README.Rmd

---
output: github_document
---

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

# campsis <img src='man/figures/logo.png' align="right" alt="" width="120" />

<!-- badges: start -->
[![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)
<!-- badges: end -->

## 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)