add tests for routes of administration #51

levenc · Jul 26, 2024 · 8fd2118 · 8fd2118
1 parent 4b03167
commit 8fd2118
Showing 1 changed file with 120 additions and 0 deletions.
diff --git a/tests/testthat/test_doseoptim_cmt.R b/tests/testthat/test_doseoptim_cmt.R
@@ -0,0 +1,120 @@
+mod_ganciclovir_Caldes_AAC2009 <- function() {
+  ini({
+    THETA_cl  <- 7.49
+    THETA_v1  <- 31.90
+    THETA_cld <- 10.20
+    THETA_v2  <- 32.0
+    THETA_ka  <- 0.895
+    THETA_baf <- 0.825
+    ETA_cl ~ 0.107
+    ETA_v1 ~ 0.227
+    ETA_ka ~ 0.464
+    ETA_baf ~ 0.049
+    add.sd <- 0.465
+    prop.sd <- 0.143
+  })
+  model({
+    TVcl  = THETA_cl*(ClCr/57);
+    TVv1  = THETA_v1;
+    TVcld = THETA_cld;
+    TVv2  = THETA_v2;
+    TVka  = THETA_ka;
+    TVbaf = THETA_baf;
+
+    cl  = TVcl*exp(ETA_cl);
+    v1  = TVv1*exp(ETA_v1);
+    cld = TVcld;
+    v2  = TVv2;
+    ka  = TVka*exp(ETA_ka);
+    baf = TVbaf*exp(ETA_baf);
+
+    k10 = cl/v1;
+    k12 = cld / v1;
+    k21 = cld / v2;
+    Cc = centr/v1;
+
+    d/dt(depot)  = -ka*depot
+    d/dt(centr)  =  ka*depot - k10*centr - k12*centr + k21*periph;
+    d/dt(periph) =                         k12*centr - k21*periph;
+    d/dt(AUC)    = Cc;
+
+    f(depot)=baf;
+    alag(depot)=0.382;
+
+    Cc ~ add(add.sd) + prop(prop.sd) + combined1()
+  })
+}
+
+df_patient <- data.frame(ID=1,TIME=c(0,1,2,6),
+                              DV=c(NA,3.4,2.7,1.4),
+                              AMT=c(450,0,0,0),
+                              EVID=c(1,0,0,0),
+                              ClCr=80)
+
+test_that("Optimal dose can be estimated for dosing in any compartment", {
+  # poso_dose_conc--------------------------------------------------------------
+  # cmt_dose = "depot"
+  expect_equal(poso_dose_conc(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                              tdm=TRUE,time_c = 25,time_dose = 24.1,
+                              target_conc = 6,cmt_dose = "depot")$dose,
+               1014.197,tolerance=1e-3)
+  expect_equal(poso_dose_conc(dat=df_patient,
+                              prior_model=mod_ganciclovir_Caldes_AAC2009,
+                              time_c=1,target_conc=6,cmt_dose = "depot")$dose,
+               928.35,tolerance=1e-3)
+  # cmt_dose="centr"
+  expect_equal(poso_dose_conc(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                              tdm=TRUE,time_c = 25,time_dose = 24.1,
+                              target_conc = 6,cmt_dose = "centr")$dose,
+               367.7199,tolerance=1e-3)
+  expect_equal(poso_dose_conc(dat=df_patient,
+                              prior_model=mod_ganciclovir_Caldes_AAC2009,
+                              time_c=1,
+                              target_conc=6,cmt_dose = "centr")$dose,
+               393.84,tolerance=1e-3)
+  # poso_time_cmin -------------------------------------------------------------
+  # cmt_dose = 1
+  expect_equal(poso_time_cmin(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                              tdm=TRUE,target_cmin = 0.5,from=1)$time,
+               13,tolerance=1e-3)
+  expect_equal(poso_time_cmin(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                              target_cmin = 0.5,from=1,dose=500)$time,
+               13.7,tolerance=1e-3)
+  # cmt_dose="centr"
+  expect_equal(poso_time_cmin(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                               tdm=TRUE,from=1,target_cmin = 0.5,
+                               cmt_dose = "centr")$time,
+               13,tolerance=1e-3)
+  expect_equal(poso_time_cmin(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                              target_cmin = 0.5,from=1,dose=500,
+                              cmt_dose = "centr")$time,
+               14.6,tolerance=1e-3)
+  # poso_dose_auc -------------------------------------------------------------
+  # cmt_dose = 1
+  expect_equal(poso_dose_auc(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                             tdm=TRUE,time_auc = 24,time_dose = 24.1,
+                             target_auc = 50)$dose,
+               924.458,tolerance=1e-3)
+  expect_equal(poso_dose_auc(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                             time_auc = 24,target_auc = 50)$dose,
+               938.59,tolerance=1e-3)
+  # cmt_dose="centr"
+  expect_equal(poso_dose_auc(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                             tdm=TRUE,time_auc = 24,time_dose = 24.1,
+                             target_auc = 50,cmt_dose = "centr")$dose,
+               645.857,tolerance=1e-3)
+  expect_equal(poso_dose_auc(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                             time_auc = 24,target_auc = 50,
+                             cmt_dose = "centr")$dose,
+               655.729,tolerance=1e-3)
+  # poso_dose_auc -------------------------------------------------------------
+  # cmt_dose = 1
+  expect_equal(poso_inter_cmin(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                               dose=500,target_cmin = 1)$interval,
+               10.69046,tolerance=1e-3)
+  # cmt_dose="centr"
+  expect_equal(poso_inter_cmin(df_patient,mod_ganciclovir_Caldes_AAC2009,
+                               dose=500,target_cmin = 1,
+                               cmt_dose = "centr")$interval,
+               11.34967,tolerance=1e-3)
+})