README.md

In asancpt/caffsim: Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model

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) and the package was published .

• 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)

• cowplot package 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)

• cowplot package 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()

asancpt/caffsim documentation built on Aug. 31, 2020, 12:49 a.m.