if (!.Call(`_rxode2_isIntel`)) { test_that("back transformation piping", { mod1 <- function() { ini({ # central KA <- 2.94E-01 backTransform("exp") CL <- 1.86E+01 V2 <- 4.02E+01 # peripheral Q <- 1.05E+01 V3 <- 2.97E+02 # effects Kin <- 1 Kout <- 1 EC50 <- 200 }) model({ C2 <- centr/V2 C3 <- peri/V3 d/dt(depot) <- -KA*depot d/dt(centr) <- KA*depot - CL*C2 - Q*C2 + Q*C3 d/dt(peri) <- Q*C2 - Q*C3 eff(0) <- 1 d/dt(eff) <- Kin - Kout*(1-C2/(EC50+C2))*eff }) } ui <- rxode(mod1) expect_equal(ui$iniDf$backTransform[ui$iniDf$name == "KA"], "exp") p1 <- ui %>% ini( KA <- backTransform("log") ) expect_equal(p1$iniDf$backTransform[ui$iniDf$name == "KA"], "log") p2 <-ui %>% ini( KA <- backTransform(log) ) expect_equal(p2$iniDf$backTransform[ui$iniDf$name == "KA"], "log") p3 <- ui |> ini(KA <- backTransform(NULL)) expect_equal(p3$iniDf$backTransform[ui$iniDf$name == "KA"], NA_character_) expect_error(ui |> ini(KA <- backTransform(matt)), "matt") }) test_that("piping with ini can update labels (rxode2/issues#351)", { mod <- function() { ini({ a <- 1 label("foo") addSd <- 2 }) model({ b <- a b ~ add(addSd) }) } ui <- rxode2(mod) expect_equal(ui$iniDf$label[ui$iniDf$name == "a"], "foo") newLabelUi <- ini(ui, a = label("bar")) expect_equal(newLabelUi$iniDf$label[newLabelUi$iniDf$name == "a"], "bar") }) test_that("piping with ini can remove labels (#627)", { mod <- function() { ini({ a <- 1 label("foo") addSd <- 2 }) model({ b <- a b ~ add(addSd) }) } ui <- rxode2(mod) expect_equal(ui$iniDf$label[ui$iniDf$name == "a"], "foo") newLabelUi <- ini(ui, a = label(NULL)) expect_equal(newLabelUi$iniDf$label[ui$iniDf$name == "a"], NA_character_) }) test_that("piping with ini gives an error pointing the user to use label for character rhs (rxode2/issues#351)", { mod <- function() { ini({ a <- 1 label("foo") addSd <- 2 }) model({ b <- a b ~ add(addSd) }) } ui <- rxode2(mod) expect_error( ini(ui, a = "bar"), regexp = "to assign a new label, use 'a <- label(\"bar\")'", fixed = TRUE ) }) test_that("piping with ini can update labels (rxode2/issues#351)", { mod <- function() { ini({ a <- 1 label("foo") addSd <- 2 }) model({ b <- a b ~ add(addSd) }) } ui <- rxode2(mod) expect_equal(ui$iniDf$label[ui$iniDf$name == "a"], "foo") newLabelUi <- ini(ui, a = label("bar")) expect_equal(newLabelUi$iniDf$label[newLabelUi$iniDf$name == "a"], "bar") }) test_that("piping with ini gives an error pointing the user to use label for character rhs (rxode2/issues#351)", { mod <- function() { ini({ a <- 1 label("foo") addSd <- 2 }) model({ b <- a b ~ add(addSd) }) } ui <- rxode2(mod) expect_error( ini(ui, a = "bar"), regexp = "to assign a new label, use 'a <- label(\"bar\")'", fixed = TRUE ) }) test_that(".iniSimplifyFixUnfix", { expect_equal( .iniSimplifyFixUnfix(str2lang("fix")), as.name("fix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("fixed")), as.name("fix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("FIX")), as.name("fix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("FIXED")), as.name("fix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("unfix")), as.name("unfix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("unfixed")), as.name("unfix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("UNFIX")), as.name("unfix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("UNFIXED")), as.name("unfix") ) expect_equal( .iniSimplifyFixUnfix(str2lang("FIXED(a)")), str2lang("fix(a)") ) expect_equal( .iniSimplifyFixUnfix(str2lang("c <- FIXED(a+b)")), str2lang("c <- fix(a + b)") ) expect_equal( .iniSimplifyFixUnfix(str2lang("c <- UNFIXED(a+b)")), str2lang("c <- unfix(a + b)") ) expect_equal( .iniSimplifyFixUnfix(str2lang("c <- NULL")), str2lang("c <- NULL") ) }) test_that(".iniSimplifyAssignArrow", { expect_equal( .iniSimplifyAssignArrow(str2lang("a <- b")), str2lang("a <- b") ) expect_equal( .iniSimplifyAssignArrow(str2lang("a = b")), str2lang("a <- b") ) # non-assignment equal signs are not modified expect_equal( .iniSimplifyAssignArrow(str2lang("a = b(c=d)")), str2lang("a <- b(c=d)") ) }) test_that("piping with ini can update reorder parameters (rxode2/issues#352)", { mod <- function() { ini({ a <- 1 b <- 2 c <- 3 addSd <- 2 }) model({ b <- a + b*log(c) b ~ add(addSd) }) } ui <- rxode2(mod) # No modification expect_equal(ui$iniDf$name, c("a", "b", "c", "addSd")) # b to the top by number expect_equal(suppressMessages(ini(ui, b <- 1, append = 0))$iniDf$name, c("b", "a", "c", "addSd")) # b to the top by logical expect_equal(suppressMessages(ini(ui, b <- 1, append = FALSE))$iniDf$name, c("b", "a", "c", "addSd")) # b to the bottom by number expect_equal(suppressMessages(ini(ui, b <- 1, append = Inf))$iniDf$name, c("a", "c", "addSd", "b")) # b to the bottom by logical expect_equal(suppressMessages(ini(ui, b <- 1, append = TRUE))$iniDf$name, c("a", "c", "addSd", "b")) # b to the bottom by name expect_equal(suppressMessages(ini(ui, b <- 1, append = "addSd"))$iniDf$name, c("a", "c", "addSd", "b")) expect_equal(suppressMessages(ini(ui, b <- 1, append = addSd))$iniDf$name, c("a", "c", "addSd", "b")) # b after c expect_equal(suppressMessages(ini(ui, b <- 1, append = "c"))$iniDf$name, c("a", "c", "b", "addSd")) # a and b after c; counter-intuitive: the order of a and b are reversed expect_equal(suppressMessages(ini(ui, a <- 1, b <- 1, append = "c"))$iniDf$name, c("c", "b", "a", "addSd")) # b to b, warn and no change expect_warning( expect_equal(suppressMessages(ini(ui, b <- 1, append = "b"))$iniDf$name, c("a", "b", "c", "addSd")), regexp = "parameter 'b' set to be moved after itself, no change in order made" ) expect_error( ini(ui, b <- 1, append = d/dt(fun)), "append") # Invalid parameter is correctly caught expect_error( ini(ui, b <- 1, append = "foo"), "append" ) }) test_that(".iniAddCovarianceBetweenTwoEtaValues", { # Promote a covariate to a correlated eta mod <- function() { ini({ a <- 1 b <- 2 c <- 3 d ~ 1 h ~ 2 addSd <- 2 }) model({ b <- a + b*log(c) f <- a + d + e i <- j + h b ~ add(addSd) }) } suppressMessages( expect_message( ini(mod, d + e ~ c(1, 0.5, 3)), regexp = "promote `e` to between subject variability" ) ) # Non-existent correlated eta suppressMessages( expect_error( ini(mod, d + g ~ c(1, 0.5, 3)), regexp = "cannot find parameter 'g'" ) ) # Update eta order suppressMessages( expect_equal( ini(mod, h + d ~ c(1, 0.5, 3))$iniDf$name, c("a", "b", "c", "addSd", "h", "d", "(h,d)") ) ) }) test_that(".iniHandleLabel", { mod <- function() { ini({ a <- 1 b <- 2 c <- 3 d ~ 1 h ~ 2 addSd <- 2 }) model({ b <- a + b*log(c) f <- a + d + e i <- j + h b ~ add(addSd) }) } # non-existent parameter expect_error( ini(mod, q = label("foo")), regexp = "cannot find parameter 'q'" ) # invalid label value expect_error( ini(mod, a = label(5)), regexp = "the new label for 'a' must be a character string" ) }) test_that(".iniHandleAppend", { mod <- function() { ini({ a <- 1 b <- 2 c <- 3 d ~ 1 h ~ 2 addSd <- 2 }) model({ b <- a + b*log(c) f <- a + d + e i <- j + h b ~ add(addSd) }) } expect_error( ini(mod, a <- 1, append=factor("A")), regexp = "'append' must be NULL, logical, numeric, or character/expression of variable in model" ) expect_error( ini(mod, q <- 1, append=0), regexp = "cannot find parameter 'q'" ) # Non-theta parameters cannot be moved expect_error( ini(mod, h ~ 1, append=0), regexp = "only theta parameters can be moved" ) }) test_that("ini tests for different types of expressions", { mod <- function() { ini({ a <- 1 b <- 2 c <- 3 d ~ 1 h ~ 2 addSd <- 2 }) model({ b <- a + b*log(c) f <- a + d + e i <- j + h b ~ add(addSd) }) } expect_error(mod %>% ini("h~3"), NA) expect_error(mod %>% ini("h~3;4*")) expect_error(mod %>% ini(factor("A"))) }) test_that("zeroRe", { modOmegaSigma <- function() { ini({ a <- 1; label("foo") #nolint iiva ~ 3 addSd <- 2 }) model({ b <- a + iiva b ~ add(addSd) }) } modOmega <- function() { ini({ a <- 1; label("foo") # nolint iiva ~ 3 }) model({ b <- a + iiva }) } modSigma <- function() { ini({ a <- 1; label("foo") # nolint addSd <- 2 }) model({ b <- a b ~ add(addSd) }) } modSigmaBound <- function() { ini({ a <- 1; label("foo") # nolint addSd <- c(1, 2) }) model({ b <- a b ~ add(addSd) }) } modNone <- function() { ini({ a <- 1; label("foo") # nolint }) model({ b <- a }) } uiOmegaSigma <- rxode2(modOmegaSigma) uiOmega <- rxode2(modOmega) uiSigma <- rxode2(modSigma) uiSigmaBound <- rxode2(modSigmaBound) uiNone <- rxode2(modNone) expect_silent( suppressMessages( newMod <- zeroRe(modOmegaSigma, which = c("omega", "sigma")) ) ) expect_silent( suppressMessages( newUi <- zeroRe(uiOmegaSigma, which = c("omega", "sigma")) ) ) expect_equal(newMod$iniDf, newUi$iniDf) # detect change expect_equal(uiOmegaSigma$iniDf$est, c(1, 2, 3)) expect_equal(newMod$iniDf$est, c(1, 0, 0)) # Confirm that you can simulate from the model suppressMessages( expect_equal( rxSolve(newMod, events = data.frame(TIME = 0:2))$b, rep(1, 3) ) ) # Confirm that the `fix` flag is respected expect_silent( suppressMessages( newUiNoFix <- zeroRe(uiOmegaSigma, which = c("omega", "sigma"), fix = FALSE) ) ) # detect change expect_equal(uiOmegaSigma$iniDf$fix, rep(FALSE, 3)) expect_equal(newUi$iniDf$fix, c(FALSE, TRUE, TRUE)) expect_equal(newUiNoFix$iniDf$fix, rep(FALSE, 3)) suppressMessages( expect_warning( newMod <- zeroRe(modOmega, which = c("omega", "sigma")), regexp = "No sigma parameters in the model" ) ) suppressMessages( expect_warning( newUi <- zeroRe(uiOmega, which = c("omega", "sigma")), regexp = "No sigma parameters in the model" ) ) expect_equal(newMod$iniDf, newUi$iniDf) # detect change expect_equal(uiOmega$iniDf$est, c(1, 3)) expect_equal(newMod$iniDf$est, c(1, 0)) suppressMessages( expect_warning( newMod <- zeroRe(modSigmaBound, which = c("omega", "sigma")), regexp = "No omega parameters in the model" ) ) suppressMessages( expect_warning( newUi <- zeroRe(uiSigmaBound, which = c("omega", "sigma")), regexp = "No omega parameters in the model" ) ) expect_equal(newMod$iniDf, newUi$iniDf) # detect change expect_equal(uiSigmaBound$iniDf$est, c(1, 2)) expect_equal(newMod$iniDf$est, c(1, 0)) # confirm lower bound change expect_equal(uiSigmaBound$iniDf$lower, c(-Inf, 1)) expect_equal(newMod$iniDf$lower, c(-Inf, 0)) suppressMessages( expect_warning( newMod <- zeroRe(modSigma, which = c("omega", "sigma")), regexp = "No omega parameters in the model" ) ) suppressMessages( expect_warning( newUi <- zeroRe(uiSigma, which = c("omega", "sigma")), regexp = "No omega parameters in the model" ) ) expect_equal(newMod$iniDf, newUi$iniDf) # detect change expect_equal(uiSigma$iniDf$est, c(1, 2)) expect_equal(newMod$iniDf$est, c(1, 0)) suppressMessages( expect_warning(expect_warning( newMod <- zeroRe(modNone, which = c("omega", "sigma")), regexp = "No omega parameters in the model"), regexp = "No sigma parameters in the model" ) ) suppressMessages( expect_warning(expect_warning( newUi <- zeroRe(uiNone, which = c("omega", "sigma")), regexp = "No omega parameters in the model"), regexp = "No sigma parameters in the model" ) ) expect_equal(newMod$iniDf, newUi$iniDf) # detect no change expect_equal(uiNone$iniDf$est, 1) expect_equal(newMod$iniDf$est, 1) # expected errors expect_error(zeroRe("A"), regexp = "'object' needs to be a rxUi model") expect_error(zeroRe(modOmegaSigma, which = "foo"), regexp = "should be one of") }) test_that("zeroRe works with correlated etas (#480)", { mod <- function() { ini({ lka <- 0.45 lcl <- 1 lvc <- 3.45 propSd <- c(0, 0.5) etalka + etalcl + etalvc ~ c(0.1, 0.2, 0.3, 0.4, 0.5, 0.6) }) model({ ka <- exp(lka + etalka) cl <- exp(lcl + etalcl) vc <- exp(lvc + etalvc) cp <- linCmt() cp ~ prop(propSd) }) } ui <- rxode2(mod) expect_equal(ui$iniDf$est[!is.na(ui$iniDf$neta1)], (1:6)/10) suppressMessages(zeroUi <- zeroRe(mod)) expect_equal(zeroUi$iniDf$est[!is.na(zeroUi$iniDf$neta1)], c(0, 0, 0)) }) test_that("Piping outside the boundaries", { m1 <- function() { ini({ x2 <- c(0, 1) x3 <- c(0, 1, 2) }) model({ f <- x2+x3*4 }) } suppressMessages({ f2 <- m1 %>% ini(x2=-1) expect_equal(f2$iniDf[f2$iniDf$name == "x2","lower"], -Inf) }) suppressMessages({ f2 <- m1 %>% ini(x3=4) expect_equal(f2$iniDf[f2$iniDf$name == "x3","upper"], Inf) }) suppressMessages({ f2 <- m1 %>% ini(x3=c(0,3)) expect_equal(f2$iniDf[f2$iniDf$name == "x3","upper"], Inf) }) }) test_that("append allows promoting from covariate (#472)", { mod <- function() { ini({ lka <- 0.45 lcl <- 1 lvc <- 3.45 propSd <- 0.5 }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc cp ~ prop(propSd) }) } suppressMessages( newmod <- mod %>% model( ka <- exp(lka + ka_dose*DOSE), auto = FALSE ) %>% ini( ka_dose <- 1, append = "lka" ) ) expect_equal(newmod$iniDf$name, c("lka", "ka_dose", "lcl", "lvc", "propSd")) }) test_that("change ini type with ~", { mod <- function() { ini({ lka <- 0.45 lcl <- 1 lvc <- 3.45 propSd <- 0.5 }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc cp ~ prop(propSd) }) } mod1 <- mod |> ini( ~ lka) expect_equal(mod1$omega, lotri(lka ~ 0.45)) mod2 <- mod1 |> ini( ~ lka) expect_equal(mod2$omega, NULL) expect_error(mod1 |> ini( ~ propSd)) expect_error(mod1 |> ini( ~ matt)) ## all etas mod <- function() { ini({ lka ~ 0.45 lcl ~ 1 lvc ~ 3.45 }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc }) } mod2 <- mod |> ini( ~ lka) expect_equal(mod2$omega, lotri(lcl ~ 1, lvc ~ 3.45)) # remove correlated eta mod <- function() { ini({ lka + lcl + lvc ~ c(0.45, 0.01, 1, 0.01, -0.01, 3.45) }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc }) } mod2 <- mod |> ini( ~ lka) expect_equal(mod2$omega, lotri(lcl + lvc ~ c(1, -0.01, 3.45))) # negative and zero mod <- function() { ini({ lka <- 0.45 lcl <- -1 lvc <- 0 }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc }) } mod2 <- mod |> ini( ~ lcl) expect_equal(mod2$omega, lotri(lcl ~ 1)) mod2 <- mod |> ini( ~ lvc) expect_equal(mod2$omega, lotri(lvc ~ 1)) mod3 <- mod2 |> ini( ~ lvc) expect_equal(mod3$omega, NULL) mod4 <- mod3 |> ini( ~ lvc) expect_equal(mod4$omega, lotri(lvc ~ 1)) }) test_that("change ini variable to covariate with -", { mod <- function() { ini({ lka + lcl + lvc ~ c(0.45, 0.01, 1, 0.01, -0.01, 3.45) }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc }) } mod2 <- mod |> ini(-lka) expect_equal(mod2$allCovs, "lka") expect_equal(mod2$omega, lotri(lcl + lvc ~ c(1, -0.01, 3.45))) mod <- function() { ini({ lka ~ 0.45 lcl ~ 1 lvc ~ 3.45 }) model({ ka <- exp(lka) cl <- exp(lcl) vc <- exp(lvc) kel <- cl / vc d/dt(depot) <- -ka*depot d/dt(central) <- ka*depot-kel*central cp <- central / vc }) } mod2 <- mod |> ini(-lka) expect_equal(mod2$allCovs, "lka") }) }