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pkpdsim

Simulate PK-PD models defined as ODE systems

https://github.com/insightrx/pkpdsim

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.2%) to scientific vocabulary

Keywords

ode pharmacodynamics pharmacokinetics pharmacometrics r

Keywords from Contributors

clinical-research
Last synced: 6 months ago · JSON representation

Repository

Simulate PK-PD models defined as ODE systems

Basic Info
Statistics
  • Stars: 42
  • Watchers: 11
  • Forks: 15
  • Open Issues: 0
  • Releases: 1
Topics
ode pharmacodynamics pharmacokinetics pharmacometrics r
Created over 8 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog License

README.md

PKPDsim

R-CMD-check CRAN status R-universe status <!-- badges: end -->

PKPDsim is a library for numerical integration of ODE systems, in particular pharmacokinetic-pharmacodynamic (PK-PD) mixed-effects models.

Installation

The development version of PKPDsim always has the most up-to-date improvements and bug fixes. We aim to release PKPDsim on CRAN at least once a year, depending on the number and impact of updates made to the development version.

The CRAN version of PKPDsim can be installed using:

r install.packages("PKPDsim")

The development version of PKPDsim can be installed from GitHub or R-universe using:

```r

Install from GitHub:

devtools::install_github("InsightRX/PKPDsim")

Install from R-universe:

install.packages("PKPDsim", repos = "https://insightrx.r-universe.dev") ```

A number of models from the literature have been made available for use in PKPD simulations. To see which models are available for installation, run:

r available_default_literature_models()

You can install these models as packages using the following commands:

```r

To install a single model:

installdefaultliteraturemodel("pkbusulfan_mccune")

To install all supplied models:

installdefaultliterature_model("all") ```

Contributing

We welcome input from the community:

  • If you think you have encountered a bug, please submit an issue on the GitHub page. Please include a reproducible example of the unexpected behavior.

  • Please open a pull request if you have a fix or updates that would improve the package. If you're not sure if your proposed changes are useful or within scope of the package, feel free to contact one of the authors of this package.

Disclaimer

The functionality in this R package is provided "as is". While its authors adhere to software development best practices, the software may still contain unintended errors.

InsightRX Inc. and the authors of this package can not be held liable for any damages resulting from any use of this software. By the use of this software package, the user waives all warranties, expressed or implied, including any warranties to the accuracy, quality or suitability of InsightRX for any particular purpose, either medical or non-medical.

© InsightRX logo

Owner

  • Name: InsightRX
  • Login: InsightRX
  • Kind: organization
  • Email: info@insight-rx.com
  • Location: San Francisco, CA

Precision dosing and clinical analytics

GitHub Events

Total
  • Create event: 24
  • Release event: 1
  • Issues event: 15
  • Watch event: 9
  • Delete event: 8
  • Issue comment event: 10
  • Push event: 48
  • Pull request review comment event: 23
  • Pull request event: 26
  • Pull request review event: 34
Last Year
  • Create event: 24
  • Release event: 1
  • Issues event: 15
  • Watch event: 9
  • Delete event: 8
  • Issue comment event: 10
  • Push event: 48
  • Pull request review comment event: 23
  • Pull request event: 26
  • Pull request review event: 34

Committers

Last synced: 9 months ago

All Time
  • Total Commits: 1,003
  • Total Committers: 13
  • Avg Commits per committer: 77.154
  • Development Distribution Score (DDS): 0.599
Past Year
  • Commits: 54
  • Committers: 5
  • Avg Commits per committer: 10.8
  • Development Distribution Score (DDS): 0.481
Top Committers
Name Email Commits
ronkeizer r****r@g****m 402
Ron Keizer r****n@i****m 320
Kara Woo k****a@i****m 129
jasmineirx j****e@i****m 96
Vikram Matange v****m@i****m 32
Jordan Brooks j****s@i****m 10
Devin Pastoor d****r@g****m 4
William Fox w****3@g****m 3
Sermet Pekin s****n@g****m 2
Michael McCarthy 5****g 2
Sungpil Han CPT s****n@a****r 1
Benjamin Rich m****l@b****t 1
Dominic Tong d****c@i****m@i****l 1
Committer Domains (Top 20 + Academic)
insight-rx.com: 6 benjaminrich.net: 1 acp.kr: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 16
  • Total pull requests: 138
  • Average time to close issues: over 4 years
  • Average time to close pull requests: 13 days
  • Total issue authors: 13
  • Total pull request authors: 9
  • Average comments per issue: 0.94
  • Average comments per pull request: 0.49
  • Merged pull requests: 115
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 27
  • Average time to close issues: N/A
  • Average time to close pull requests: 11 days
  • Issue authors: 0
  • Pull request authors: 4
  • Average comments per issue: 0
  • Average comments per pull request: 0.19
  • Merged pull requests: 18
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • thomasjsln (2)
  • melmelie (2)
  • ronkeizer (2)
  • roninsightrx (1)
  • lostinpkpd (1)
  • kkradtke (1)
  • philipdelff (1)
  • KyleBarrett (1)
  • kenujen (1)
  • e-molitor (1)
  • jeslo328 (1)
  • cohendnli (1)
  • zcutts (1)
Pull Request Authors
  • roninsightrx (67)
  • karawoo (29)
  • jasmineirx (28)
  • JordanBrooks33 (4)
  • mccarthy-m-g (4)
  • WillFox (2)
  • SermetPekin (2)
  • shanmdphd (1)
  • lemonardo1 (1)
Top Labels
Issue Labels
Pull Request Labels
documentation (2) bug (1)

Packages

  • Total packages: 1
  • Total downloads:
    • cran 719 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 5
  • Total maintainers: 1
cran.r-project.org: PKPDsim

Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 719 Last month
Rankings
Forks count: 6.8%
Stargazers count: 10.2%
Average: 17.7%
Downloads: 18.8%
Dependent repos count: 24.0%
Dependent packages count: 28.8%
Maintainers (1)
ron@insight-rx.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.2 depends
  • BH * imports
  • MASS * imports
  • Rcpp >= 0.12.9 imports
  • data.table * imports
  • jsonlite * imports
  • magrittr * imports
  • parallel * imports
  • randtoolbox * imports
  • stats * imports
  • stringr * imports
  • httr * suggests
  • knitr * suggests
  • mockery * suggests
  • rmarkdown * suggests
  • testthat >= 3.0.0 suggests
inst/template/DESCRIPTION cran
  • BH * imports
  • Rcpp >= 0.11.5 imports
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action 4.1.4 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
Dockerfile docker
  • 579831337053.dkr.ecr.us-west-2.amazonaws.com/irx-r-base latest build