachem cellranger checkmate class cli clipr cluster colorspace cpp11 crayon curl data.table Deriv DescTools digest dplyr e1071 evaluate Exact expm farver fastmap fontawesome forcats foreign Formula fs generics ggplot2 gld glue gridExtra gtable haven highr Hmisc hms htmlTable htmltools htmlwidgets httr isoband jquerylib jsonlite knitr labeling lattice lifecycle lmom magrittr MASS Matrix memoise mime minpack.lm mvtnorm nnet openssl pander pillar pkgconfig png prettyunits progress proxy R6 rappdirs RColorBrewer Rcpp RCurl readr readxl rematch rlang rmarkdown rootSolve rpart rstudioapi S7 sass scales stringi stringr sys tibble tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr xfun yaml

xgxr Overview

Rendered fromxgxr_overview.Rmdusingknitr::rmarkdown

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

Help page	Topics
Case 1 PKPD Data Set	case1_pkpd
Edit a Rmd Template from xgx	edit_rmd_template_str
Determine the name of a Rmd template	get_rmd_name
'get_rmd_str' returns a Rmd template string, based on the desired PKPD parameters	get_rmd_str
Multiple Ascending Dose Data Set	mad
Multiple Ascending Dose Data Set (Duplicates Removed)	mad_missing_duplicates
Multiple Ascending Dose Noncompartmental Analysis (NCA) dataset	mad_nca
nlmixr Theophylline SD Data Set	nlmixr_theo_sd
predict.nls	predict.nls
Prediction data frame from ggplot2 Get predictions with standard errors into data frame	predictdf
Prediction data frame for nls	predictdf.nls
Prediction data frame for polr	predictdf.polr
Single Ascending Dose Data Set	sad
Stat object for producing smooths through ordinal data	StatSmoothOrdinal
Stat ggproto object for binning by quantile for xgx_stat_ci	StatSummaryBinQuant
Stat ggproto object for creating ggplot layers of binned confidence intervals for probabiliities of classes in ordinal data	StatSummaryOrdinal
Calls the standard theme for xGx graphics	theme_xgx
Append filenames to bottom of the plot	xgx_annotate_filenames
Create a status (e.g. DRAFT) annotation layer	xgx_annotate_status
Annotate a png file or directory of png files	xgx_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 log10	xgx_breaks_log10
Sets the default breaks for a time axis	xgx_breaks_time
Check data for various issues	xgx_check_data
'xgx_conf_int' returns a dataframe with mean +/- confidence intervals	xgx_conf_int
Append filenames to bottom of the plot	xgx_dirs2char
Plot data with mean and confidence intervals	xgx_geom_ci
Plot data with median and percent intervals	xgx_geom_pi
Nice labels for log10.	xgx_labels_log10
Sets the default minor_breaks for log10 scales	xgx_minor_breaks_log10
Create a new xgx plot	xgx_plot
Saving plot, automatically annotating the status and denoting the filenames	xgx_save
Saving table as an image, also labeling the program that created the table and where the table is stored	xgx_save_table
log10 scales the x axis with a "pretty" set of breaks	xgx_scale_x_log10
Reverse-log transform for the x scale.	xgx_scale_x_reverselog10
Convert time units for plotting	xgx_scale_x_time_units xgx_scale_y_time_units
log10 scales the y axis with a "pretty" set of breaks	xgx_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 intervals	xgx_stat_ci
Plot data with median and percent intervals	xgx_stat_pi
Wrapper for stat_smooth	xgx_geom_smooth xgx_geom_smooth_emax xgx_stat_smooth
Summarize Covariate information in a dataset	xgx_summarize_covariates
Check data for various issues	xgx_summarize_data
Calls the standard theme for xGx graphics	xgx_theme
Sets the standard theme for xGx graphics	xgx_theme_set

Package: xgxr 1.1.5

xgxr: Exploratory Graphics for Pharmacometrics

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