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mrgsolve

Simulate from ODE-based population PK/PD and QSP models in R

https://github.com/metrumresearchgroup/mrgsolve

Science Score: 26.0%

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

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    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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  • ○
    Scientific vocabulary similarity
    Low similarity (18.1%) to scientific vocabulary

Keywords

mrgsolve ode r rstats

Keywords from Contributors

data-manipulation
Last synced: 6 months ago · JSON representation

Repository

Simulate from ODE-based population PK/PD and QSP models in R

Basic Info
  • Host: GitHub
  • Owner: metrumresearchgroup
  • License: gpl-2.0
  • Language: R
  • Default Branch: main
  • Homepage: https://mrgsolve.org
  • Size: 36.2 MB
Statistics
  • Stars: 141
  • Watchers: 24
  • Forks: 35
  • Open Issues: 82
  • Releases: 54
Topics
mrgsolve ode r rstats
Created about 10 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
pagetitle: "mrgsolve"
date: ""
author: ""
output: github_document
---


```{r,echo=FALSE}
library(lattice)
library(knitr)
```

```{r, include = FALSE}
knitr::opts_chunk$set(
  comment = ".",
  fig.path = "man/figures/README-"
)
options(tibble.print_min = 5, tibble.print_max = 5)
```



# mrgsolve 

[![Build Status](https://github.com/metrumresearchgroup/mrgsolve/actions/workflows/main.yaml/badge.svg)](https://github.com/metrumresearchgroup/mrgsolve/actions/workflows/main.yaml)
[![CRAN](http://www.r-pkg.org/badges/version/mrgsolve)](https://cran.r-project.org/package=mrgsolve)
[![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html)
[![questions](https://img.shields.io/badge/ask_for-Help-brightgreen.svg)](https://github.com/metrumresearchgroup/mrgsolve/issues)
[![MetrumRG](https://img.shields.io/badge/contact-MetrumRG-brightgreen.svg)](http://metrumrg.com)



mrgsolve is an R package for simulation from hierarchical, ordinary differential
equation (ODE) based models typically employed in drug development.  mrgsolve
is free and open-source software.  


## Resources
Please see [mrgsolve.github.io](https://mrgsolve.github.io) for additional
resources, including:

- [User Guide](https://mrgsolve.github.io/user_guide)
- [R Documentation](https://mrgsolve.github.io/docs)
- [Vignettes](https://mrgsolve.github.io/vignettes) 
- [Gallery](https://github.com/mrgsolve/gallery) 


## Installation

Install the latest release on CRAN
```{r,eval=FALSE}
install.packages("mrgsolve")
```

__Please__ be sure to see important install-related information 
[here](https://github.com/metrumresearchgroup/mrgsolve/wiki/mrgsolve-Installation).


Install the current development version

```{r,eval=FALSE}
remotes::install_github("metrumresearchgroup/mrgsolve")
```

## Interaction

We welcome __questions__ about anything mrgsolve: installation, getting your 
model to work, understanding better how mrgsolve works. We also welcome __suggestions__ 
for how to make mrgsolve more useful to you and to the pharmacometrics community. 

Please interact with us at the [Issue Tracker](https://github.com/metrumresearchgroup/mrgsolve/issues). 
This requires a GitHub account. 


## Some examples

### A simple simulation
```{r,echo=FALSE}
options(mrgsolve_mread_quiet = TRUE)
```


```{r,message=FALSE}
library(mrgsolve)
```

Load a model from the internal library
```{r}
mod <- mread("pk1", modlib())
```

Simulate a simple regimen
```{r,pk-figure}
mod %>% 
  ev(amt = 100, ii = 24, addl = 9) %>%
  mrgsim(end = 300, delta = 0.1) %>% 
  plot(CP~time)
```


A more complicated regimen: 100 mg infusions over 2 hours every 24 hours
for one week, followed by 50 mg boluses every 12 hours for 10 days:

```{r,regimen-figure}
mod %>% 
  ev_rx("100 over 2h q 24 x 7 then 50 q 12 x 20") %>%
  mrgsim(end = 600, delta = 0.1) %>% 
  plot(CP~time)
```


### Population simulation

```{r}
mod <- mread("popex", modlib()) %>% zero_re()
```


A data set looking at different patient weights and doses

```{r, message=FALSE}
library(dplyr)

data <- expand.ev(amt = c(100,150), WT = seq(40,140,20)) %>% mutate(dose = amt)

head(data)
```

Simulate
```{r, population-figure}
mod %>% 
  data_set(data) %>% 
  carry_out(dose,WT) %>%
  mrgsim(delta = 0.1, end = 72) %>% 
  plot(IPRED~time|factor(dose),scales = "same")
```


