tests/Test-pdfPQ.R

In ncar: Noncompartmental Analysis for Pharmacokinetic Report

require(ncar)

# Regression test for the expected-value comparator in pdfPQ(), which carries the same
# code as NonCompart::PQNCA(). A parameter that was NA on BOTH sides - not estimable for
# that profile, and not expected to be - was counted as a difference, so feeding the
# analysis its own output back in as `expected` produced "expected-values DIFFER" and an
# overall NOT QUALIFIED for a correct analysis.

Fail = function(msg) stop(paste("Test Failed!", msg))

pdfOut = tempfile(fileext = ".pdf")
on.exit(unlink(pdfOut), add = TRUE)

d = data.frame(ID   = rep(1:2, each = 6),
               Time = rep(c(0, 1, 2, 4, 8, 24), 2),
               Conc = c(0, 10, 16, 12, 8, 1,
                        0,  0,  5,  0, 0, 0))

r = NonCompart::tblNCA(d, key = "ID", colTime = "Time", colConc = "Conc", dose = 1, R2ADJ = 0)
if (!is.na(r$LAMZHL[2])) Fail("fixture is wrong: subject 2 should have no terminal phase")

expected = r[, c("ID", "CMAX", "AUCLST", "AUCIFO", "LAMZHL")]

pq = pdfPQ(fileName = pdfOut, concData = d, key = "ID", colTime = "Time", colConc = "Conc",
           dose = 1, R2ADJ = 0, expected = expected)

bad = Filter(function(e) !isTRUE(e$ok), pq$expected)
if (length(bad) > 0) {
  Fail(paste("self-comparison reported", length(bad), "difference(s); first:",
             bad[[1]]$param, "expected =", bad[[1]]$exp, "observed =", bad[[1]]$obs))
}
if (!isTRUE(pq$reproducible)) Fail("re-running the same analysis was reported as irreproducible")

## a genuine disagreement must still be caught
e2 = expected
e2$AUCLST[1] = e2$AUCLST[1] * 2
pq = pdfPQ(fileName = pdfOut, concData = d, key = "ID", colTime = "Time", colConc = "Conc",
           dose = 1, R2ADJ = 0, expected = e2)
bad = Filter(function(e) !isTRUE(e$ok), pq$expected)
if (length(bad) != 1) Fail(paste("a doubled AUCLST should be 1 difference, got", length(bad)))
if (bad[[1]]$param != "AUCLST") Fail(paste("wrong parameter flagged:", bad[[1]]$param))

cat("Test-pdfPQ.R: OK\n")