Translate formation fractions to nlmixr language

Works for the dimethenamid data, at least for FOCEI. Very little testing
yet. The summary function does not yet handle the new transformations
of formation fractions (that are in fact very old, as they were used
in the very first version of mkin). The test file has no tests yet, just
some code that may be used for testing.

1 files changed, 99 insertions, 0 deletions

diff --git a/tests/testthat/test_nlmixr.r b/tests/testthat/test_nlmixr.r
new file mode 100644
index 00000000..e3bd3d66
--- /dev/null
+++ b/tests/testthat/test_nlmixr.r
@@ -0,0 +1,99 @@
+
+
+dmta_ds <- lapply(1:8, function(i) {
+  ds_i <- dimethenamid_2018$ds[[i]]$data
+  ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+  ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+  ds_i
+})
+names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+dmta_ds[["Borstel"]] <- rbind(dmta_ds[["Borstel 1"]], dmta_ds[["Borstel 2"]])
+dmta_ds[["Borstel 1"]] <- NULL
+dmta_ds[["Borstel 2"]] <- NULL
+dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+dmta_ds[["Elliot 1"]] <- NULL
+dmta_ds[["Elliot 2"]] <- NULL
+dfop_sfo3_plus <- mkinmod(
+  DMTA = mkinsub("DFOP", c("M23", "M27", "M31")),
+  M23 = mkinsub("SFO"),
+  M27 = mkinsub("SFO"),
+  M31 = mkinsub("SFO", "M27", sink = FALSE),
+  quiet = TRUE
+)
+f_dmta_mkin_tc <- mmkin(
+  list("DFOP-SFO3+" = dfop_sfo3_plus),
+  dmta_ds, quiet = TRUE, error_model = "tc")
+
+d_dmta_nlmixr <- nlmixr_data(f_dmta_mkin_tc)
+m_dmta_nlmixr <- function ()
+{
+    ini({
+        DMTA_0 = 98.7697627680706
+        eta.DMTA_0 ~ 2.35171765917765
+        log_k_M23 = -3.92162409637283
+        eta.log_k_M23 ~ 0.549278519419884
+        log_k_M27 = -4.33774620773911
+        eta.log_k_M27 ~ 0.864474956685295
+        log_k_M31 = -4.24767627688461
+        eta.log_k_M31 ~ 0.750297149164171
+        f_DMTA_tffm0_1_qlogis = -2.092409
+        eta.f_DMTA_tffm0_1_qlogis ~ 0.3
+        f_DMTA_tffm0_2_qlogis = -2.180576
+        eta.f_DMTA_tffm0_2_qlogis ~ 0.3
+        f_DMTA_tffm0_3_qlogis = -2.142672
+        eta.f_DMTA_tffm0_3_qlogis ~ 0.3
+        log_k1 = -2.2341008812259
+        eta.log_k1 ~ 0.902976221565793
+        log_k2 = -3.7762779983269
+        eta.log_k2 ~ 1.57684519529298
+        g_qlogis = 0.450175725479389
+        eta.g_qlogis ~ 3.0851335687675
+        sigma_low_DMTA = 0.697933852349996
+        rsd_high_DMTA = 0.0257724286053519
+        sigma_low_M23 = 0.697933852349996
+        rsd_high_M23 = 0.0257724286053519
+        sigma_low_M27 = 0.697933852349996
+        rsd_high_M27 = 0.0257724286053519
+        sigma_low_M31 = 0.697933852349996
+        rsd_high_M31 = 0.0257724286053519
+    })
+    model({
+        DMTA_0_model = DMTA_0 + eta.DMTA_0
+        DMTA(0) = DMTA_0_model
+        k_M23 = exp(log_k_M23 + eta.log_k_M23)
+        k_M27 = exp(log_k_M27 + eta.log_k_M27)
+        k_M31 = exp(log_k_M31 + eta.log_k_M31)
+        k1 = exp(log_k1 + eta.log_k1)
+        k2 = exp(log_k2 + eta.log_k2)
+        g = expit(g_qlogis + eta.g_qlogis)
+        f_DMTA_tffm0_1 = expit(f_DMTA_tffm0_1_qlogis + eta.f_DMTA_tffm0_1_qlogis)
+        f_DMTA_tffm0_2 = expit(f_DMTA_tffm0_2_qlogis + eta.f_DMTA_tffm0_2_qlogis)
+        f_DMTA_tffm0_3 = expit(f_DMTA_tffm0_3_qlogis + eta.f_DMTA_tffm0_3_qlogis)
+        f_DMTA_to_M23 = f_DMTA_tffm0_1
+        f_DMTA_to_M27 = (1 - f_DMTA_tffm0_1) * f_DMTA_tffm0_2
+        f_DMTA_to_M31 = (1 - f_DMTA_tffm0_1) * (1 - f_DMTA_tffm0_2) * f_DMTA_tffm0_3
+        d/dt(DMTA) = -((k1 * g * exp(-k1 * time) + k2 * (1 -
+            g) * exp(-k2 * time))/(g * exp(-k1 * time) + (1 -
+            g) * exp(-k2 * time))) * DMTA
+        d/dt(M23) = +f_DMTA_to_M23 * ((k1 * g * exp(-k1 * time) +
+            k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) +
+            (1 - g) * exp(-k2 * time))) * DMTA - k_M23 * M23
+        d/dt(M27) = +f_DMTA_to_M27 * ((k1 * g * exp(-k1 * time) +
+            k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) +
+            (1 - g) * exp(-k2 * time))) * DMTA - k_M27 * M27 +
+            k_M31 * M31
+        d/dt(M31) = +f_DMTA_to_M31 * ((k1 * g * exp(-k1 * time) +
+            k2 * (1 - g) * exp(-k2 * time))/(g * exp(-k1 * time) +
+            (1 - g) * exp(-k2 * time))) * DMTA - k_M31 * M31
+        DMTA ~ add(sigma_low_DMTA) + prop(rsd_high_DMTA)
+        M23 ~ add(sigma_low_M23) + prop(rsd_high_M23)
+        M27 ~ add(sigma_low_M27) + prop(rsd_high_M27)
+        M31 ~ add(sigma_low_M31) + prop(rsd_high_M31)
+    })
+}
+m_dmta_nlmixr_mkin <- nlmixr_model(f_dmta_mkin_tc, test_log_parms = TRUE)
+f_dmta_nlmixr_saem <- nlmixr(f_dmta_mkin_tc, est = "saem", control = saemControl(print = 250))
+f_dmta_nlmixr_focei <- nlmixr(f_dmta_mkin_tc, est = "focei", control = foceiControl(print = 250))
+plot(f_dmta_nlmixr_saem)
+plot(f_dmta_nlmixr_focei)
+