RXR-2598: consolidate model compilations in test setup

tests/testthat/setup.R

@@ -1,6 +1,13 @@
+# =============================================================================
+# Shared models compiled once at test session startup
+# =============================================================================
+
+# --- Library models (standard PK models) ---
 mod_1cmt_iv <- new_ode_model("pk_1cmt_iv")
 mod_2cmt_iv <- new_ode_model("pk_2cmt_iv")
 mod_1cmt_oral <- new_ode_model("pk_1cmt_oral")
+
+# --- Custom 1cmt oral with lagtime ---
 mod_1cmt_oral_lagtime <- new_ode_model(
   code = "
     dAdt[0] = -KA * A[0]
@@ -11,7 +18,9 @@ mod_1cmt_oral_lagtime <- new_ode_model(
   dose = list(cmt = 1, bioav = 1),
   parameters = list(CL = 5, V = 50, KA = 0.5, TLAG = 0.83)
 )
-oral_1cmt_allometric <- new_ode_model( # also timevarying and dose-dependence factor
+
+# --- 1cmt oral with allometric scaling, time-varying CL, dose-dependent V ---
+oral_1cmt_allometric <- new_ode_model(
   code = "
       if(t<168.0) {
         CLi = CL * pow(WT/70, 0.75)
@@ -32,3 +41,174 @@ oral_1cmt_allometric <- new_ode_model( # also timevarying and dose-dependence fa
   declare_variables = c("CLi", "Vi"),
   parameters = list(KA = 0.5, CL = 5, V = 50)
 )
+
+# --- From test_iov.R: IOV models ---
+pars_iov <- list(
+  "kappa_CL_1" = 0,
+  "kappa_CL_2" = 0,
+  "kappa_CL_3" = 0,
+  "eta_CL" = 0,
+  "CL" = 5,
+  "V" = 50,
+  "KA" = 1
+)
+pars_iov_no_iov <- list(
+  "CL" = 5,
+  "V" = 50,
+  "KA" = 1
+)
+pk_iov_none <- new_ode_model(
+  code = "
+      dAdt[1] = -KA * A[1]
+      dAdt[2] = +KA * A[1] -(CL/V) * A[2]
+    ",
+  obs = list(cmt = 2, scale = "V"),
+  dose = list(cmt = 1, bioav = 1),
+  parameters = names(pars_iov_no_iov),
+  cpp_show_code = FALSE
+)
+pk_iov <- new_ode_model(
+  code = "
+      CL_iov = CL * exp(kappa_CL + eta_CL);
+      dAdt[1] = -KA * A[1]
+      dAdt[2] = +KA * A[1] -(CL_iov/V) * A[2]
+    ",
+  iov = list(
+    cv = list(CL = 0.2),
+    n_bins = 3
+  ),
+  obs = list(cmt = 2, scale = "V"),
+  dose = list(cmt = 1, bioav = 1),
+  declare_variables = c("kappa_CL", "CL_iov"),
+  parameters = names(pars_iov),
+  cpp_show_code = FALSE
+)
+
+# --- From test_compare_results.R ---
+dose_in_cmt_2 <- new_ode_model(
+  code = "
+      dAdt[1] = -KA * A[1];
+      dAdt[2] = KA*A[1] -(CL/V) * A[2]
+      dAdt[3] = S2*(A[2]-A[3])
+    ",
+  obs = list(cmt = 2, scale = "V"),
+  dose = list(cmt = 2),
+  cpp_show_code = FALSE
+)
+
+# --- From test_cmt_mapping.R: 1cmt oral with cmt_mapping ---
+pk1cmt_oral_cmt_mapping <- new_ode_model(
+  code = "dAdt[1] = -KA*A[1]; dAdt[2] = KA*A[1] - (CL/V)*A[2];",
+  obs = list(cmt = 2, scale = "V"),
+  cmt_mapping = list(oral = 1, infusion = 2, bolus = 2)
+)
+
+# --- From test_multi_obs.R: Multi-observation model ---
+vars_multi_obs <- c("CONC", "METAB", "METAB2", "ACT")
+pk_multi_obs <- new_ode_model(
+  code = "dAdt[1] = -(CL/V)*A[1]; CONC = 1000*A[1]/V; METAB = CONC/2; METAB2 = CONC * t; ACT = 15",
+  obs = list(variable = vars_multi_obs),
+  declare_variables = vars_multi_obs,
+  cpp_show_code = FALSE
+)
+
+# --- From test_mixture_model.R ---
+covs_mixture <- list(WT = new_covariate(70))
