{"Package":"ruminate","Title":"A Pharmacometrics Data Transformation and Analysis Tool","Version":"0.3.1","Authors@R":"person(\"John\", \"Harrold\", , \"john.m.harrold@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = 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.","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,\nonbrand (>= 1.0.3), PKNCA (>= 0.10.2), plotly, rhandsontable,\nrlang, shiny, shinyAce, shinyWidgets, stats, stringr, tidyr,\nutils, yaml, zip","Suggests":"babelmixr2, cli, clipr, gridExtra, knitr, nlmixr2lib(>=\n0.3.0), nonmem2rx, nlmixr2(>= 3.0.0), prompter, rmarkdown,\nreadxl, rxode2 (>= 3.0.0), shinybusy, shinydashboard, testthat\n(>= 3.0.0), ubiquity","RoxygenNote":"7.3.2","Config/testthat/edition":"3","VignetteBuilder":"knitr","NeedsCompilation":"no","Packaged":"2025-01-10 14:59:10 UTC; jmh","Author":"John Harrold [aut, cre] ()","Maintainer":"John Harrold ","Repository":"CRAN","Date/Publication":"2025-01-10 15:50:06 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/ruminate_0.3.1.tar.gz","jsonAuthors":[{"name":"John Harrold","email":"john.m.harrold@gmail.com","maintainer":true}],"readme":"\n\n\n# ruminate

\n\n\n\n\n\n[![Codecov test\ncoverage](https://codecov.io/gh/john-harrold/ruminate/branch/master/graph/badge.svg)](https://app.codecov.io/gh/john-harrold/ruminate?branch=master)\n![cranlogs](https://cranlogs.r-pkg.org/badges/ruminate)\n![Active](https://www.repostatus.org/badges/latest/active.svg)\n[![Lifecycle:\nExperimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html)\n[![R-CMD-check](https://github.com/john-harrold/ruminate/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/john-harrold/ruminate/actions/workflows/R-CMD-check.yaml)\n\n\n\nThe goal of `{ruminate}` is to facilitate exploration of pharmacometrics\ndata. This is done by creating a Shiny interface to different tools for\ndata transformation (`{dplyr}` and `{tidyr}`), plotting (`{ggplot2}`),\nnoncompartmental analysis (`{PKNCA}`), and ODE-based adaptive trial\nsimulations (`{rxode2}`). These results can be reported in Excel, Word\nor PowerPoint. The state of the app can be saved and loaded at a later\ndate. When saved, a script is generated to reproduce the different\nactions in the Shiny interface.\n\n# Deployed example in the cloud\n\nYou can point your web browser to\n[runrumiate.ubiquity.tools](https://runruminate.ubiquity.tools) and try\nthe development version of ruminate. Keep in mind this is a public\nserver. No data is tracked or kept, but it is open to the public. So be\ncareful about uploading confidential data. Also know this is a single\ninstance and if many people are using it at once it can be slow.\n\n# Local installation\n\n## From CRAN\n\nYou can install the released version of `ruminate` from\n[CRAN](https://cran.r-project.org/package=ruminate) with:\n\n``` r\n# Actual package\ninstall.packages(\"ruminate\", dependencies=TRUE)\n```\n\n## Development version\n\nYou can install the development version from\n[GitHub](https://github.com/john-harrold/ruminate/) with the following:\n\n``` r\n# Installing devtools if it's not already installed\nif(system.file(package=\"devtools\") == \"\"){\n install.packages(\"devtools\") \n}\n\ndevtools::install_github(\"john-harrold/onbrand\", dependencies=TRUE)\ndevtools::install_github(\"john-harrold/formods\", dependencies=TRUE)\ndevtools::install_github(\"john-harrold/ruminate\", dependencies=TRUE)\n```\n\nNote that because `{ruminate}` depends on `{formods}` and `{onbrand}`\nyou will need to first install the development versions of `{onbrand}`\nand `{formods}`.\n\n# Running ruminate\n\n## In RStudio\n\nThis will run the default/stable version of ruminate:\n\n``` r\nlibrary(ruminate)\nruminate()\n```\n\nAs new modules are developed they can be found in the development app.\nThis command will run the ruminate with any development modules enabled:\n\n``` r\nlibrary(ruminate)\nlibrary(shiny)\nrunApp(system.file(package=\"ruminate\",\"templates\", \"ruminate_devel.R\"))\n```\n\n**If you are running this you should probably be using the development\nversion off of github to make sure you have the latest version.**\n\n## In a Docker container\n\nThis kind of assumes a basic familiarity with Docker. Keep in mind that\nthese containers are built for ‘x86’ images. Essentially Intel/AMD cpus.\nThis means that if you have a Mac with Apple Silicon (M1, M2,etc.) it\nmay not work or the performance may not be that good.\n\n### Pull a container from Docker\n\nThis will pull container from docker and run it locally\n\n docker pull johnmharrold/ruminate:latest\n docker run -p 3838:3838 johnmharrold/ruminate:latest &\n\nIf that worked you can put the following into a web browser and then use\nruminate there:\n\n http://127.0.0.1:3838/\n\n### Create your own container\n\nIf you want to create your own container you can do the following:\n\n``` bash\ndocker build -t ruminate --no-cache https://raw.githubusercontent.com/john-harrold/ruminate/main/inst/docker/local_container\n```\n\nThis will run the Docker image locally:\n\n``` bash\ndocker run --name ruminate --rm -p 3838:3838 ruminate\n```\n\nIf everything worked you can then point your web browser to:\n\n http://127.0.0.1:3838/\n\nThis will push the image to DockerHub:\n\n``` bash\ndocker tag ruminate /ruminate:latest\ndocker push /ruminate:latest\n```\n\nYou can use this to pull the image from DockerHub:\n\n``` bash\ndocker pull /ruminate:latest\n```\n\n## Deployment and Customization\n\nIf you want to deploy and customize ruminate, please see the [Deployment\nvignette](https://ruminate.ubiquity.tools/articles/deployment.html).","jobInfo":{"package":"ruminate","version":"0.3.1","parsingStatus":"success","parserVersion":2,"parsedAt":"2025-01-10T17:29:53+0000"}}

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