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RxODE

RxODE is an R package that facilitates easy simulations in R

https://github.com/nlmixrdevelopment/rxode

Science Score: 10.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 17 committers (5.9%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.5%) to scientific vocabulary

Keywords from Contributors

data-manipulation grammar c-plus-plus-11 c-plus-plus-14 c-plus-plus-17 c-plus-plus-20 r-packages rcpp
Last synced: 11 months ago · JSON representation

Repository

RxODE is an R package that facilitates easy simulations in R

Basic Info
Statistics
  • Stars: 54
  • Watchers: 5
  • Forks: 14
  • Open Issues: 25
  • Releases: 0
Created over 9 years ago · Last pushed over 4 years ago
Metadata Files
Readme License

README.Rmd 





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

# RxODE


[![R build status](https://github.com/nlmixrdevelopment/RxODE/workflows/R-CMD-check/badge.svg)](https://github.com/nlmixrdevelopment/RxODE/actions)
[![codecov.io](https://codecov.io/github/nlmixrdevelopment/RxODE/coverage.svg)](https://codecov.io/github/nlmixrdevelopment/RxODE?branch=master)
[![CRAN version](http://www.r-pkg.org/badges/version/RxODE)](https://cran.r-project.org/package=RxODE)
[![CRAN checks](https://cranchecks.info/badges/worst/RxODE)](https://cran.r-project.org/web/checks/check_results_RxODE.html)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/RxODE)](https://cran.r-project.org/package=RxODE)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/RxODE)](https://cran.r-project.org/package=RxODE)
[![CodeFactor](https://www.codefactor.io/repository/github/nlmixrdevelopment/rxode/badge)](https://www.codefactor.io/repository/github/nlmixrdevelopment/rxode)


## Overview

**RxODE** is an R package for solving and simulating from ode-based
models. These models are convert the RxODE mini-language to C and
create a compiled dll for fast solving. ODE solving using RxODE has a
few key parts:

 - `RxODE()` which creates the C code for fast ODE solving based on a
   [simple syntax](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-syntax.html) related to Leibnitz notation.
 - The event data, which can be:
   - a `NONMEM` or `deSolve` [compatible data frame](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-event-types.html), or
   - created with `et()` or `EventTable()` for [easy simulation of events](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-event-table.html)
   - The data frame can be augmented by adding
     [time-varying](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-covariates.html#time-varying-covariates)
     or adding [individual covariates](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-covariates.html#individual-covariates) (`iCov=` as needed)
 - `rxSolve()` which solves the system of equations using initial
   conditions and parameters to make predictions
   - With multiple subject data, [this may be
     parallelized](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-speed.html).
   - With single subject the [output data frame is adaptive](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-data-frame.html)
   - Covariances and other metrics of uncertanty can be used to
     [simulate while solving](https://nlmixrdevelopment.github.io/RxODE/articles/RxODE-sim-var.html)

