tests/testthat/test-ui.R

In nlmixr2/rxode2: Facilities for Simulating from ODE-Based Models

rxTest({
  test_that("comments are parsed correctly", {
    cmt <- c("function() {", "      ini({", "        ## You may label each parameter with a comment",
             "        tka <- 0.45 # Log Ka", "        tcl <- log(c(0, 2.7, 100)) # Log Cl",
             "        ## This works with interactive models", "        ## You may also label the preceding line with label(\"label text\")",
             "        tv <- 3.45; label(\"log V\")", "        ## the label(\"Label name\") works with all models",
             "        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)", "      })", "    }")

    eq <- c("function () ", "{", "    ini({", "        tka <- 0.45", "        label(\"Log Ka\")",
            "        tcl <- log(c(0, 2.7, 100))", "        label(\"Log Cl\")",
            "        tv <- 3.45", "        label(\"log V\")", "        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)",
            "    })", "}")

    suppressMessages(
      expect_equal(.rxReplaceCommentWithLabel(cmt), eq)
    )

    # Leave comment labels in here as they are required for equality testing below
    one.cmt <- function() {
      ini({
        ## You may label each parameter with a comment
        tka <- 0.45 # Log Ka
        tcl <- log(c(0, 2.7, 100)) # Log Cl
        ## This works with interactive models
        ## You may also label the preceding line with label("label text")
        tv <- 3.45; label("log V")
        ## the label("Label name") works with all models
        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)
      })
    }

    suppressMessages(
      str <- .rxFunction2string(one.cmt)
    )
    if (!is.null(attr(one.cmt, "srcref"))) {
      expect_equal(str, eq)
      attr(one.cmt, "srcref") <- NULL
    }

    # Leave comment labels in here as they are required for equality testing below
    one.cmt <- function() {
      ini({
        ## You may label each parameter with a comment
        tka <- 0.45 # Log Ka
        tcl <- log(c(0, 2.7, 100)) # Log Cl
        ## This works with interactive models
        ## You may also label the preceding line with label("label text")
        tv <- 3.45; label("log V")
        ## the label("Label name") works with all models
        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) | tmp
      })
    }

    suppressMessages(
      mkstr <- .rxFunction2string(one.cmt)
    )
    expect_equal(mkstr,
                 c("function () ", "{", "    ini({", "        tka <- 0.45", "        label(\"Log Ka\")",
                   "        tcl <- log(c(0, 2.7, 100))", "        label(\"Log Cl\")",
                   "        tv <- 3.45", "        label(\"log V\")", "        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) | tmp",
                   "    })", "}"))

  })

  test_that("meta information parsing", {

    one.cmt <- function() {
      meta1 <- "meta"
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        eta.ka ~ 0.6
        eta.cl ~ 0.3
        eta.v ~ 0.1
        add.sd <- 0.7
      })
      meta2 <- "meta2"
      model({
        ka <- exp(tka + eta.ka)
        cl <- exp(tcl + eta.cl)
        v <- exp(tv + eta.v)
        linCmt() ~ add(add.sd)
      })
    }

    tmp1 <- one.cmt()

    expect_true(inherits(as.function(tmp1), "function"))

    expect_equal(tmp1$meta$meta1, "meta")
    expect_equal(tmp1$meta$meta2, "meta2")

    one.cmt <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        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)
      })
    }

    one.cmt <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        eta.ka ~ 0.6
        eta.cl ~ 0.3
        eta.v ~ 0.1
        add.sd <- 0.7
        lambda <- c(-2, 1, 2)
      })
      model({
        ka <- exp(tka + eta.ka)
        cl <- exp(tcl + eta.cl)
        v <- exp(tv + eta.v)
        linCmt() ~ add(add.sd) + boxCox(lambda) | tmp
      })
    }

    one.cmt <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        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)
        lambda <- 3 + v
        linCmt() ~ add(add.sd) + boxCox(lambda) | tmp
      })
    }

    one.cmt <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        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() ~ lnorm(add.sd) | tmp
      })
    }

    one.cmt <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        eta.ka ~ 0.6
        eta.cl ~ 0.3
        eta.v ~ 0.1
        add.sd <- 0.7
        bLambda <- c(0, 3)
      })
      model({
        ka <- exp(tka + eta.ka)
        cl <- exp(tcl + eta.cl)
        v <- exp(tv + eta.v)
        linCmt() ~ lnorm(add.sd) | tmp
        tmp2 ~ dpois(bLambda)
      })
    }

    cov <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        tvp <- 3.45
        cl.wt <- 0.1
        v.wt <- 0.1
        cl.sex <- 0.1
        v.sex <- 0.1
        cl.age <- 0.1
        v.age <- 0.1
        vp.wt <- 1
        vp.sex <- 1
        vp.age <- 1
        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 + log(wt / 70) * cl.wt + sex * cl.sex + age * cl.age + 3)
        v  <- exp(tv + eta.v + wt * v.wt + sex * v.sex + age * v.age + 2)
        vp <- exp(tvp + wt * vp.wt + sex * vp.sex + age * vp.age)
        d/dt(depot) = -ka * depot
        d/dt(center) = ka * depot - cl/v * center
        cp = center/v
        cp ~ add(add.sd)
      })
    }

