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pharmr

R wrapper to Pharmpy

https://github.com/pharmpy/pharmr

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
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    Academic publication links
  • ○
    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.4%) to scientific vocabulary

Keywords from Contributors

interpretability standardization animal hack autograder report
Last synced: 10 months ago · JSON representation

Repository

R wrapper to Pharmpy

Basic Info
  • Host: GitHub
  • Owner: pharmpy
  • License: lgpl-3.0
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 889 KB
Statistics
  • Stars: 22
  • Watchers: 3
  • Forks: 5
  • Open Issues: 68
  • Releases: 0
Created over 5 years ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

CRAN status check <!-- badges: end -->

pharmr is an R wrapper to Pharmpy: an open-source software package for pharmacometric modeling. It provides an R interface to all functions found in the modeling and tools modules (documented here). The documentation for each function is also available via the help-function (or ?).

For comprehensive information and documentation, see: https://pharmpy.github.io

Installation and setup

The current CRAN version (1.7.2) of pharmr does not work with the CRAN version of the altair package to be able to display plots generated by pharmr. If you are interested in plotting with pharmr you need to install the latest version from github with:

R remotes::install_github("vegawidget/altair")

This does not apply to the pharmr version on github.

Install from CRAN

The latest stable version of pharmr is available via CRAN, and can be installed via:

R install.packages("pharmr")

After installing pharmr, Pharmpy needs to be set up:

R pharmr::install_pharmpy()

For a more comprehensive description of the process of setting up, see the following guide.

Install from GitHub

It is also possible to install the development version of pharmr from GitHub, with the following command:

R remotes::install_github("pharmpy/pharmr", ref="main")

Pharmpy can then be installed:

R pharmr::install_pharmpy()

Using pharmr

```R

library(pharmr) model <- loadexamplemodel("pheno") model$parameters value lower upper fix POPCL 0.004693 0.00 ∞ False POPVC 1.009160 0.00 ∞ False COVAPGR 0.100000 -0.99 ∞ False IIVCL 0.030963 0.00 ∞ False IIVVC 0.031128 0.00 ∞ False SIGMA 0.013086 0.00 ∞ False res <- loadexamplemodelfitresults("pheno") res$parameterestimates POPCL POPVC COVAPGR IIVCL IIVVC SIGMA 0.00469555 0.98425800 0.15892000 0.02935080 0.02790600 0.01324100

```

A simple example of reading a model, performing a simple transformation, and running the model in NONMEM. Note that you need NONMEM installed to be able to fit the model, see the following guide on how to set up the config file.

```R model <- loadexamplemodel('pheno') %>% addperipheralcompartment()

res <- fit(model) ```

Owner

  • Name: pharmpy
  • Login: pharmpy
  • Kind: organization

GitHub Events

Total
  • Issues event: 18
  • Watch event: 3
  • Issue comment event: 9
  • Push event: 40
  • Create event: 10
Last Year
  • Issues event: 18
  • Watch event: 3
  • Issue comment event: 9
  • Push event: 40
  • Create event: 10

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 457
  • Total Committers: 5
  • Avg Commits per committer: 91.4
  • Development Distribution Score (DDS): 0.359
Past Year
  • Commits: 95
  • Committers: 3
  • Avg Commits per committer: 31.667
  • Development Distribution Score (DDS): 0.347
Top Committers
Name Email Commits
Stella s****n@f****e 293
github-actions[bot] 4****] 105
Rikard Nordgren r****n@f****e 56
Stella Belin 6****n 2
pharmpy-dev-123 1****3 1
Committer Domains (Top 20 + Academic)
farmaci.uu.se: 2

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 118
  • Total pull requests: 7
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 21 hours
  • Total issue authors: 18
  • Total pull request authors: 2
  • Average comments per issue: 1.47
  • Average comments per pull request: 0.14
  • Merged pull requests: 7
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 16
  • Pull requests: 0
  • Average time to close issues: 11 days
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • stellabelin (50)
  • rikardn (21)
  • joaoabr (14)
  • schaedeli (7)
  • artikandms (5)
  • SimonBuatois (4)
  • cossonvalerie (3)
  • SylvieRetout (3)
  • emiliesg (2)
  • hugo-maas (2)
  • Orwa-bit (2)
  • king-of-poppk (1)
  • liuxl17 (1)
  • klosinho00 (1)
  • yahanhsutw (1)
Pull Request Authors
  • stellabelin (6)
  • pharmpy-dev-123 (1)
Top Labels
Issue Labels
bug (19) dx (6) documentation (4) enhancement (3) waiting for information (2) question (1) dependencies (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 634 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: pharmr

Interface to the 'Pharmpy' 'Pharmacometrics' Library

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 634 Last month
Rankings
Stargazers count: 14.6%
Forks count: 14.9%
Dependent packages count: 29.8%
Average: 33.2%
Dependent repos count: 35.5%
Downloads: 71.5%
Maintainers (1)
rikard.nordgren@uu.se
Last synced: 11 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
.github/workflows/build_docs.yaml actions
  • actions/cache v2 composite
  • actions/checkout v3 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
DESCRIPTION cran
  • R >= 3.6.0 depends
  • altair >= 4.0.0 depends
  • reticulate >= 1.19 imports
  • utils * imports
  • here * suggests
  • knitr * suggests
  • magrittr * suggests
  • testthat * suggests