+mod_mixture <- new_ode_model(
+  code = "
+      dAdt[0] = -(CL*(WT/70.0)/V)*A[0];
+    ",
+  pk_code = " ",
+  obs = list(cmt = 1, scale = "V"),
+  mixture = list(CL = list(values = c(5, 15), probability = 0.3)),
+  covariates = covs_mixture
+)
+
+# --- Conditional models (skip on CRAN due to compilation time) ---
+if (identical(Sys.getenv("NOT_CRAN"), "true")) {
+
+  # Library models
+  pk_3cmt_iv <- new_ode_model("pk_3cmt_iv")
+  pk_2cmt_oral <- new_ode_model("pk_2cmt_oral")
+  pk_3cmt_oral <- new_ode_model("pk_3cmt_oral")
+  mod_1cmt_iv_mm <- new_ode_model("pk_1cmt_iv_mm")
+
+  # --- From test_advan_with_auc.R: Models with AUC compartments ---
+  parameters_advan_auc <- list(
+    CL = 10, V = 50, KA = 0.5, Q = 5, V2 = 100, Q2 = 3, V3 = 150, F1 = 1
+  )
+  mod_1cmt_auc <- new_ode_model(
+    code = "dAdt[1] = -(CL/V)*A[1]; dAdt[2] = A[1]/V;",
+    parameters = parameters_advan_auc
+  )
+  mod_2cmt_auc <- new_ode_model(
+    code = "
+    dAdt[1] = -(CL/V)*A[1] - (Q/V)*A[1] + (Q/V2)*A[2];
+    dAdt[2] = +(Q/V)*A[1] - (Q/V2)*A[2];
+    dAdt[3] = A[1]/V;
+  ",
+    parameters = parameters_advan_auc
+  )
+  mod_3cmt_auc <- new_ode_model(
+    code = "
+    dAdt[1] = -(CL/V)*A[1] - (Q/V)*A[1] + (Q/V2)*A[2] - (Q2/V)*A[1] + (Q2/V3)*A[3];
+    dAdt[2] =                (Q/V)*A[1]  -(Q/V2)*A[2]                             ;
+    dAdt[3] =                                           (Q2/V)*A[1] - (Q2/V3)*A[3];
+    dAdt[4] = A[1]/V;
+  ",
+    parameters = parameters_advan_auc
+  )
+
+  # --- From test_timevar_cov.R: 2cmt with time-varying covariates ---
+  mod_2cmt_timevar <- new_ode_model(
+    code = "
+      dAdt[1] = -(Q/V)*A[1] + (Q/V2)*A[2] -(CLi/V)*A[1];
+      dAdt[2] = -(Q/V2)*A[2] + (Q/V)*A[1];
+    ",
+    pk_code = "CLi = CL + CRCL",
+    obs = list(cmt = 2, scale = "V"),
+    covariates = list(CRCL = new_covariate(5)),
+    declare_variables = "CLi",
+    cpp = FALSE
+  )
+
+  # --- From test_t_init.R: Model with state initialization ---
+  mod_t_init <- new_ode_model(
+    code = "CLi = CL; Vi = V; dAdt[1] = -(CLi/Vi)*A[1]; CONC = A[1]/Vi",
+    state_init = "A[1] = TDM_INIT * Vi",
+    parameters = list(CL = 7.67, V = 97.7, TDM_INIT = 500),
+    obs = list(cmt = 1, scale = "Vi"),
+    declare_variables = c("CONC", "CLi", "Vi"),
+    cpp_show_code = FALSE
+  )
+
+  # --- From test_reparametrization.R: Carreno 2cmt model ---
+  covs_carreno <- list(
+    CRCL = new_covariate(5),
+    CL_HEMO = new_covariate(0)
+  )
+  model_carreno <- new_ode_model(
+    code = "
+    CLi = SCLInter + SCLSlope * (CRCL*16.667) + CL_HEMO \
+    Vi = V \
+    Qi = K12 * Vi \
+    V2i = Qi / K21 \
+    dAdt[0] = -(CLi/V)*A[0] - K12*A[0] + K21*A[1] \
+    dAdt[1] = K12*A[0] - K21*A[1] \
+    dAdt[2] = A[0]/V
+  ",
+    parameters = list(
+      V = 25.76, SCLSlope = 0.036, K12 = 2.29, K21 = 1.44,
+      SCLInter = 0.18, TDM_INIT = 0
+    ),
+    declare_variables = c("CLi", "Qi", "Vi", "V2i"),
+    covariates = covs_carreno,
+    obs = list(cmt = 1, scale = "V"),
+    reparametrization = list(
+      "CL" = "SCLInter + SCLSlope * (CRCL*16.667) + CL_HEMO",
+      "V" = "V",
+      "Q" = "K12 * V",
+      "V2" = "(K12 * V) / K21"
+    )
+  )
+}

