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caffsim R package: Simulation of Plasma Caffeine Concentrations by Using Population Pharmacokinetic Model

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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.

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()

Read the original on github.com ↗