nmTest({ test_that("integerish error focei", { PKdata <- nlmixr2data::warfarin %>% dplyr::filter(dvid == "cp") %>% dplyr::select(-dvid) %>% dplyr::mutate(sex = ifelse(sex == "male", 1, 0)) One.comp.KA.ODE <- function() { ini({ # Where initial conditions/variables are specified lka <- log(1.15) #log ka (1/h) lcl <- log(0.135) #log Cl (L/h) lv <- log(8) #log V (L) prop.err <- 0.15 #proportional error (SD/mean) add.err <- 0.6 #additive error (mg/L) eta.ka ~ 0.5 #IIV ka eta.cl ~ 0.1 #IIV cl eta.v ~ 0.1 #IIV v }) model({ # Where the model is specified cl <- exp(lcl + eta.cl) v <- exp(lv + eta.v) ka <- exp(lka + eta.ka) ## ODE example d/dt(depot) = -ka * depot d/dt(central) = ka * depot - (cl/v) * central ## Concentration is calculated cp = central/v ## And is assumed to follow proportional and additive error cp ~ prop(prop.err) + add(add.err) }) } ## estimate parameters using nlmixr/FOCEI: fitOne.comp.KA.ODE_F <- nlmixr(One.comp.KA.ODE, #the model definition PKdata, #the data set est = "focei", #the estimation algorithm (FOCEi) #FOCEi options: foceiControl(print = 5)) #only print every 5th estimation step }) })