tests/testthat/test_advan_with_auc.R

@@ -1,43 +1,14 @@
+# Uses models and parameters defined in setup.R (conditional, NOT_CRAN only):
+# - mod_1cmt_auc, mod_2cmt_auc, mod_3cmt_auc
+# - parameters_advan_auc
+
 if (identical(Sys.getenv("NOT_CRAN"), "true")) {
   dose <- 100
   interval <- 12
   n_days <- 5
   t_inf <- 1.5
-  parameters <- list(
-    CL = 10,
-    V = 50,
-    KA = 0.5,
-    Q = 5,
-    V2 = 100,
-    Q2 = 3,
-    V3 = 150,
-    F1 = 1
-  )
   t_obs <- c(3, 6, 8, 23, 47)
 
-  ## ODE models for testing
-  mod_1cmt <- new_ode_model(
-    code="dAdt[1] = -(CL/V)*A[1]; dAdt[2] = A[1]/V;",
-    parameters = parameters
-  )
-  mod_2cmt <- new_ode_model(
-    code="
-    dAdt[1] = -(CL/V)*A[1] - (Q/V)*A[1] + (Q/V2)*A[2];
-    dAdt[2] = +(Q/V)*A[1] - (Q/V2)*A[2];
-    dAdt[3] = A[1]/V;
-  ",
-  parameters = parameters
-  )
-  mod_3cmt <- new_ode_model(
-    code="
-    dAdt[1] = -(CL/V)*A[1] - (Q/V)*A[1] + (Q/V2)*A[2] - (Q2/V)*A[1] + (Q2/V3)*A[3];
-    dAdt[2] =                (Q/V)*A[1]  -(Q/V2)*A[2]                             ;
-    dAdt[3] =                                           (Q2/V)*A[1] - (Q2/V3)*A[3];
-    dAdt[4] = A[1]/V;
-  ",
-  parameters = parameters
-  )
-
   ## bolus dataset
   reg_bolus <- new_regimen(
     amt = dose,
@@ -47,7 +18,7 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
   )
   data_bolus <- advan_create_data(
     reg_bolus,
-    parameters = parameters,
+    parameters = parameters_advan_auc,
     cmts = 5,
     t_obs = t_obs
   )
@@ -61,7 +32,7 @@ if (identical(Sys.getenv("NOT_CRAN"), "true")) {
   )
   data_infusion <- advan_create_data(
     reg_infusion,
-    parameters = parameters,
+    parameters = parameters_advan_auc,
     cmts = 6,
     t_obs = t_obs
   )
@@ -71,7 +42,7 @@ test_that("One compartment bolus ADVAN runs", {
   skip_on_cran()
   res1_iv_r <- advan("1cmt_iv_bolus", cpp=FALSE)(data_bolus)
   res1_iv_c <- advan("1cmt_iv_bolus", cpp=TRUE)(data_bolus)
-  res1_iv_ode <- sim(ode = mod_1cmt, regimen = reg_bolus, parameters = parameters, t_obs = t_obs)
+  res1_iv_ode <- sim(ode = mod_1cmt_auc, regimen = reg_bolus, parameters = parameters_advan_auc, t_obs = t_obs)
 
