Data

Tools

Indexes

Applications

Experiments

Open Source Science

campsis

A generic PK/PD simulation platform based on rxode2 and mrgsolve engines.

https://github.com/calvagone/campsis

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 (14.9%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

A generic PK/PD simulation platform based on rxode2 and mrgsolve engines.

Basic Info
Statistics
  • Stars: 9
  • Watchers: 3
  • Forks: 4
  • Open Issues: 9
  • Releases: 29
Created over 5 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/"
)
```

# campsis 


[![R-CMD-check](https://github.com/Calvagone/campsis/workflows/R-CMD-check/badge.svg)](https://github.com/Calvagone/campsis/actions)
[![Codecov test coverage](https://codecov.io/gh/Calvagone/campsis/graph/badge.svg)](https://app.codecov.io/gh/Calvagone/campsis)
[![CRAN version](http://www.r-pkg.org/badges/version/campsis)](https://cran.r-project.org/package=campsis)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/campsis)](https://cran.r-project.org/package=campsis)
[![CRAN total downloads](https://cranlogs.r-pkg.org/badges/campsis)](https://cran.r-project.org/package=campsis)


## Requirements

* R package `campsismod` must be installed beforehand
* Simulation engine must be installed too (`rxode2` or `mrgsolve`)

## Installation
Install the latest stable release using `devtools`:
  
```{r, eval=FALSE}
devtools::install_github("Calvagone/campsis")
```

## Basic example

Import the `campsis` package:

```{r, message=F, warning=F}
library(campsis)
```

Create your dataset:

```{r}
ds <- Dataset(50) %>%
  add(Bolus(time=0, amount=1000, ii=12, addl=2)) %>%
  add(Observations(times=seq(0, 36, by=0.5)))
```

Load your own model or use a built-in model from the library:

```{r}
model <- model_suite$pk$`2cpt_fo`
```

Simulate your results with your preferred simulation engine (`rxode2` or `mrgsolve`):

```{r, message=F}
results <- model %>% simulate(dataset=ds, dest="rxode2", seed=1)
```

Plot your results:

```{r readme_plot, fig.show='hide'}
shadedPlot(results, "CONC")
```

```{r, eval=FALSE, echo=FALSE, results='hide'}
file_vignette <- "vignettes/resources/readme_plot.png"
ggplot2::ggsave(filename=file_vignette, width=8, height=4, dpi=100)
```

```{r, eval=FALSE, echo=FALSE, results='hide'}
file.copy(file_vignette, "docs/articles/resources/")
```

![](vignettes/resources/readme_plot.png)

Owner

  • Name: Calvagone
  • Login: Calvagone
  • Kind: organization

GitHub Events

Total
  • Create event: 4
  • Release event: 3
  • Issues event: 48
  • Watch event: 2
  • Issue comment event: 29
  • Push event: 51
  • Pull request event: 6
  • Fork event: 2
Last Year
  • Create event: 4
  • Release event: 3
  • Issues event: 48
  • Watch event: 2
  • Issue comment event: 29
  • Push event: 51
  • Pull request event: 6
  • Fork event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 452
  • Total Committers: 2
  • Avg Commits per committer: 226.0
  • Development Distribution Score (DDS): 0.004
Past Year
  • Commits: 64
  • Committers: 1
  • Avg Commits per committer: 64.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Nicolas Luyckx n****x@c****m 450
luyckxn 4****n 2
Committer Domains (Top 20 + Academic)
calvagone.com: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 135
  • Total pull requests: 29
  • Average time to close issues: about 1 month
  • Average time to close pull requests: about 20 hours
  • Total issue authors: 6
  • Total pull request authors: 2
  • Average comments per issue: 0.58
  • Average comments per pull request: 0.38
  • Merged pull requests: 27
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 24
  • Pull requests: 5
  • Average time to close issues: 14 days
  • Average time to close pull requests: about 1 hour
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.83
  • Average comments per pull request: 0.0
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • luyckxn (115)
  • AndreasCalvagone (14)
  • jsmccune14 (3)
  • jmccune14 (1)
  • mattfidler (1)
  • Amaranthfan (1)
Pull Request Authors
  • luyckxn (33)
  • mattfidler (1)
Top Labels
Issue Labels
enhancement (16) bug (4)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 507 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 13
  • Total maintainers: 1
cran.r-project.org: campsis

Generic PK/PD Simulation Platform CAMPSIS

  • Versions: 13
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 507 Last month
Rankings
Forks count: 17.8%
Stargazers count: 22.5%
Dependent packages count: 29.8%
Average: 31.8%
Dependent repos count: 35.5%
Downloads: 53.3%
Maintainers (1)
nicolas.luyckx@calvagone.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 4.0.0 depends
  • campsismod * depends
  • MASS * imports
  • assertthat * imports
  • digest * imports
  • dplyr * imports
  • ggplot2 * imports
  • methods * imports
  • plyr * imports
  • progress * imports
  • purrr * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
  • RxODE * suggests
  • bookdown * suggests
  • devtools * suggests
  • gridExtra * suggests
  • knitr * suggests
  • mrgsolve * suggests
  • pkgdown * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • rxode2 * suggests
  • stringr * 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