    pk.turnover.emax <- function() {
      ini({
        tktr <- log(1)
        tka <- log(1)
        tcl <- log(0.1)
        tv <- log(10)
        ##
        eta.ktr ~ 1
        eta.ka ~ 1
        eta.cl ~ 2
        eta.v ~ 1
        prop.err <- 0.1
        pkadd.err <- 0.1
        ##
        temax <- logit(0.8)
        #temax <- 7.5
        tec50 <- log(0.5)
        tkout <- log(0.05)
        te0 <- log(100)
        ##
        eta.emax ~ .5
        eta.ec50  ~ .5
        eta.kout ~ .5
        eta.e0 ~ .5
        ##
        pdadd.err <- 10
      })
      model({
        ktr <- exp(tktr + eta.ktr)
        ka <- exp(tka + eta.ka)
        cl <- exp(tcl + eta.cl)
        v <- exp(tv + eta.v)
        ##
        #poplogit = log(temax/(1-temax))
        emax=expit(temax+eta.emax)
        #logit=temax+eta.emax
        ec50 =  exp(tec50 + eta.ec50)
        kout = exp(tkout + eta.kout)
        e0 = exp(te0 + eta.e0)
        ##
        DCP = center/v
        PD=1-emax*DCP/(ec50+DCP)
        ##
        effect(0) = e0
        kin = e0*kout
        ##
        d/dt(depot) = -ktr * depot
        d/dt(gut) =  ktr * depot -ka * gut
        d/dt(center) =  ka * gut - cl / v * center
        d/dt(effect) = kin*PD -kout*effect
        ##
        cp = center / v
        cp ~ prop(prop.err) + add(pkadd.err)
        effect ~ add(pdadd.err)
      })
    }

    turnover.emax.noeta <- function() {
      ini({
        tktr <- log(1)
        tka <- log(1)
        tcl <- log(0.1)
        tv <- log(10)
        ##
        prop.err <- 0.1
        pkadd.err <- 0.1
        ##
        temax <- logit(0.8)
        #temax <- 7.5
        tec50 <- log(0.5)
        tkout <- log(0.05)
        te0 <- log(100)
        ##
        pdadd.err <- 10
      })
      model({
        ktr <- exp(tktr)
        ka <- exp(tka)
        cl <- exp(tcl)
        v <- exp(tv)
        ##
        #poplogit = log(temax/(1-temax))
        emax=expit(temax)
        ec50 =  exp(tec50)
        kout = exp(tkout)
        e0 = exp(te0)
        ##
        DCP = center/v
        PD=1-emax*DCP/(ec50+DCP)
        ##
        effect(0) = e0
        kin = e0*kout
        ##
        d/dt(depot) = -ktr * depot
        d/dt(gut) =  ktr * depot -ka * gut
        d/dt(center) =  ka * gut - cl / v * center
        d/dt(effect) = kin*PD -kout*effect
        ##
        cp = center / v
        cp ~ prop(prop.err) + add(pkadd.err)
        effect ~ add(pdadd.err)
      })
    }

    f <- function() {
      ini({
        lKA <- log(0.294)
        CL <- 18.6
        V2 <- 40.2
        Q <- 10.5
        V3 <- 297
        Kin <- 1
        Kout <- 1
        EC50 <- 200
        eta.ka ~ 0.12
        prop.sd ~ 0.2
      })
      model({
        KA <- exp(lKA + eta.ka)
        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
        d/dt(eff) <- Kin - Kout*(1-C2/(EC50+C2))*eff
        eff(0) <- 1
        C2 ~ prop(prop.sd)
      })
    }

    expect_error(f(), "prop.sd")

    one.cmt <- function() {
      ini({
        tka <- 0.45
        tcl <- log(c(0, 2.7, 100))
        tv <- 3.45
        eta.ka + eta.cl ~ c(0.6,
                            0.001, 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) | tmp
        vv ~ add(add.sd)
      })
    }

    expect_error(one.cmt())
  })


  test_that("model only", {

    one.cmt <- function() {
      model({
        ka <- exp(tka + eta.ka)
        cl <- exp(tcl + eta.cl)
        v <- exp(tv + eta.v)
        add.sd <- 4 + 3
        linCmt() ~ add(add.sd)
      })
    }

    expect_error(one.cmt(), NA)


    one.cmt <- function() {
      model({
        ka <- exp(tka + eta.ka)
        cl <- exp(tcl + eta.cl)
        v <- exp(tv + eta.v)
        add.sd <- 4
        linCmt() ~ add(add.sd)
      })
    }

    expect_error(one.cmt(), NA)

  })
})