rxTest({
  rxWithSeed(
    42,
    {
      m1 <- rxode2({
        CL ~ (1 - 0.2 * SEX) * (0.807 + 0.00514 * (CRCL - 91.2)) * exp(eta.cl)
        V1 ~ 4.8 * exp(eta.v1)
        Q ~ (3.46 + 0.0593 * (WT - 75.1)) * exp(eta.q)
        V2 ~ 1.93 * (3.13 + 0.0458 * (WT - 75.1)) * exp(eta.v2)
        cp <- max(linCmt() + err.sd, 0.01)
        if (cp == 0.01) cp <- NA
        mSEX <- SEX
        mWT <- WT
        mCRCL <- CRCL
      })

      # Make non-random covariates for testing
      AGE <- round(seq(18, 18 + 29))
      SEX <- c(rep(0, 15), rep(1, 15))
      WT <- seq(60, 60 + 29)
      CRCL <- seq(30, 30 + 29)
      ## id is in lower case to match the event table
      cov.df <- dplyr::tibble(id = seq_along(AGE), AGE = AGE, SEX = SEX, WT = WT, CRCL = CRCL)

      s <- c(0, 0.25, 0.5, 0.75, 1, 1.5, seq(2, 24, by = 1))
      ## Add 10% diff
      s <- lapply(s, function(x) {
        d <- x * 0.1
        c(x - d, x + d)
      })

      e <- et() %>%
        ## Specify the id and weight based dosing from covariate data.frame
        ## This requires rxode2 XXX
        et(id = cov.df$id, amt = 6 * cov.df$WT, rate = 6 * cov.df$WT) %>%
        ## Sampling is added for each ID
        et(s) %>%
        as.data.frame() %>%
        ## Merge the event table with the covarite information
        merge(cov.df, by = "id") %>%
        dplyr::as_tibble()

      e2 <- et() %>%
        ## Specify the id and weight based dosing from covariate data.frame
        ## This requires rxode2 XXX
        et(id = cov.df$id, amt = 6 * cov.df$WT, rate = 6 * cov.df$WT) %>%
        ## Sampling is added for each ID
        et(s)

      e$WT <- e$WT + e$time / 30
      e$CRCL <- e$CRCL + e$time / 30

      test_that("test resampleID behavior", {
        for (nStud in c(1, 2)) {
          f1 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        addDosing = TRUE, nStud = nStud
                        )

          if (nStud == 1) {
            expect_equal(f1$WT, e$WT)
            expect_equal(f1$CRCL, e$CRCL)
            expect_equal(f1$SEX, e$SEX)
          }

          f2 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        resample = c("SEX", "WT", "CRCL"),
                        resampleID = TRUE,
                        addDosing = TRUE, nStud = nStud
                        )

          expect_equal(f2$mWT, f2$WT)
          expect_equal(f2$mCRCL, f2$CRCL)
          expect_equal(f2$mSEX, f2$SEX)

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r2 <- f2[!duplicated(f2$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1, r2)))

          ## now test that the covariates are all shifted correctly
          expect_true(all(r1$WT - r1$CRCL == 30))
          expect_true(all(r2$WT - r2$CRCL == 30))

          expect_true(all(r1$SEX[r1$CRCL <= 44] == 0))
          expect_true(all(r1$SEX[r1$CRCL > 44] == 1))

          expect_true(all(r2$SEX[r2$CRCL <= 44] == 0))
          expect_true(all(r2$SEX[r2$CRCL > 44] == 1))

          f3 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        resample = c("SEX", "WT", "CRCL"),
                        resampleID = FALSE,
                        addDosing = TRUE, nStud = nStud
                        )

          expect_equal(f3$mWT, f3$WT)
          expect_equal(f3$mCRCL, f3$CRCL)
          expect_equal(f3$mSEX, f3$SEX)

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r3 <- f3[!duplicated(f3$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1, r3)))

          ## Now these should be false
          expect_false(all(r3$WT - r3$CRCL == 30))

          expect_false(all(r3$SEX[r3$CRCL <= 44] == 0))
          expect_false(all(r3$SEX[r3$CRCL > 44] == 1))


          f3 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        resample = TRUE,
                        resampleID = FALSE,
                        addDosing = TRUE, nStud = nStud
                        )

          expect_equal(f3$mWT, f3$WT)
          expect_equal(f3$mCRCL, f3$CRCL)
          expect_equal(f3$mSEX, f3$SEX)

