rxTest({ test_that("mixing omega and sigma with parameter data frame; RxODE#375", { lognCv <- function(x) { log((x / 100)^2 + 1) } mod2 <- rxode2({ ## the order of variables do not matter, the type of compartmental ## model is determined by the parameters specified. CL ~ TCL * exp(eta.Cl) * (WT / 70)^0.75 C2 ~ linCmt(KA, CL, V2, Q, V3) eff(0) <- 1 ## This specifies that the effect compartment starts at 1. d / dt(eff) ~ Kin - Kout * (1 - C2 / (EC50 + C2)) * eff ## resp <- eff + err1 pk <- C2 * exp(err2) }) ev <- eventTable(amount.units = "mg", time.units = "hours") %>% add.dosing(dose = 10000, nbr.doses = 10, dosing.interval = 12, dosing.to = 2) %>% add.dosing(dose = 20000, nbr.doses = 5, start.time = 120, dosing.interval = 24, dosing.to = 2) %>% add.sampling(0:240) ## Add Residual differences sigma <- diag(2) * 0.05 dimnames(sigma) <- list(c("err1", "err2"), c("err1", "err2")) omega <- matrix(0.2, dimnames = list("eta.Cl", "eta.Cl")) theta <- c( KA = 2.94E-01, TCL = 1.86E+01, V2 = 4.02E+01, Q = 1.05E+01, V3 = 2.97E+02, Kin = 1, Kout = 1, EC50 = 200 ) thetaMat <- diag(length(theta)) * lognCv(5) dimnames(thetaMat) <- list(names(theta), names(theta)) nStud <- 3 nSub <- 12 par <- rxRmvn(nStud, theta, thetaMat) par <- rxCbindStudyIndividual(par, data.frame(WT = rnorm(nStud * nSub, 70, 10))) expect_error(rxSolve(mod2, ev, par, omega = omega, sigma = sigma, dfSub = 100, dfObs = 400, nStud = nStud, nSub = nSub ), NA) # Nesting: ## mod <- rxode2({ ## ## Clearance with individuals ## eff(0) = 1 ## C2 = centr/V2*(1+prop.sd); ## C3 = peri/V3; ## CL = TCl*exp(eta.Cl + eye.Cl + iov.Cl + inv.Cl) * (WT / 70)^0.75 ## KA = TKA * exp(eta.Ka + eye.Ka + iov.Cl + inv.Ka) ## d/dt(depot) =-KA*depot; ## d/dt(centr) = KA*depot - CL*C2 - Q*C2 + Q*C3; ## d/dt(peri) = Q*C2 - Q*C3; ## d/dt(eff) = Kin - Kout*(1-C2/(EC50+C2))*eff; ## ef0 = eff + add.sd ## }) ## et(amountUnits="mg", timeUnits="hours") %>% ## et(amt=10000, addl=9,ii=12,cmt="depot") %>% ## et(time=120, amt=2000, addl=4, ii=14, cmt="depot") %>% ## et(seq(0, 240, by=4)) %>% # Assumes sampling when there is no dosing information ## et(seq(0, 240, by=4) + 0.1) %>% ## adds 0.1 for separate eye ## et(id=1:20) %>% ## ## Add an occasion per dose ## dplyr::mutate(occ=cumsum(!is.na(amt))) %>% ## dplyr::mutate(occ=ifelse(occ == 0, 1, occ)) %>% ## dplyr::mutate(occ=2- occ %% 2) %>% ## dplyr::mutate(eye=ifelse(round(time) == time, 1, 2)) %>% ## dplyr::mutate(inv=ifelse(id < 10, 1, 2)) %>% ## dplyr::as_tibble() -> ## ev ## theta <- c("TKA"=0.294, "TCl"=18.6, "V2"=40.2, ## "Q"=10.5, "V3"=297, "Kin"=1, "Kout"=1, "EC50"=200) ## ## Creating covariance matrix ## tmp <- matrix(rnorm(8^2), 8, 8) ## tMat <- tcrossprod(tmp, tmp) / (8 ^ 2) ## dimnames(tMat) <- list(names(theta), names(theta)) ## tMat ## nStud <- 4 ## nSub <- 20 ## par <- rxCbindStudyIndividual(rxRmvn(nStud, theta, tMat), ## data.frame(WT=rnorm(nStud * nSub, 70, 10))) ## omega <- lotri(lotri(eta.Cl ~ 0.1, ## eta.Ka ~ 0.1) | id(nu=100), ## lotri(eye.Cl ~ 0.05, ## eye.Ka ~ 0.05) | eye(nu=200), ## lotri(iov.Cl ~ 0.01, ## iov.Ka ~ 0.01) | occ(nu=200), ## lotri(inv.Cl ~ 0.02, ## inv.Ka ~ 0.02) | inv(nu=10)) ## sigma <- lotri(prop.sd ~ .25, ## add.sd~ 0.125) ## s <- rxSolve(mod, par, ev, omega=omega, ## sigma=sigma, sigmaDf=400, ## nStud=nStud) }) })