   # AUC R
   expect_equal(round(res1_iv_r[res1_iv_r$TIME %in% t_obs,]$AUC, 5), round(res1_iv_ode[res1_iv_ode$comp == 2,]$y, 5))
@@ -84,7 +55,7 @@ test_that("Two compartment bolus ADVAN runs", {
   skip_on_cran()
   res2_iv_r <- advan("2cmt_iv_bolus", cpp=FALSE)(data_bolus)
   res2_iv_c <- advan("2cmt_iv_bolus", cpp=TRUE)(data_bolus)
-  res2_iv_ode <- sim(ode = mod_2cmt, regimen = reg_bolus, parameters = parameters, t_obs = t_obs)
+  res2_iv_ode <- sim(ode = mod_2cmt_auc, regimen = reg_bolus, parameters = parameters_advan_auc, t_obs = t_obs)
   expect_equal(
     round(res2_iv_r[res2_iv_r$TIME %in% t_obs,]$AUC, 5),
     round(res2_iv_c[res2_iv_c$TIME %in% t_obs,]$AUC, 5)
@@ -106,7 +77,7 @@ test_that("Two compartment infusion ADVAN runs", {
   skip_on_cran()
   res2_inf_r <- advan("2cmt_iv_infusion", cpp=FALSE)(data_infusion)
   res2_inf_c <- advan("2cmt_iv_infusion", cpp=TRUE)(data_infusion)
-  res2_inf_ode <- sim(ode = mod_2cmt, regimen = reg_infusion, parameters = parameters, t_obs = t_obs)
+  res2_inf_ode <- sim(ode = mod_2cmt_auc, regimen = reg_infusion, parameters = parameters_advan_auc, t_obs = t_obs)
 
   expect_equal(
     round(res2_inf_r[res2_inf_r$TIME %in% t_obs,]$AUC, 5),
@@ -131,7 +102,7 @@ test_that("Three compartment bolus ADVAN runs", {
   skip_on_cran()
   res3_iv_r <- advan("3cmt_iv_bolus", cpp=FALSE)(data_bolus)
   res3_iv_c <- advan("3cmt_iv_bolus", cpp=TRUE)(data_bolus)
-  res3_iv_ode <- sim(ode = mod_3cmt, regimen = reg_bolus, parameters = parameters, t_obs = t_obs)
+  res3_iv_ode <- sim(ode = mod_3cmt_auc, regimen = reg_bolus, parameters = parameters_advan_auc, t_obs = t_obs)
   expect_equal(
     round(res3_iv_r[res3_iv_r$TIME %in% t_obs,]$AUC, 5),
     round(res3_iv_c[res3_iv_c$TIME %in% t_obs,]$AUC, 5)
@@ -153,7 +124,7 @@ test_that("Three compartment iv ADVAN runs", {
   skip_on_cran()
   res3_iv_r <- advan("3cmt_iv_infusion", cpp=FALSE)(data_infusion)
   res3_iv_c <- advan("3cmt_iv_infusion", cpp=TRUE)(data_infusion)
-  res3_iv_ode <- sim(ode = mod_3cmt, regimen = reg_infusion, parameters = parameters, t_obs = t_obs)
+  res3_iv_ode <- sim(ode = mod_3cmt_auc, regimen = reg_infusion, parameters = parameters_advan_auc, t_obs = t_obs)
   expect_equal(
     round(res3_iv_r[res3_iv_r$TIME %in% t_obs,]$AUC, 5),
     round(res3_iv_c[res3_iv_c$TIME %in% t_obs,]$AUC, 5)
@@ -170,4 +141,3 @@ test_that("Three compartment iv ADVAN runs", {
     round(res3_iv_ode[res3_iv_ode$comp == 4,]$y, 5)
   )
 })
-

