README.md

In asancpt/busulfansim: Simulation of Plasma Busulfan Concentrations by Using Population Pharmacokinetic Model

busulfansim R package: Simulation of Plasma Busulfan Concentrations by Using Population Pharmacokinetic Model

Simulate plasma busulfan concentrations using population pharmacokinetic model described in Choe, Kim, Lim, Cho, Ghim, Jung, Kim, Noh, Bae and Lee (2012) .

• Github: https://github.com/asancpt/busulfansim
• Package vignettes and references by pkgdown: http://asancpt.github.io/busulfansim

Installation

install.pacakges("devtools")
devtools::install_github("asancpt/busulfansim")

# Simply create single dose dataset
busulfansim::bsfnPkparam(Weight = 20, Dose = 200, N = 20) 

# Simply create multiple dose dataset
busulfansim::bsfnPkparamMulti(Weight = 20, Dose = 200, N = 20, Tau = 12) 

Single dose

Create a PK dataset for busulfan single dose

library(busulfansim)
MyDataset <- bsfnPkparam(Weight = 20, Dose = 200, N = 20)
knitr::kable(head(MyDataset), format = 'markdown')

| subjid| Tmax| Cmax| AUC| Half_life| CL| V| Ka| Ke| |------:|---------:|--------:|---------:|---------:|--------:|--------:|---------:|---------:| | 1| 0.5767079| 3.856945| 12.750493| 1.8447004| 15.68567| 41.75376| 4.789441| 0.3756708| | 2| 0.5538237| 3.184901| 5.392561| 0.6503104| 37.08813| 34.80346| 2.827778| 1.0656449| | 3| 0.5772617| 4.216626| 11.617549| 1.4486013| 17.21534| 35.98580| 4.270547| 0.4783925| | 4| 0.1728366| 2.323294| 3.167900| 0.8159181| 63.13331| 74.33133| 18.754942| 0.8493499| | 5| 1.0199484| 3.282203| 13.044898| 1.8978537| 15.33166| 41.98738| 2.062794| 0.3651493| | 6| 0.4464045| 3.985585| 9.753881| 1.3482443| 20.50466| 39.89219| 6.029677| 0.5140018|

Create a dataset for concentration-time curve

MyConcTime <- bsfnConcTime(Weight = 20, Dose = 200, N = 20)
knitr::kable(head(MyConcTime), format = 'markdown') 

| Subject| Time| Conc| |-------:|----:|--------:| | 1| 0.0| 0.000000| | 1| 0.1| 2.965643| | 1| 0.2| 4.203926| | 1| 0.3| 4.650275| | 1| 0.4| 4.736440| | 1| 0.5| 4.661575|

Create a concentration-time curve

bsfnPlot(MyConcTime)

Create plots for publication (according to the amount of busulfan)

• 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) bsfnPlotMulti(bsfnConcTime(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 busulfan multiple doses

MyDatasetMulti <- bsfnPkparamMulti(Weight = 20, Dose = 200, N = 20, Tau = 12)
knitr::kable(head(MyDatasetMulti), format = 'markdown') 

| subjid| TmaxS| CmaxS| AUCS| AI| Aavss| Cavss| Cmaxss| Cminss| |------:|---------:|--------:|---------:|--------:|--------:|---------:|--------:|---------:| | 1| 0.7888594| 3.467596| 10.851480| 1.004072| 36.23804| 0.9042900| 5.000735| 0.0202825| | 2| 0.9324679| 3.158090| 13.937638| 1.028223| 55.51025| 1.1614698| 4.293860| 0.1178600| | 3| 0.8673877| 2.677137| 7.541794| 1.000798| 27.97736| 0.6284828| 4.487030| 0.0035793| | 4| 0.2297815| 3.665982| 5.987100| 1.000171| 23.00505| 0.4989250| 4.329242| 0.0007390| | 5| 0.1789700| 4.948107| 10.601323| 1.002164| 32.51695| 0.8834436| 5.434176| 0.0117355| | 6| 0.8579808| 3.741281| 13.129701| 1.008054| 41.32498| 1.0941418| 5.326850| 0.0425591|

Create a dataset for concentration-time curve

MyConcTimeMulti <- bsfnConcTimeMulti(Weight = 20, Dose = 200, N = 20, Tau = 12, Repeat = 10)
knitr::kable(head(MyConcTimeMulti), format = 'markdown')

| Subject| Time| Conc| |-------:|----:|--------:| | 1| 0.0| 0.000000| | 1| 0.1| 2.340878| | 1| 0.2| 3.132843| | 1| 0.3| 3.328890| | 1| 0.4| 3.299005| | 1| 0.5| 3.186662|

Create a concentration-time curve

bsfnPlotMulti(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) bsfnPlotMulti(bsfnConcTimeMulti(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

bsfnShiny()

asancpt/busulfansim documentation built on May 31, 2019, 8:40 a.m.