Let backtransform_odeparms handle nlmixr formation fractions

Also adapt summary.nlmixr.mmkin to correctly handle the way
formation fractions are translated to nlmixr

1 files changed, 97 insertions, 97 deletions

diff --git a/tests/testthat/test_nlmixr.r b/tests/testthat/test_nlmixr.r
index e3bd3d66..dcbb50ac 100644
--- a/tests/testthat/test_nlmixr.r
+++ b/tests/testthat/test_nlmixr.r
@@ -1,99 +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)
-
+# 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)
+#