tests/testthat/test_calc_ss_analytic.R

@@ -1,3 +1,7 @@
+# Uses models defined in setup.R:
+# - mod_1cmt_iv, mod_2cmt_iv, mod_1cmt_oral
+# - pk_3cmt_iv, pk_2cmt_oral, pk_3cmt_oral (conditional, NOT_CRAN only)
+
 # shared parameters
 dose <- 100
 interval <- 12
@@ -6,13 +10,6 @@ reg_oral <- new_regimen(amt = dose, interval = interval, n = n_ss, type = "oral"
 reg_bolus <- new_regimen(amt = dose, interval = interval, n = n_ss, type = "bolus")
 reg_inf <- new_regimen(amt = dose, interval = interval, n = n_ss, type = "infusion")
 t_obs <- max(reg_oral$dose_times) + interval
-# Uses models defined in setup.R
-
-if (identical(Sys.getenv("NOT_CRAN"), "true")) {
-  pk_3cmt_iv <- new_ode_model("pk_3cmt_iv")
-}
-
-#delta <- function(x, ref) { abs(x-ref)/ref }
 
 test_that("1 cmt oral", {
   par <- list(CL = 5, V = 100, KA = 1)
@@ -72,7 +69,6 @@ test_that("1-cmt iv infusion", {
 
 test_that("2-cmt oral", {
   skip_on_cran()
-  pk_2cmt_oral <- new_ode_model("pk_2cmt_oral")
   par <- list(CL = 5, V = 100, Q = 3, V2 = 150, KA = 1)
   res_ana <- calc_ss_analytic(f = "2cmt_oral", dose = dose, interval = interval, parameters = par)
   res_ode <- sim(pk_2cmt_oral, parameters = par, regimen = reg_oral, t_obs = t_obs, only_obs = F)$y
@@ -98,7 +94,6 @@ test_that("2-cmt infusion", {
 
 test_that("3-cmt oral", {
   skip_on_cran()
-  pk_3cmt_oral <- new_ode_model("pk_3cmt_oral")
   par <- list(CL = 5, V = 100, Q = 3, V2 = 150, Q2 = 6, V3 = 250, KA = 1)
   res_ana <- calc_ss_analytic(f = "3cmt_oral", dose = dose, interval = interval, parameters = par)
   res_ode <- sim(pk_3cmt_oral, parameters = par, regimen = reg_oral, t_obs = t_obs, only_obs = F)$y

tests/testthat/test_cmt_mapping.R

@@ -1,12 +1,9 @@
-pk1cmt_oral_code <- new_ode_model(
-  code = "dAdt[1] = -KA*A[1]; dAdt[2] = KA*A[1] - (CL/V)*A[2];",
-  obs = list(cmt = 2, scale="V"),
-  cmt_mapping = list(oral = 1, infusion = 2, bolus = 2)
-)
+# Uses model defined in setup.R:
+# - pk1cmt_oral_cmt_mapping
 
 test_that("Compartment mapping is added to attributes", {
-  expect_equal(attr(pk1cmt_oral_code, "cmt_mapping")[["oral"]], 1)
-  expect_equal(attr(pk1cmt_oral_code, "cmt_mapping")[["infusion"]], 2)
+  expect_equal(attr(pk1cmt_oral_cmt_mapping, "cmt_mapping")[["oral"]], 1)
+  expect_equal(attr(pk1cmt_oral_cmt_mapping, "cmt_mapping")[["infusion"]], 2)
 })
 
 test_that("Admin route is interpreted and simulated correctly", {
@@ -18,7 +15,7 @@ test_that("Admin route is interpreted and simulated correctly", {
   )
   p <- list(KA = 1, CL = 5, V = 50)
   res <-  sim_ode(
-    ode = pk1cmt_oral_code,
+    ode = pk1cmt_oral_cmt_mapping,
     parameters = p,
     regimen = regimen,
     only_obs = FALSE