### Sensitivity analysis with PBPK model

```{r}
mod <- modlib("pbpk")
```

Reference

```{r, comment = " ", echo=FALSE}
blocks(mod,PROB) 
```

Model parameters

```{r}
param(mod)
```


Set up a  batch to simulate
```{r}
idata <- expand.idata(Kpli = seq(4,20,2))

idata
```


```{r, pbpk-figure}
mod %>% 
  ev(amt = 150) %>% 
  idata_set(idata) %>%
  mrgsim(end = 6, delta = 0.1) %>%
  plot(Cp~time)
```

Owner

  • Name: Metrum Research Group
  • Login: metrumresearchgroup
  • Kind: organization

GitHub Events

Total
  • Issues event: 37
  • Watch event: 16
  • Delete event: 12
  • Issue comment event: 50
  • Push event: 73
  • Pull request review comment event: 54
  • Pull request event: 25
  • Pull request review event: 64
  • Create event: 21
Last Year
  • Issues event: 37
  • Watch event: 16
  • Delete event: 12
  • Issue comment event: 50
  • Push event: 73
  • Pull request review comment event: 54
  • Pull request event: 25
  • Pull request review event: 64
  • Create event: 21

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 2,384
  • Total Committers: 8
  • Avg Commits per committer: 298.0
  • Development Distribution Score (DDS): 0.078
Past Year
  • Commits: 165
  • Committers: 2
  • Avg Commits per committer: 82.5
  • Development Distribution Score (DDS): 0.248
Top Committers
Name Email Commits
Kyle Baron k****b@m****m 2,198
Kyle Baron k****n@i****c 124
Devin Pastoor d****r@g****m 38
copernican c****n@g****m 13
kyleb k****b@c****e 6
harshb h****b@m****m 3
Bill Denney w****y@h****m 1
Romain Francois r****n@r****m 1
Committer Domains (Top 20 + Academic)
metrumrg.com: 2 rstudio.com: 1 humanpredictions.com: 1 choline.home: 1 imap.cc: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 156
  • Total pull requests: 147
  • Average time to close issues: 8 months
  • Average time to close pull requests: 29 days
  • Total issue authors: 43
  • Total pull request authors: 4
  • Average comments per issue: 1.54
  • Average comments per pull request: 0.85
  • Merged pull requests: 123
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 31
  • Pull requests: 34
  • Average time to close issues: 3 months
  • Average time to close pull requests: 6 days
  • Issue authors: 9
  • Pull request authors: 2
  • Average comments per issue: 0.65
  • Average comments per pull request: 0.41
  • Merged pull requests: 22
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kylebaron (102)
  • FelicienLL (4)
  • kevin199011 (3)
  • bergsmat (2)
  • farmacyst99 (2)
  • mark0935git (2)
  • Andy00000000000 (2)
  • jeslo328 (1)
  • AprilCCC (1)
  • benjaminrich (1)
  • nguyenjq (1)
  • XuefenYin (1)
  • AMCasablancas (1)
  • algaloo (1)
  • marianklose (1)
Pull Request Authors
  • kylebaron (179)
  • kyleam (10)
  • barrettk (2)
  • marianklose (1)
Top Labels
Issue Labels
bug (23) low-risk (9) enhancement (8) refactor (6) bug-fixed (4) housekeeping (3) question (2) change (2) feature_request (1) needs-test (1) documentation (1) dependencies (1) think_about (1) bug? (1)
Pull Request Labels
bug (6) enhancement (4) refactor (4) low-risk (2) housekeeping (2) change (2) bug-fixed (1)

Packages

  • Total packages: 3
  • Total downloads:
    • cran 1,151 last-month
  • Total docker downloads: 21,825
  • Total dependent packages: 7
    (may contain duplicates)
  • Total dependent repositories: 13
    (may contain duplicates)
  • Total versions: 60
  • Total maintainers: 1
proxy.golang.org: github.com/metrumresearchgroup/mrgsolve
  • Versions: 25
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
cran.r-project.org: mrgsolve

Simulate from ODE-Based Models

  • Versions: 29
  • Dependent Packages: 7
  • Dependent Repositories: 13
  • Downloads: 1,151 Last month
  • Docker Downloads: 21,825
Rankings
Forks count: 2.4%
Stargazers count: 3.4%
Dependent packages count: 6.6%
Average: 7.8%
Dependent repos count: 8.0%
Docker downloads count: 12.5%
Downloads: 13.6%
Maintainers (1)
kyleb@metrumrg.com
Last synced: 6 months ago
conda-forge.org: r-mrgsolve
  • Versions: 6
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 27.9%
Stargazers count: 30.6%
Dependent repos count: 34.0%
Average: 35.9%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5 depends
  • methods * depends
  • Rcpp >= 1.0.7 imports
  • dplyr >= 1.0.8 imports
  • glue * imports
  • lifecycle * imports
  • magrittr >= 2.0.1 imports
  • rlang >= 1.0.1 imports
  • tibble >= 3.1.6 imports
  • tidyselect >= 1.1.1 imports
  • data.table >= 1.14.2 suggests
  • knitr * suggests
  • lattice * suggests
  • pmxTools * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • xml2 >= 1.3.2 suggests
  • yaml * suggests