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r3 <- f3[!duplicated(f3$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1, r3)))

          ## Now these should be false
          expect_false(all(r3$WT - r3$CRCL == 30))

          expect_false(all(r3$SEX[r3$CRCL <= 44] == 0))
          expect_false(all(r3$SEX[r3$CRCL > 44] == 1))

          f2 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        resample = TRUE,
                        resampleID = TRUE,
                        addDosing = TRUE, nStud = nStud
                        )

          expect_equal(f2$mWT, f2$WT)
          expect_equal(f2$mCRCL, f2$CRCL)
          expect_equal(f2$mSEX, f2$SEX)

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r2 <- f2[!duplicated(f2$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1, r2)))

          ## now test that the covariates are all shifted correctly
          expect_true(all(r1$WT - r1$CRCL == 30))
          expect_true(all(r2$WT - r2$CRCL == 30))

          expect_true(all(r1$SEX[r1$CRCL <= 44] == 0))
          expect_true(all(r1$SEX[r1$CRCL > 44] == 1))

          expect_true(all(r2$SEX[r2$CRCL <= 44] == 0))
          expect_true(all(r2$SEX[r2$CRCL > 44] == 1))

          if (nStud == 1) {
            f1 <- rxSolve(m1, e,
                          ## Lotri uses lower-triangular matrix rep. for named matrix
                          omega = lotri(
                            eta.cl ~ .306,
                            eta.q ~ 0.0652,
                            eta.v1 ~ .567,
                            eta.v2 ~ .191
                          ),
                          sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                          resample = FALSE,
                          addDosing = TRUE, nStud = nStud
                          )

            expect_equal(f1$WT, e$WT)
            expect_equal(f1$CRCL, e$CRCL)
            expect_equal(f1$SEX, e$SEX)
          }
        }
      })


      # resample tests; time invariant

      nsub <- 30
      # Simulate Weight based on age and gender
      AGE <- round(runif(nsub, min = 18, max = 70))
      SEX <- round(runif(nsub, min = 0, max = 1))
      HTm <- round(rnorm(nsub, 176.3, 0.17 * sqrt(4482)), digits = 1)
      HTf <- round(rnorm(nsub, 162.2, 0.16 * sqrt(4857)), digits = 1)
      WTm <- round(exp(3.28 + 1.92 * log(HTm / 100)) * exp(rnorm(nsub, 0, 0.14)), digits = 1)
      WTf <- round(exp(3.49 + 1.45 * log(HTf / 100)) * exp(rnorm(nsub, 0, 0.17)), digits = 1)
      WT <- ifelse(SEX == 1, WTf, WTm)
      CRCL <- round(runif(nsub, 30, 140))
      ## id is in lower case to match the event table
      cov.df <- dplyr::tibble(id = seq_along(AGE), AGE = AGE, SEX = SEX, WT = WT, CRCL = CRCL)

      s <- c(0, 0.25, 0.5, 0.75, 1, 1.5, seq(2, 24, by = 1))
      ## Add 10% diff
      s <- lapply(s, function(x) {
        d <- x * 0.1
        c(x - d, x + d)
      })

      e <- et(time.units = "hr") %>%
        ## Specify the id and weight based dosing from covariate data.frame
        ## This requires rxode2 XXX
        et(id = cov.df$id, amt = 6 * cov.df$WT, rate = 6 * cov.df$WT) %>%
        ## Sampling is added for each ID
        et(s) %>%
        as.data.frame() %>%
        ## Merge the event table with the covarite information
        merge(cov.df, by = "id") %>%
        dplyr::as_tibble()

      e2 <- et(time.units = "hr") %>%
        ## Specify the id and weight based dosing from covariate data.frame
        ## This requires rxode2 XXX
        et(id = cov.df$id, amt = 6 * cov.df$WT, rate = 6 * cov.df$WT) %>%
        ## Sampling is added for each ID
        et(s)


      test_that("resample tests: time invariant", {
        for (resampleID in c(TRUE, FALSE)) {
          f1 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE
                        )

          expect_equal(f1$mWT, f1$WT)
          expect_equal(f1$mCRCL, f1$CRCL)

          f2 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        resample = c("SEX", "WT", "CRCL"),
                        resampleID = resampleID
                        )

          expect_equal(f2$mWT, f2$WT)
          expect_equal(f2$mCRCL, f2$CRCL)

          f3 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), keep = c("SEX", "WT", "CRCL"),
                        resample = c("SEX", "WT", "CRCL"),
                        resampleID = resampleID
                        )

          expect_equal(f3$mWT, f3$WT)
          expect_equal(f3$mCRCL, f3$CRCL)

