test_that("manual back-transform", { t100 <- function(x) { x * 100 } one.cmt <- function() { ini({ tka <- fix(0.45); backTransform("t100") tcl <- log(c(0, 2.7, 100)); backTransform("t100") tv <- 3.45; backTransform("none") eta.ka ~ 0.6 eta.cl ~ 0.3 eta.v ~ 0.1 add.sd <- 0.7 }) model({ ka <- exp(tka + eta.ka) cl <- exp(tcl + eta.cl) v <- exp(tv + eta.v) linCmt() ~ add(add.sd) }) } skip_if_not(rxode2parse::.linCmtSens()) fit <- nlmixr(one.cmt, theo_sd, est="saem", control=saemControl(print=0, nBurn = 1, nEm = 1)) expect_equal(setNames(fit$parFixedDf["tka", "Estimate"] * 100, NULL), setNames(fit$parFixedDf["tka", "Back-transformed"], NULL)) expect_equal(fit$parFixed["tka", "Back-transformed(95%CI)"], sprintf("%3g", fit$parFixedDf["tka", "Estimate"] * 100)) expect_equal(NA_real_, setNames(fit$parFixedDf["tka", "CI Lower"], NULL)) expect_equal(NA_real_, setNames(fit$parFixedDf["tka", "CI Upper"], NULL)) expect_equal(setNames(fit$parFixedDf["tcl", "Estimate"] * 100, NULL), setNames(fit$parFixedDf["tcl", "Back-transformed"], NULL)) qn <- qnorm(1.0 - (1 - 0.95) / 2) expect_equal(setNames(t100(fit$parFixedDf["tcl", "Estimate"] + qn * fit$parFixedDf["tcl", "SE"]), NULL), setNames(fit$parFixedDf["tcl", "CI Upper"], NULL)) expect_equal(setNames(t100(fit$parFixedDf["tcl", "Estimate"] - qn * fit$parFixedDf["tcl", "SE"]), NULL), setNames(fit$parFixedDf["tcl", "CI Lower"], NULL)) expect_equal(fit$parFixed["tcl", "Back-transformed(95%CI)"], sprintf("%3g (%3g, %3g)", t100(fit$parFixedDf["tcl", "Estimate"]), setNames(t100(fit$parFixedDf["tcl", "Estimate"] - qn * fit$parFixedDf["tcl", "SE"]), NULL), setNames(t100(fit$parFixedDf["tcl", "Estimate"] + qn * fit$parFixedDf["tcl", "SE"]), NULL))) expect_equal(setNames(exp(fit$parFixedDf["tv", "Estimate"] + qn * fit$parFixedDf["tv", "SE"]), NULL), setNames(fit$parFixedDf["tv", "CI Upper"], NULL)) expect_equal(setNames(exp(fit$parFixedDf["tv", "Estimate"] - qn * fit$parFixedDf["tv", "SE"]), NULL), setNames(fit$parFixedDf["tv", "CI Lower"], NULL)) qn <- qnorm(1.0 - (1 - 0.80) / 2) fit <- nlmixr(one.cmt, theo_sd, est="saem", control=saemControl(print=0, nBurn = 1, nEm = 1, ci=0.8)) expect_equal(setNames(fit$parFixedDf["tka", "Estimate"] * 100, NULL), setNames(fit$parFixedDf["tka", "Back-transformed"], NULL)) expect_equal(fit$parFixed["tka", "Back-transformed(80%CI)"], sprintf("%3g", fit$parFixedDf["tka", "Estimate"] * 100)) expect_equal(NA_real_, setNames(fit$parFixedDf["tka", "CI Lower"], NULL)) expect_equal(NA_real_, setNames(fit$parFixedDf["tka", "CI Upper"], NULL)) expect_equal(setNames(fit$parFixedDf["tcl", "Estimate"] * 100, NULL), setNames(fit$parFixedDf["tcl", "Back-transformed"], NULL)) expect_equal(setNames(t100(fit$parFixedDf["tcl", "Estimate"] + qn * fit$parFixedDf["tcl", "SE"]), NULL), setNames(fit$parFixedDf["tcl", "CI Upper"], NULL)) expect_equal(setNames(t100(fit$parFixedDf["tcl", "Estimate"] - qn * fit$parFixedDf["tcl", "SE"]), NULL), setNames(fit$parFixedDf["tcl", "CI Lower"], NULL)) expect_equal(fit$parFixed["tcl", "Back-transformed(80%CI)"], sprintf("%3g (%3g, %3g)", t100(fit$parFixedDf["tcl", "Estimate"]), setNames(t100(fit$parFixedDf["tcl", "Estimate"] - qn * fit$parFixedDf["tcl", "SE"]), NULL), setNames(t100(fit$parFixedDf["tcl", "Estimate"] + qn * fit$parFixedDf["tcl", "SE"]), NULL))) expect_equal(setNames(exp(fit$parFixedDf["tv", "Estimate"] + qn * fit$parFixedDf["tv", "SE"]), NULL), setNames(fit$parFixedDf["tv", "CI Upper"], NULL)) expect_equal(setNames(exp(fit$parFixedDf["tv", "Estimate"] - qn * fit$parFixedDf["tv", "SE"]), NULL), setNames(fit$parFixedDf["tv", "CI Lower"], NULL)) expect_error(nlmixr(one.cmt, theo_sd, est="focei", control=foceiControl(print=0, maxOuterIterations = 0, maxInnerIterations = 0, covMethod = "")), NA) })