Package: ruminate
Title: A Pharmacometrics Data Transformation and Analysis Tool
Version: 0.4.0
Authors@R: 
    person("John", "Harrold", , "john.m.harrold@gmail.com", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-2052-4373"))
Description: Exploration of pharmacometrics data involves both general
        tools (transformation and plotting) and specific techniques
        (non-compartmental analysis). This kind of exploration is
        generally accomplished by utilizing different packages. The
        purpose of 'ruminate' is to create a 'shiny' interface to make
        these tools more broadly available while creating reproducible
        results.  Currently there are modules for uploading one or more
        datasets, data wrangling, plot genreation, non-compartmental
        analysis, construction of ODE-based models, and constructing
        and running adaptive trial simualtions. Analyses can be saved
        and reloaded later. It's possible to create workflows to
        automate analyses.  There is integrated reporting in Word,
        Powerpoint and Excel. You can also generate scripts to
        replicate what was done in the app to create a stand-alone
        script to run in validated environments.
License: BSD_2_clause + file LICENSE
BugReports: https://github.com/john-harrold/ruminate/issues
URL: https://ruminate.ubiquity.tools/
Encoding: UTF-8
Depends: R (>= 4.2.0)
Imports: digest, dplyr, DT, flextable, formods (>= 0.2.0), ggplot2,
        onbrand (>= 1.0.8), PKNCA (>= 0.10.2), plotly (>= 4.11.0),
        rhandsontable, rlang, shiny, shinyAce, shinyWidgets, stats,
        stringr, tidyr, utils, zip
Suggests: babelmixr2(>= 0.1.8), cli, clipr, gridExtra, knitr,
        nlmixr2lib(>= 0.3.0), nonmem2rx, nlmixr2(>= 3.0.4), prompter,
        rmarkdown, readxl, rxode2 (>= 3.0.0), shinybusy,
        shinydashboard, shinytest2, testthat (>= 3.0.0), ubiquity
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev make libharfbuzz-dev libicu-dev
        libjpeg-dev libpng-dev libtiff-dev libuv1-dev libwebp-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://john-harrold.r-universe.dev
Date/Publication: 2026-02-11 04:55:23 UTC
RemoteUrl: https://github.com/john-harrold/ruminate
RemoteRef: HEAD
RemoteSha: 2b58cceec27d0ed72f243dc2f27bb45f1aa737b2
NeedsCompilation: no
Packaged: 2026-06-11 09:30:30 UTC; root
Author: John Harrold [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2052-4373>)
Maintainer: John Harrold <john.m.harrold@gmail.com>