## Installation

```{r child='man-roxygen/rmdhunks/RxODE-install-hunk.Rmd'}
```

# Illustrated Example

```{r child='man/rmdhunks/RxODE-intro-chunk.Rmd'}
```

# Related R Packages
```{r child='man-roxygen/rmdhunks/related-R-chunk.Rmd'}
```

Owner

  • Name: nlmixr
  • Login: nlmixrdevelopment
  • Kind: organization

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 4,664
  • Total Committers: 17
  • Avg Commits per committer: 274.353
  • Development Distribution Score (DDS): 0.402
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Matthew Fidler 5****r 2,788
Fidler m****r@g****m 1,771
wwang-at-github w****8@g****m 63
Fidler F****3@n****t 7
daj d****5@g****m 7
hallowkm h****m@u****u 6
wwang-at-github w****g@o****m 5
Bill Denney w****y@h****m 5
hallowkm m****w@g****m 2
kestrel99 j****l@g****m 2
daj j****4@P****t 2
Tim Waterhouse t****e@g****m 1
Justin Wilkins j****s@o****m 1
Kirill Müller k****r@m****g 1
wwang-at-github w****z@l****n 1
Dirk Eddelbuettel e****d@d****g 1
Matthew Fidler m****r@M****l 1
Committer Domains (Top 20 + Academic)
debian.org: 1 localhost.localdomain: 1 mailbox.org: 1 occams.com: 1 phuseh-l04634.na.novartis.net: 1 humanpredictions.com: 1 uga.edu: 1 novartis.net: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 76
  • Total pull requests: 24
  • Average time to close issues: 20 days
  • Average time to close pull requests: 2 days
  • Total issue authors: 25
  • Total pull request authors: 4
  • Average comments per issue: 2.63
  • Average comments per pull request: 0.67
  • Merged pull requests: 19
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 0
  • Average time to close issues: 6 days
  • Average time to close pull requests: N/A
  • Issue authors: 6
  • Pull request authors: 0
  • Average comments per issue: 2.13
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • mattfidler (37)
  • billdenney (6)
  • snailittle (4)
  • lirui0321 (3)
  • sckott (2)
  • krinaj (2)
  • levenc (2)
  • namtien0312 (2)
  • nitkaila (2)
  • mbatgh (1)
  • sliao999 (1)
  • frbrz (1)
  • wchg1980 (1)
  • Slow-Walker66 (1)
  • ftuhin2828 (1)
Pull Request Authors
  • mattfidler (21)
  • andrjohns (1)
  • eddelbuettel (1)
  • krlmlr (1)
Top Labels
Issue Labels
enhancement (9) wontfix (2)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total docker downloads: 43,438
  • Total dependent packages: 5
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 49
cran.r-project.org: RxODE

Facilities for Simulating from ODE-Based Models

  • Versions: 35
  • Dependent Packages: 4
  • Dependent Repositories: 4
  • Docker Downloads: 43,438
Rankings
Forks count: 5.6%
Stargazers count: 6.4%
Average: 9.3%
Dependent packages count: 9.6%
Dependent repos count: 15.5%
Last synced: about 1 year ago
conda-forge.org: r-rxode
  • Versions: 14
  • Dependent Packages: 1
  • Dependent Repositories: 0
Rankings
Dependent packages count: 28.8%
Dependent repos count: 34.0%
Average: 34.2%
Stargazers count: 35.6%
Forks count: 38.1%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • PreciseSums >= 0.3 imports
  • Rcpp >= 0.12.3 imports
  • assertthat * imports
  • backports * imports
  • checkmate * imports
  • cli >= 2.0.0 imports
  • dparser >= 0.1.8 imports
  • ggplot2 * imports
  • inline * imports
  • lotri >= 0.3.0 imports
  • magrittr * imports
  • memoise * imports
  • methods * imports
  • qs * imports
  • rex * imports
  • sys * imports
  • tools * imports
  • utils * imports
  • DT * suggests
  • Matrix * suggests
  • covr * suggests
  • crayon * suggests
  • curl * suggests
  • data.table >= 1.12.4 suggests
  • devtools * suggests
  • digest * suggests
  • dplyr >= 0.8.0 suggests
  • ggrepel * suggests
  • gridExtra * suggests
  • htmltools * suggests
  • knitr * suggests
  • learnr * suggests
  • microbenchmark * suggests
  • nlme * suggests
  • patchwork * suggests
  • pillar * suggests
  • remotes * suggests
  • rlang * suggests
  • rmarkdown * suggests
  • rsconnect * suggests
  • scales * suggests
  • shiny * suggests
  • spelling * suggests
  • stringi * suggests
  • symengine * suggests
  • testthat * suggests
  • tibble * suggests
  • tidyr * suggests
  • units >= 0.6 suggests
  • usethis * suggests
  • vdiffr * suggests
  • xgxr * suggests