tests/testthat/test-plot.R

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

rxTest({

  expect_plotlog <- function(o, timex, logx, logy, dat) {
    # Checking for the correct type for logx and logy is nontrivial, so j
    expect_named(o, c("timex", "logx", "logy", "dat"))
    if (is.null(timex)) {
      expect_null(o$timex)
    } else {
      expect_equal(o$timex, timex)
    }
    if (is.null(logx)) {
      expect_null(o$logx)
    } else {
      expect_type(o$logx, "list")
      expect_length(o$logx, 1)
      expect_s3_class(o$logx[[1]], logx)
    }
    if (is.null(logy)) {
      expect_null(o$logy)
    } else {
      expect_type(o$logy, "list")
      expect_length(o$logy, 1)
      expect_s3_class(o$logy[[1]], logy)
    }
    expect_equal(o$dat, dat)
  }

  test_that(".plotLog works without xgxr", {
    skip_on_os("mac")
    d <- data.frame(time=-1:2, conc=0:3)
    expect_equal(
      .plotLog(.dat=d, .timex="A", log=""),
      list(
        timex="A",
        logx=NULL,
        logy=NULL,
        dat=d
      )
    )
    expect_plotlog(
      .plotLog(.dat=d, .timex="A", log="x"),
      timex=NULL, logx="ScaleContinuousPosition", logy=NULL, dat=d[-(1:2), ]
    )
    expect_plotlog(
      .plotLog(.dat=d, .timex="A", log="y"),
      timex="A", logx=NULL, logy="ScaleContinuousPosition", dat=d
    )
    expect_plotlog(
      .plotLog(.dat=d, .timex="A", log="xy"),
      timex=NULL, logx="ScaleContinuousPosition", logy="ScaleContinuousPosition", dat=d[-(1:2), ]
    )
  })

  test_that(".plotLog works with xgxr", {
    skip_if_not_installed("xgxr")
    skip_on_os("mac")
    skip("See https://github.com/Novartis/xgxr/issues/50 for why xgxr is not uniquely tested as of 2022-03-15")
    current_xgxr_option <- getOption("rxode2.xgxr")
    withr::with_options(
      list(rxode2.xgxr=TRUE), {
        d <- data.frame(time=-1:2, conc=0:3)
        # Insert tests here
      }
    )
  })

  test_that(".plotLog gives expected errors", {
    skip_on_os("mac")
    expect_error(.plotLog(log=c("x", "y")))
    expect_error(.plotLog(log=1))
    expect_error(.plotLog(log="foo"))
    expect_error(.plotLog(log=c("x", "y")))
    expect_error(.plotLog(.dat=data.frame(A=1), log="x", .timex="A"))
    # Time column is only required when log="x"
    expect_silent(.plotLog(.dat=data.frame(A=1), log="y", .timex="A"))
  })

  test_that("plot() with invalid component throws an error", {
    skip_on_os("mac")

    pheno2 <- function() {
      ini({
        tcl <- log(0.008)
        tv <-  log(0.6)
        eta.cl + eta.v ~ c(1,
                           0.01, 1)
        add.err <- 0.1
      })
      model({
        cl <- exp(tcl + eta.cl) # individual value of clearance
        v <- exp(tv + eta.v)    # individual value of volume
        ke <- cl / v            # elimination rate constant
        d/dt(A1) = - ke * A1    # model differential equation
        cp = A1 / v             # concentration in plasma
        cp ~ add(add.err)  # define error model
      })
    }

    simdata <- data.frame(time=1:10, ID=factor(c("A", "B")))

    sim <- rxSolve(pheno2, events=simdata)

    expect_error(plot(sim, "foo"))
    expect_warning(plot(sim, sim, "foo"))
    expect_error(plot(sim), NA)
  })

})