Add example 2

inst/poped/ex.2.a.warfarin.evaluate.babelmixr2.R

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+## Warfarin example from software comparison in:
+## Nyberg et al., "Methods and software tools for design evaluation
+##   for population pharmacokinetics-pharmacodynamics studies",
+##   Br. J. Clin. Pharm., 2014.
+
+library(babelmixr2)
+library(PopED)
+
+##-- Model: One comp first order absorption
+
+f <- function() {
+  ini({
+    tCl <- 0.15
+    tV <- 8
+    tKA <- 1.0
+    tFavail <- fix(1)
+    eta.cl ~ 0.07
+    eta.v ~ 0.02
+    eta.ka ~ 0.6
+
+    prop.sd <- sqrt(0.01)
+  })
+  model({
+    CL <- tCl*exp(eta.cl)
+    V <- tV*exp(eta.v)
+    KA <- tKA*exp(eta.ka)
+    Favail <- tFavail
+    y <- (DOSE*Favail*KA/(V*(KA-CL/V)))*(exp(-CL/V*time)-exp(-KA*time))
+    y ~ prop(prop.sd)
+
+  })
+}
+
+e <- et(list(c(0, 120))) %>%
+  et(c(1,2,6,24,36,72,120))
+
+e$time <- c(0.5,1,2,6,24,36,72,120)
+e$low <- 0
+e$high <- 120
+
+e <- as.data.frame(e)
+
+## -- Define initial design  and design space
+babel.db <- nlmixr2(f, e, "poped",
+                    control=popedControl(
+                                  groupsize=32,
+                                  a=list(c(DOSE=70))))
+
+##  create plot of model without variability
+plot_model_prediction(babel.db)
+
+##  create plot of model with variability
+plot_model_prediction(babel.db,IPRED=T,DV=T)
+
+## get predictions from model
+model_prediction(babel.db)
+
+## evaluate initial design
+evaluate_design(babel.db)
+shrinkage(babel.db)
+
+## Evaluate with full FIM
+evaluate_design(babel.db, fim.calc.type=0)
+
+# Examine efficiency of sampling windows
+plot_efficiency_of_windows(babel.db,xt_windows=0.5)