caffsim R package: Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model
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
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
library(caffsim)
MyDataset <- caffPkparam(Weight = 20, Dose = 200, N = 20)
head(MyDataset)
| subjid | Tmax | Cmax | AUC | Half\_life | CL | V | Ka | Ke |
| -----: | --------: | --------: | --------: | ---------: | -------: | -------: | ---------: | --------: |
| 1 | 0.9858664 | 15.006075 | 115.44184 | 4.594639 | 1.732474 | 11.48643 | 3.2719387 | 0.1508280 |
| 2 | 3.8148250 | 7.699503 | 107.02942 | 6.354802 | 1.868645 | 17.13545 | 0.5169846 | 0.1090514 |
| 3 | 0.8826191 | 12.147005 | 107.60372 | 5.491894 | 1.858672 | 14.72962 | 4.0586205 | 0.1261860 |
| 4 | 0.2567103 | 13.950749 | 139.11091 | 6.730028 | 1.437702 | 13.96215 | 20.7765914 | 0.1029713 |
| 5 | 1.1563495 | 8.302007 | 65.44492 | 4.587332 | 3.056005 | 20.22931 | 2.6177408 | 0.1510682 |
| 6 | 1.2026953 | 9.445008 | 55.68603 | 3.130858 | 3.591565 | 16.22609 | 2.0869246 | 0.2213451 |
Create a dataset for concentration-time curve
MyConcTime <- caffConcTime(Weight = 20, Dose = 200, N = 20)
head(MyConcTime)
| Subject | Time | Conc |
| ------: | ---: | --------: |
| 1 | 0.0 | 0.000000 |
| 1 | 0.1 | 4.129452 |
| 1 | 0.2 | 7.174502 |
| 1 | 0.3 | 9.410497 |
| 1 | 0.4 | 11.042950 |
| 1 | 0.5 | 12.225252 |
Create a concentration-time curve
caffPlot(MyConcTime)
Create plots for publication (according to the amount of caffeine)
cowplotpackage is required
#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
MyDatasetMulti <- caffPkparamMulti(Weight = 20, Dose = 200, N = 20, Tau = 12)
head(MyDatasetMulti)
| subjid | TmaxS | CmaxS | AUCS | AI | Aavss | Cavss | Cmaxss | Cminss |
| -----: | --------: | -------: | --------: | -------: | --------: | --------: | -------: | -------: |
| 1 | 0.9548818 | 14.35410 | 78.14388 | 1.068908 | 72.79768 | 6.511990 | 19.08368 | 1.230238 |
| 2 | 1.1467783 | 11.52173 | 89.29910 | 1.187191 | 108.04592 | 7.441592 | 16.31939 | 2.573172 |
| 3 | 0.6768031 | 16.69770 | 136.35979 | 1.250128 | 124.04012 | 11.363316 | 22.85721 | 4.573316 |
| 4 | 0.7753311 | 14.44837 | 119.92576 | 1.251847 | 124.46355 | 9.993813 | 20.06162 | 4.036002 |
| 5 | 0.2400863 | 13.36207 | 65.42138 | 1.081913 | 77.33312 | 5.451782 | 15.22267 | 1.152520 |
| 6 | 0.6535510 | 10.73536 | 76.56109 | 1.183885 | 107.17374 | 6.380091 | 14.06610 | 2.184791 |
Create a dataset for concentration-time curve
MyConcTimeMulti <- caffConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 12, Repeat = 10)
head(MyConcTimeMulti)
| Subject | Time | Conc |
| ------: | ---: | --------: |
| 1 | 0.0 | 0.000000 |
| 1 | 0.1 | 4.915431 |
| 1 | 0.2 | 8.455652 |
| 1 | 0.3 | 10.989413 |
| 1 | 0.4 | 12.786772 |
| 1 | 0.5 | 14.045507 |
Create a concentration-time curve
caffPlotMulti(MyConcTimeMulti)
Create plots for publication (according to dosing interval)
cowplotpackage is required
#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
caffShiny()