diff options
Diffstat (limited to 'tests/testthat')
| -rw-r--r-- | tests/testthat/test_nlmixr.r | 194 |
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) +# |