nmTest({ # M2 all observations dat <- Wang2007 dat$DV <- dat$Y # Add the required DV data item f <- function() { ini({ tvK <- 0.5 # Typical Value of K bsvK ~ 0.04 # Between Subject Variance of K prop.sd <- sqrt(0.1) }) model({ ke <- tvK * exp(bsvK) v <- 1 ipre <- 10 * exp(-ke * t) ipre ~ prop(prop.sd) }) } ct <- function(model, censInfo) { expect_equal(as.character(model$censInformation), censInfo) } dat2 <- dat dat2$limit <- 0 dat3 <- dat dat3$limit <- 3 dat4 <- dat dat4$limit <- 12 f.foce <- suppressMessages(suppressWarnings(nlmixr(f, dat, "posthoc", control = list(interaction = FALSE)))) f.focei <- suppressWarnings(suppressMessages(nlmixr(f, dat, "posthoc"))) test_that("censoring information is correct", { ct(f.foce, "No censoring") ct(f.focei, "No censoring") }) f.focei2 <- suppressWarnings(suppressMessages(nlmixr(f, dat2, "posthoc"))) f.saem2 <- suppressWarnings(suppressMessages(nlmixr(f, dat2, "saem"))) test_that("censoring changes results", { expect_false(isTRUE(all.equal(f.focei$objf, f.focei2$objf))) ct(f.focei2, "M2 censoring") ct(f.saem2, "M2 censoring") }) test_that("Limit affects values", { f.focei3 <- suppressMessages(suppressWarnings(nlmixr(f, dat3, "posthoc"))) expect_false(isTRUE(all.equal(f.focei2$objf, f.focei3$objf))) ct(f.focei3, "M2 censoring") f.focei4 <- suppressMessages(suppressWarnings(nlmixr(f, dat4, "posthoc"))) ct(f.focei4, "M2 censoring") f.foce2 <- suppressMessages(suppressWarnings(nlmixr(f, dat2, "posthoc", control = list(interaction = FALSE)))) expect_false(isTRUE(all.equal(f.foce$objf, f.foce2$objf))) ct(f.foce2, "M2 censoring") f.foce3 <- suppressMessages(suppressWarnings(nlmixr(f, dat3, "posthoc", control = list(interaction = FALSE)))) expect_false(isTRUE(all.equal(f.foce2$objf, f.foce3$objf))) ct(f.foce3, "M2 censoring") }) test_that("M3/M4 -- Missing, assume LLOQ=3 at t=1.5", { skip_if(Sys.getenv("R_ARCH") == "/i386", "windows32") datL <- rbind(dat[, names(dat) != "Y"], data.frame(ID = 1:10, Time = 1.5, DV = 3)) datL$cens <- ifelse(datL$Time == 1.5, 1, 0) datL <- datL[order(datL$ID, datL$Time), ] datL4 <- datL datL4$limit <- 0 f.foceiL <- suppressMessages(suppressWarnings(nlmixr(f, datL, "posthoc"))) expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL$objf))) ct(f.foceiL, "M3 censoring") datL2o3 <- datL datL2o3$limit <- NA datL2o3$limit[1] <- 0 f.foceiL2o3 <- suppressMessages(suppressWarnings(nlmixr(f, datL2o3, "posthoc"))) ct(f.foceiL2o3, "M2 and M3 censoring") f.foceiL <- suppressMessages(suppressWarnings(nlmixr(f, datL, "posthoc"))) expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL$objf))) ct(f.foceiL, "M3 censoring") f.foceiL4 <- suppressMessages(suppressWarnings(nlmixr(f, datL4, "posthoc"))) expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL4$objf))) expect_false(isTRUE(all.equal(f.foceiL$objf, f.foceiL4$objf))) ct(f.foceiL4, "M2 and M4 censoring") datL4only <- datL4 datL4only$limit <- ifelse(datL4only$cens == 0, NA, 0) f.foceiL4only <- suppressMessages(suppressWarnings(nlmixr(f, datL4only, "posthoc"))) ct(f.foceiL4only, "M4 censoring") w <- which(datL4only$cens == 1) datL4and3 <- datL4only datL4and3$limit[w[1]] <- NA f.foceiL4and3 <- suppressMessages(suppressWarnings(nlmixr(f, datL4and3, "posthoc"))) ct(f.foceiL4and3, "M3 and M4 censoring") datL4o3o2 <- datL4and3 datL4o3o2$limit[1] <- 0 f.foceiL4o3o2 <- suppressMessages(suppressWarnings(nlmixr(f, datL4o3o2, "posthoc"))) ct(f.foceiL4o3o2, "M2, M3 and M4 censoring") datL <- rbind(dat[, names(dat) != "Y"], data.frame(ID = 1:10, Time = 1.5, DV = 3)) datL$cens <- ifelse(datL$Time == 1.5, 1, 0) datL <- datL[order(datL$ID, datL$Time), ] datL4 <- datL datL4$limit <- 0 f.foceiL <- suppressMessages(suppressWarnings(nlmixr(f, datL, "posthoc"))) expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL$objf))) ct(f.foceiL, "M3 censoring") f.foceiL4 <- suppressMessages(suppressWarnings(nlmixr(f, datL4, "posthoc"))) expect_false(isTRUE(all.equal(f.focei$objf, f.foceiL4$objf))) expect_false(isTRUE(all.equal(f.foceiL$objf, f.foceiL4$objf))) ct(f.foceiL, "M3 censoring") ## foce datL <- rbind(dat[, names(dat) != "Y"], data.frame(ID = 1:10, Time = 1.5, DV = 3)) datL$cens <- ifelse(datL$Time == 1.5, 1, 0) datL <- datL[order(datL$ID, datL$Time), ] datL4 <- datL datL4$limit <- 0 f.foceL <- suppressMessages(suppressWarnings(nlmixr(f, datL, "posthoc", control = list(interaction = FALSE)))) expect_false(isTRUE(all.equal(f.foce$objf, f.foceL$objf))) ct(f.foceiL4, "M2 and M4 censoring") f.foceL4 <- suppressMessages(suppressWarnings(nlmixr(f, datL4, "posthoc", control = list(interaction = FALSE)))) expect_false(isTRUE(all.equal(f.foce$objf, f.foceL4$objf))) expect_false(isTRUE(all.equal(f.foceL$objf, f.foceL4$objf))) ct(f.foceiL4, "M2 and M4 censoring") upperDat <- datL4 names(upperDat)[4] <- "CENS" names(upperDat)[5] <- "LIMIT" f.foceL4u <- suppressMessages(suppressWarnings(nlmixr(f, datL4, "posthoc", control = list(interaction = FALSE)))) expect_equal(names(f.foceL4u), names(f.foceL4)) }) })