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r2 <- f2[!duplicated(f2$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1, r2)))

          r3 <- f3[!duplicated(f3$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1, r3)))

          ## Now try icov option

          f1 <-
            expect_warning(
              rxSolve(m1, e2,
                      iCov = cov.df,
                      ## Lotri uses lower-triangular matrix rep. for named matrix
                      omega = lotri(
                        eta.cl ~ .306,
                        eta.q ~ 0.0652,
                        eta.v1 ~ .567,
                        eta.v2 ~ .191
                      ),
                      sigma = lotri(err.sd ~ 0.5), addCov = TRUE
                      )
            )

          expect_equal(f1$mWT, f1$WT)
          expect_equal(f1$mCRCL, f1$CRCL)

          f2 <-
            expect_warning(
              rxSolve(m1, e2,
                      iCov = cov.df,
                      ## Lotri uses lower-triangular matrix rep. for named matrix
                      omega = lotri(
                        eta.cl ~ .306,
                        eta.q ~ 0.0652,
                        eta.v1 ~ .567,
                        eta.v2 ~ .191
                      ),
                      sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                      resample = c("SEX", "WT", "CRCL"),
                      resampleID = resampleID
                      )
            )

          expect_equal(f2$mWT, f2$WT)
          expect_equal(f2$mCRCL, f2$CRCL)

          f3 <-
            expect_warning(
              rxSolve(m1, e2,
                      iCov = cov.df,
                      ## Lotri uses lower-triangular matrix rep. for named matrix
                      omega = lotri(
                        eta.cl ~ .306,
                        eta.q ~ 0.0652,
                        eta.v1 ~ .567,
                        eta.v2 ~ .191
                      ),
                      sigma = lotri(err.sd ~ 0.5),
                      keep = c("SEX", "WT", "CRCL"),
                      resample = c("SEX", "WT", "CRCL"),
                      resampleID = resampleID
                      )
            )

          expect_equal(f3$mWT, f3$WT)
          expect_equal(f3$mCRCL, f3$CRCL)
        }
      })

      # resample tests; time varying

      # Make these time-varying covariates

      e$WT <- e$WT + rnorm(length(e$WT), sd = 1)
      e$CRCL <- e$CRCL + rnorm(length(e$CRCL), sd = 1)

      test_that("resample tests: time varying", {
        for (resampleID in c(TRUE, FALSE)) {
          f1 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE
                        )

          expect_equal(f1$mWT, f1$WT)
          expect_equal(f1$mCRCL, f1$CRCL)

          f2 <- rxSolve(m1, e,
                        ## Lotri uses lower-triangular matrix rep. for named matrix
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), addCov = TRUE,
                        resample = c("SEX", "WT", "CRCL"),
                        resampleID = resampleID
                        )

          expect_equal(f2$mWT, f2$WT)
          expect_equal(f2$mCRCL, f2$CRCL)

          f3 <- rxSolve(m1, e,
                        omega = lotri(
                          eta.cl ~ .306,
                          eta.q ~ 0.0652,
                          eta.v1 ~ .567,
                          eta.v2 ~ .191
                        ),
                        sigma = lotri(err.sd ~ 0.5), keep = c("SEX", "WT", "CRCL"),
                        resample = c("SEX", "WT", "CRCL"),
                        resampleID = resampleID
                        )

          expect_equal(f3$mWT, f3$WT)
          expect_equal(f3$mCRCL, f3$CRCL)

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r2 <- f2[!duplicated(f2$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1$WT, r2$WT)))

          ## Now test keep case

          r1 <- f1[!duplicated(f1$id), c("id", "SEX", "WT", "CRCL")]
          r3 <- f3[!duplicated(f3$id), c("id", "SEX", "WT", "CRCL")]

          expect_false(isTRUE(all.equal(r1$WT, r3$WT)))
        }
      })
    }
  )
})