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PopED

Population Experimental Design (PopED) in R

https://github.com/andrewhooker/poped

Science Score: 13.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (16.0%) to scientific vocabulary

Keywords

cran nlme optimal-design pharmacodynamics pharmacokinetics pharmacometrics pkpd population population-model r
Last synced: 6 months ago · JSON representation

Repository

Population Experimental Design (PopED) in R

Basic Info
Statistics
  • Stars: 34
  • Watchers: 14
  • Forks: 21
  • Open Issues: 29
  • Releases: 10
Topics
cran nlme optimal-design pharmacodynamics pharmacokinetics pharmacometrics pkpd population population-model r
Created about 12 years ago · Last pushed over 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# PopED 

[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/PopED)](https://CRAN.R-project.org/package=PopED)
[![R-CMD-check](https://github.com/andrewhooker/PopED/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/andrewhooker/PopED/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/andrewhooker/PopED/graph/badge.svg)](https://app.codecov.io/gh/andrewhooker/PopED)


PopED computes optimal experimental designs for both population 
and individual studies based on nonlinear mixed-effect models. 
Often this is based on a computation of the Fisher Information Matrix (FIM). 

## Installation

You need to have R installed.  Download the latest version of R from www.r-project.org.
You can install the released version of PopED from [CRAN](https://CRAN.R-project.org) with:

``` r
install.packages("PopED")
```

And the development version from [GitHub](https://github.com/) with:

``` r
# install.packages("devtools")
devtools::install_github("andrewhooker/PopED")
```
## Getting started

To get started you need to define 

1. A model.
2. An initial design (and design space if you want to optimize). 
3. The tasks to perform. 

Learn more in this [introduction to PopED](https://andrewhooker.github.io/PopED/articles/intro-poped.html)

## Contact

You are welcome to:

* Ask questions at: https://github.com/andrewhooker/PopED/discussions
* submit suggestions and bug-reports at: https://github.com/andrewhooker/PopED/issues 
* send a pull request on: https://github.com/andrewhooker/PopED
* compose a friendly e-mail to: andrew.hooker@farmaci.uu.se

Owner

  • Name: Andrew Hooker
  • Login: andrewhooker
  • Kind: user
  • Location: Uppsala, Sweden
  • Company: Uppsala University

GitHub Events

Total
  • Watch event: 3
  • Issue comment event: 6
  • Pull request event: 1
Last Year
  • Watch event: 3
  • Issue comment event: 6
  • Pull request event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 824
  • Total Committers: 6
  • Avg Commits per committer: 137.333
  • Development Distribution Score (DDS): 0.1
Past Year
  • Commits: 5
  • Committers: 1
  • Avg Commits per committer: 5.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Andrew Hooker a****r@g****m 742
martin-gmx m****k@g****t 59
giulialestini g****i@g****m 19
Vincent Aranzana-Climent v****t@f****e 2
Vincent-AC v****t@a****g 1
Matthew Fidler 5****r 1
Committer Domains (Top 20 + Academic)
aracli.org: 1 farmbio.uu.se: 1 gmx.at: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 51
  • Total pull requests: 22
  • Average time to close issues: 3 months
  • Average time to close pull requests: about 1 month
  • Total issue authors: 32
  • Total pull request authors: 4
  • Average comments per issue: 2.49
  • Average comments per pull request: 1.41
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 5
  • Pull requests: 1
  • Average time to close issues: 14 days
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 3.4
  • Average comments per pull request: 5.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • Sibojang9 (6)
  • mattfidler (5)
  • Anks2030 (5)
  • Vincent-AC (3)
  • Mark-Tepeck (2)
  • andrewhooker (2)
  • krimobe (2)
  • vjd (2)
  • michielve (1)
  • amitvtaneja (1)
  • FelicienLL (1)
  • krinaj (1)
  • Mike-Hood (1)
  • the-magister (1)
  • UNCcrawler (1)
Pull Request Authors
  • martin-gmx (14)
  • Vincent-AC (3)
  • mattfidler (3)
  • andrewhooker (3)
Top Labels
Issue Labels
enhancement (1) bug (1) question (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 484 last-month
  • Total docker downloads: 43,438
  • Total dependent packages: 1
  • Total dependent repositories: 2
  • Total versions: 11
  • Total maintainers: 1
cran.r-project.org: PopED

Population (and Individual) Optimal Experimental Design

  • Versions: 11
  • Dependent Packages: 1
  • Dependent Repositories: 2
  • Downloads: 484 Last month
  • Docker Downloads: 43,438
Rankings
Docker downloads count: 0.6%
Forks count: 3.5%
Stargazers count: 8.8%
Average: 12.9%
Dependent packages count: 18.2%
Dependent repos count: 19.2%
Downloads: 27.1%
Maintainers (1)
andrew.hooker@farmaci.uu.se
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.14 depends
  • MASS * imports
  • boot * imports
  • codetools * imports
  • dplyr >= 0.7.0 imports
  • ggplot2 * imports
  • gtools * imports
  • magrittr * imports
  • mvtnorm * imports
  • purrr * imports
  • stats * imports
  • stringr * imports
  • tibble * imports
  • utils * imports
  • GA * suggests
  • Hmisc * suggests
  • Rcpp * suggests
  • covr * suggests
  • deSolve * suggests
  • devtools * suggests
  • gridExtra * suggests
  • knitr * suggests
  • mrgsolve * suggests
  • nlme * suggests
  • rhandsontable * suggests
  • rmarkdown * suggests
  • shiny * suggests
  • testthat * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact main composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite