## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( echo = TRUE, warning = FALSE, collapse = TRUE, comment = "#>" ) ## ----echo = FALSE, fig.cap = "Figure 1: A simple PBPK model", out.width = "50%"---- knitr::include_graphics("pbpk_basic_model_schematic.png") ## ----table1, echo=FALSE, message=FALSE, warnings=FALSE, results='asis'-------- tabl <- " | Parameter | Units | Rat Value | Human Value | |-------------------|:-----------------:|:---------:|:-----------:| | $M$ | kg | 0.25 | 80 | | $Q_\\textrm{CC}$ | L/h/kg${}^{0.75}$ | 15 | 15 | | $Q_\\textrm{LC}$ | -- | 0.21 | 0.26 | | $Q_\\textrm{FC}$ | -- | 0.06 | 0.05 | | $V_\\textrm{LC}$ | L/kg | 0.04 | 0.02 | | $V_\\textrm{FC}$ | L/kg | 0.07 | 0.21 | | $V_\\textrm{ABC}$ | L/kg | 0.02 | 0.02 | | $V_\\textrm{VBC}$ | L/kg | 0.05 | 0.05 | " cat(tabl) # Output the table in a format good for HTML/PDF/docx conversion. ## ----eval = FALSE------------------------------------------------------------- # library(MCSimMod) ## ----eval = FALSE------------------------------------------------------------- # # Get the full name of the package directory that contains the example MCSim # # model specification file. # mod_path <- file.path(system.file(package = "MCSimMod"), "extdata") # # # Create a model object using the example MCSim model specification file # # "pbpk_simple.model" included in the MCSimMod package. # pbpk_mod_name <- file.path(mod_path, "pbpk_simple") # pbpk_mod <- createModel(pbpk_mod_name) ## ----eval = FALSE------------------------------------------------------------- # # Load the model. # pbpk_mod$loadModel() ## ----eval = FALSE------------------------------------------------------------- # pbpk_mod$parms # #> M Q_CC Q_LC Q_FC V_LC V_FC V_ABC # #> 0.2500000 15.0000000 0.2100000 0.0600000 0.0400000 0.0700000 0.0200000 # #> V_VBC P_L P_F P_R V_maxC K_m k_abs # #> 0.0500000 3.5000000 86.5000000 2.3000000 10.0000000 6.0000000 1.2500000 # #> D_oral D_IV Q_C Q_L Q_F Q_RC Q_R # #> 0.0000000 0.0000000 5.3033009 1.1136932 0.3181981 0.7300000 3.8714096 # #> V_L V_F V_AB V_VB V_RC V_R V_max # #> 0.0100000 0.0175000 0.0050000 0.0125000 0.8200000 0.2050000 3.5355339 # #> R_oral R_IV # #> 0.0000000 0.0000000 ## ----eval = FALSE------------------------------------------------------------- # pbpk_mod$updateParms(c(D_oral = 1)) ## ----eval = FALSE------------------------------------------------------------- # pbpk_mod$parms # #> M Q_CC Q_LC Q_FC V_LC V_FC # #> 0.25000000 15.00000000 0.21000000 0.06000000 0.04000000 0.07000000 # #> V_ABC V_VBC P_L P_F P_R V_maxC # #> 0.02000000 0.05000000 3.50000000 86.50000000 2.30000000 10.00000000 # #> K_m k_abs D_oral D_IV Q_C Q_L # #> 6.00000000 1.25000000 1.00000000 0.00000000 5.30330086 1.11369318 # #> Q_F Q_RC Q_R V_L V_F V_AB # #> 0.31819805 0.73000000 3.87140963 0.01000000 0.01750000 0.00500000 # #> V_VB V_RC V_R V_max R_oral R_IV # #> 0.01250000 0.82000000 0.20500000 3.53553391 0.01041667 0.00000000 ## ----eval = FALSE------------------------------------------------------------- # pbpk_mod$Y0 # #> A_G A_L A_F A_AB A_VB A_R A_dose A_m AUC # #> 0 0 0 0 0 0 0 0 0 ## ----eval = FALSE------------------------------------------------------------- # times <- seq(from = 0, to = 100, by = 0.1) ## ----eval = FALSE------------------------------------------------------------- # out_oral <- pbpk_mod$runModel(times) ## ----eval = FALSE------------------------------------------------------------- # plot(out_oral[, "time"], out_oral[, "A_tot"], # type = "l", lty = 1, lwd = 2, # xlab = "Time (h)", ylab = "Amount (mg)" # ) ## ----echo = FALSE, out.width = "100%"----------------------------------------- knitr::include_graphics("amount_lost_vs_time.png") ## ----eval = FALSE------------------------------------------------------------- # cat( # "Total blood flow to compartments:", # pbpk_mod$parms[["Q_L"]] + pbpk_mod$parms[["Q_F"]] + pbpk_mod$parms[["Q_R"]], # "L/h\n" # ) # #> Total blood flow to compartments: 5.303301 L/h # cat("Total cardiac output:", pbpk_mod$parms[["Q_C"]], "L/h\n") # #> Total cardiac output: 5.303301 L/h ## ----eval = FALSE------------------------------------------------------------- # plot(out_oral[, "time"], out_oral[, "C_VB"], # type = "l", lty = 1, lwd = 2, # xlab = "Time (h)", ylab = "Concentration (mg/L)" # ) ## ----echo = FALSE, out.width = "100%"----------------------------------------- knitr::include_graphics("conc_vb_vs_time.png") ## ----eval = FALSE------------------------------------------------------------- # plot(out_oral[, "time"], out_oral[, "C_L"], # type = "l", lty = 1, lwd = 2, # log = "y", ylim = c(0.0001, 10), # xlab = "Time (h)", ylab = "Concentration (mg/L)" # ) # lines(out_oral[, "time"], out_oral[, "C_F"], # lty = 2, lwd = 2 # ) # lines(out_oral[, "time"], out_oral[, "C_R"], # lty = 3, lwd = 2 # ) # legend("bottomright", # legend = c("Liver", "Fat", "Rest of Body"), # lty = c(1, 2, 3), lwd = 2 # ) ## ----echo = FALSE, out.width = "100%"----------------------------------------- knitr::include_graphics("conc_comp_vs_time.png")