Add set_nd_nq previously in pfm

pfm depends on mkin anyways, so reexporting set_nd_nq and
set_nd_nq_focus in pfm should provide reasonable continuity.

3 files changed, 90 insertions, 4 deletions

diff --git a/tests/testthat/print_sfo_saem_1.txt b/tests/testthat/print_sfo_saem_1.txt
index a11e1e96..34eea058 100644
--- a/tests/testthat/print_sfo_saem_1.txt
+++ b/tests/testthat/print_sfo_saem_1.txt
@@ -7,13 +7,13 @@ Data:
 
 Likelihood computed by importance sampling
    AIC  BIC logLik
-  1311 1315   -649
+  1312 1316   -650
 
 Fitted parameters:
             estimate lower upper
-parent_0       1e+02 99.13 1e+02
+parent_0       1e+02 99.28 1e+02
 k_parent       4e-02  0.03 4e-02
 a.1            9e-01  0.75 1e+00
 b.1            5e-02  0.04 5e-02
-SD.parent_0    7e-01 -1.09 3e+00
+SD.parent_0    2e-01 -6.33 7e+00
 SD.k_parent    3e-01  0.20 4e-01
diff --git a/tests/testthat/summary_hfit_sfo_tc.txt b/tests/testthat/summary_hfit_sfo_tc.txt
index ad701cee..e3e2f7e4 100644
--- a/tests/testthat/summary_hfit_sfo_tc.txt
+++ b/tests/testthat/summary_hfit_sfo_tc.txt
@@ -45,7 +45,7 @@ SD.log_k_parent  0.3   0.1   0.4
 
 Variance model:
     est. lower upper
-a.1 0.91  0.64  1.17
+a.1 0.90  0.64  1.17
 b.1 0.05  0.04  0.06
 
 Backtransformed parameters:
diff --git a/tests/testthat/test_set_nd.R b/tests/testthat/test_set_nd.R
new file mode 100644
index 00000000..232e7c62
--- /dev/null
+++ b/tests/testthat/test_set_nd.R
@@ -0,0 +1,86 @@
+context("Processing of residue series")
+
+# FOCUS (2014) page 76 (parent) and page 132 (metabolite)
+
+parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")
+parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")
+parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")
+metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")
+
+test_that("Simple residue series are processed as intended", {
+
+  expect_equal(set_nd_nq(parent_1, 0.02),
+    c(.12, .09, .05, .03, .01, rep(NA, 5)))
+
+  expect_equal(set_nd_nq(parent_2, 0.02, loq = 0.05),
+    c(.12, .09, .05, .03, .01, .01, .03, .01, NA, NA))
+
+  expect_equal(set_nd_nq(metabolite, 0.02, loq = 0.05),
+    c(NA, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
+
+  expect_equal(set_nd_nq(c("nd", 1, 0.2, "nd"), 0.1),
+    c(NA, 1, 0.2, 0.05))
+
+})
+
+test_that("Simple residue series are processed as in the FOCUS guidance", {
+
+  # Parent 1
+  expect_error(set_nd_nq_focus(parent_1, 0.02),
+    "You need to specify an LOQ")
+  expect_equal(set_nd_nq_focus(parent_1, 0.02, 0.05),
+    c(.12, .09, .05, .03, .01, rep(NA, 5)))
+
+  # Parent 2
+  expect_equal(set_nd_nq_focus(parent_2, 0.02, loq = 0.05),
+    c(.12, .09, .05, .03, .01, rep(NA, 5)))
+
+  # Parent 3
+  expect_equal(set_nd_nq_focus(parent_3, 0.02, loq = 0.05),
+    c(.12, .09, .05, .03, .01, .01, .06, .01, NA, NA))
+
+  # Metabolite
+  expect_equal(set_nd_nq_focus(metabolite, 0.02, loq = 0.05),
+    c(0, NA, .01, .03, .06, .1, .11, .1, .09, .05, .03, .01, NA))
+
+})
+
+test_that("Examples Boesten et al. (2015, p. 57/58) are correctly processed", {
+  table_8 <- matrix(
+    c(10, 10, rep("nd", 4),
+      10, 10, rep("nq", 2), rep("nd", 2),
+      10, 10, 10, "nq", "nd", "nd",
+      "nq", 10, "nq", rep("nd", 3),
+      "nd", "nq", "nq", rep("nd", 3),
+      rep("nd", 6), rep("nd", 6)),
+    ncol = 6, byrow = TRUE)
+  table_8_processed <- set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)
+  table_9 <- matrix(
+    c(10, 10, 0.25, 0.25, NA, NA,
+      10, 10, 1, 1, 0.25, NA,
+      10, 10, 10, 1, 0.25, NA,
+      1, 10, 1, 0.25, NA, NA,
+      0.25, 1, 1, 0.25, NA, NA,
+      NA, 0.25, 0.25, NA, NA, NA,
+      rep(NA, 6)),
+    ncol = 6, byrow = TRUE)
+  expect_equal(table_8_processed, table_9)
+
+  table_10 <- matrix(
+    c(10, 10, rep("nd", 4),
+      10, 10, rep("nd", 4),
+      10, 10, 10, rep("nd", 3),
+      "nd", 10, rep("nd", 4),
+      rep("nd", 18)),
+    ncol = 6, byrow = TRUE)
+  table_10_processed <- set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)
+  table_11 <- matrix(
+    c(10, 10, 0.25, rep(NA, 3),
+      10, 10, 0.25, rep(NA, 3),
+      10, 10, 10, 0.25, NA, NA,
+      0.25, 10, 0.25, rep(NA, 3),
+      NA, 0.25, rep(NA, 4),
+      rep(NA, 12)),
+    ncol = 6, byrow = TRUE)
+  expect_equal(table_10_processed, table_11)
+})