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README.Rmd
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---
output:
html_document:
self_contained: no
keep_md: yes
df_print: kable
github_document:
df_print: kable
editor_options:
chunk_output_type: console
---
```{r setup, include = FALSE}
library(knitr)
knitr::opts_chunk$set(fig.width=8, fig.height=4, dev = 'png', dpi = 150,
fig.path='assets/figures/',
echo=TRUE, warning=FALSE, message=FALSE, cache = FALSE)
#results = 'asis',
```
# `caffsim` R package: Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model
[](https://doi.org/10.5281/zenodo.842649)
[](https://cran.r-project.org/package=caffsim)
> Simulate plasma caffeine concentrations using population pharmacokinetic model described in Lee, Kim, Perera, McLachlan and Bae (2015) <doi:10.1007/s00431-015-2581-x> and the package was published <doi:10.12793/tcp.2017.25.3.141>.
- Github: <https://github.com/asancpt/caffsim>
- Package vignettes and references by `pkgdown`: <http://asancpt.github.io/caffsim>
## Installation
```{r eval = FALSE}
install.pacakges("devtools")
devtools::install_github("asancpt/caffsim")
# Simply create single dose dataset
caffsim::caffPkparam(Weight = 20, Dose = 200, N = 20)
# Simply create multiple dose dataset
caffsim::caffPkparamMulti(Weight = 20, Dose = 200, N = 20, Tau = 12)
```
## Single dose
### Create a PK dataset for caffeine single dose
```{r}
library(caffsim)
MyDataset <- caffPkparam(Weight = 20, Dose = 200, N = 20)
head(MyDataset)
```
### Create a dataset for concentration-time curve
```{r}
MyConcTime <- caffConcTime(Weight = 20, Dose = 200, N = 20)
head(MyConcTime)
```
### Create a concentration-time curve
```{r MyPlotMyConcTime}
caffPlot(MyConcTime)
```
### Create plots for publication (according to the amount of caffeine)
- `cowplot` package is required
```{r MyPlotPub, fig.width = 8, fig.height = 12}
#install.packages("cowplot") # if you don't have it
library(cowplot)
MyPlotPub <- lapply(
c(seq(100, 800, by = 100)),
function(x) caffPlotMulti(caffConcTime(20, x, 20)) +
theme(legend.position="none") +
labs(title = paste0("Single Dose ", x, "mg")))
plot_grid(MyPlotPub[[1]], MyPlotPub[[2]],
MyPlotPub[[3]], MyPlotPub[[4]],
MyPlotPub[[5]], MyPlotPub[[6]],
MyPlotPub[[7]], MyPlotPub[[8]],
labels=LETTERS[1:8], ncol = 2, nrow = 4)
```
## Multiple dose
### Create a PK dataset for caffeine multiple doses
```{r}
MyDatasetMulti <- caffPkparamMulti(Weight = 20, Dose = 200, N = 20, Tau = 12)
head(MyDatasetMulti)
```
### Create a dataset for concentration-time curve
```{r}
MyConcTimeMulti <- caffConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 12, Repeat = 10)
head(MyConcTimeMulti)
```
### Create a concentration-time curve
```{r MyPlotMultiMyConcTimeMulti}
caffPlotMulti(MyConcTimeMulti)
```
### Create plots for publication (according to dosing interval)
- `cowplot` package is required
```{r MyPlotMultiPub, fig.width = 8, fig.height = 12}
#install.packages("cowplot") # if you don't have it
library(cowplot)
MyPlotMultiPub <- lapply(
c(seq(4, 32, by = 4)),
function(x) caffPlotMulti(caffConcTimeMulti(20, 250, 20, x, 15)) +
theme(legend.position="none") +
labs(title = paste0("q", x, "hr" )))
plot_grid(MyPlotMultiPub[[1]], MyPlotMultiPub[[2]],
MyPlotMultiPub[[3]], MyPlotMultiPub[[4]],
MyPlotMultiPub[[5]], MyPlotMultiPub[[6]],
MyPlotMultiPub[[7]], MyPlotMultiPub[[8]],
labels=LETTERS[1:8], ncol = 2, nrow = 4)
```
## Interactive shiny app
```r
caffShiny()
```