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Diffstat (limited to 'tests/testthat')
| -rw-r--r-- | tests/testthat/test_nlmixr.r | 99 |
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) + |