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Diffstat (limited to 'tests/testthat/test_nlmixr.r')
| -rw-r--r-- | tests/testthat/test_nlmixr.r | 99 |
1 files changed, 0 insertions, 99 deletions
diff --git a/tests/testthat/test_nlmixr.r b/tests/testthat/test_nlmixr.r deleted file mode 100644 index dcbb50ac..00000000 --- a/tests/testthat/test_nlmixr.r +++ /dev/null @@ -1,99 +0,0 @@ - - -# 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) -# |