Merge pull request #97 from john-harrold/main

Cc was defined after it was used resulting in it being flagged as a covariate.
nlmixr2 · Jan 2, 2025 · 223d4a7 · 223d4a7
2 parents 7f1eef6 + 9796281
commit 223d4a7
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Showing 13 changed files with 13 additions and 13 deletions.
diff --git a/inst/modeldb/pharmacodynamics/indirect_1cpt_inhi_kout_r0rmaxcrmax.R b/inst/modeldb/pharmacodynamics/indirect_1cpt_inhi_kout_r0rmaxcrmax.R
@@ -28,13 +28,13 @@ indirect_1cpt_inhi_kout_r0rmaxcrmax <- function() {
     kin <- s1/imax
     kout <- kin/r0
     IC50 <- crmax*(r0-(1-imax)*rmax)/(rmax-r0)
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -(kel)*central
     d/dt(effect) <- kin - kout*(1-imax*Cc/(Cc + IC50))*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kin_kin_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kin_kin_t.R
@@ -26,14 +26,14 @@ indirect_circ_1cpt_inhi_kin_kin_t  <- function() {
     fdepot   <- exp(lfdepot)
 
     kin_t <- kout*rm+kout*ra*cos(0.2616*(t-tz))-0.2616*ra*sin(0.2616*(t-tz))
+    Cc <-  central/vc
 
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -(cl/vc)*central
     d/dt(effect) <- kin_t*(1-imax*Cc/(Cc + IC50)) - kout*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kin_kout_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kin_kout_t.R
@@ -24,6 +24,7 @@ indirect_circ_1cpt_inhi_kin_kout_t  <- function() {
     fdepot   <- exp(lfdepot)
 
     kout_t <- kin + 0.2616*ra*sin(0.2616*(t-tz))/(rm+ra*cos*(0.2616*(t-tz)))
+    Cc <-  central/vc
 
 
 
@@ -32,7 +33,6 @@ indirect_circ_1cpt_inhi_kin_kout_t  <- function() {
     d/dt(central)    <- ka*depot -(cl/vc)*central
     d/dt(effect) <- kin - kout_t*(1-imax*Cc/(Cc + IC50))*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kout_kin_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kout_kin_t.R
@@ -24,14 +24,14 @@ indirect_circ_1cpt_inhi_kout_kin_t  <- function() {
     fdepot   <- exp(lfdepot)
 
     kin_t <- kout*rm+kout*ra*cos(0.2616*(t-tz))-0.2616*ra*sin(0.2616*(t-tz))
+    Cc <-  central/vc
 
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -(cl/vc)*central
     d/dt(effect) <- kin_t - kout*(1-imax*Cc/(Cc + IC50))*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kout_kout_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_inhi_kout_kout_t.R
@@ -24,14 +24,14 @@ indirect_circ_1cpt_inhi_kout_kout_t  <- function() {
     fdepot   <- exp(lfdepot)
 
     kout_t <- kin + 0.2616*ra*sin(0.2616*(t-tz))/(rm+ra*cos*(0.2616*(t-tz)))
+    Cc <-  central/vc
 
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -(cl/vc)*central
     d/dt(effect) <- kin - kout_t*(1-imax*Cc/(Cc + IC50))*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kin_kin_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kin_kin_t.R
@@ -24,13 +24,13 @@ indirect_circ_1cpt_stim_kin_kin_t <- function() {
     fdepot   <- exp(lfdepot)
 
     kin_t <- kout*rm+kout*ra*cos(0.2616*(t-tz))-0.2616*ra*sin(0.2616*(t-tz))
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -kel*central
     d/dt(effect) <- kin_t*(1+Emax*Cc/(Cc + IC50)) - kout*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kin_kout_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kin_kout_t.R
@@ -24,13 +24,13 @@ indirect_circ_1cpt_stim_kin_kout_t <- function() {
     fdepot   <- exp(lfdepot)
 
     kout_t <- kin + 0.2616*ra*sin(0.2616*(t-tz))/(rm+ra*cos*(0.2616*(t-tz)))
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -kel*central
     d/dt(effect) <- kin*(1+Emax*Cc/(Cc + IC50)) - kout_t*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kout_kin_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kout_kin_t.R
@@ -24,13 +24,13 @@ indirect_circ_1cpt_stim_kout_kin_t <- function() {
     fdepot   <- exp(lfdepot)
 
     kin_t <- kout*rm+kout*ra*cos(0.2616*(t-tz))-0.2616*ra*sin(0.2616*(t-tz))
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -kel*central
     d/dt(effect) <- kin_t - kout*(1+Emax*Cc/(Cc + IC50))*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kout_kout_t.R b/inst/modeldb/pharmacodynamics/indirect_circ_1cpt_stim_kout_kout_t.R
@@ -24,13 +24,13 @@ indirect_circ_1cpt_stim_kout_kout_t <- function() {
     fdepot   <- exp(lfdepot)
 
     kout_t <- kin + 0.2616*ra*sin(0.2616*(t-tz))/(rm+ra*cos*(0.2616*(t-tz)))
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot -kel*central
     d/dt(effect) <- kin_t - kout*(1+Emax*Cc/(Cc + IC50))*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_inhi_CLV.R b/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_inhi_CLV.R
@@ -26,14 +26,14 @@ indirect_prec_1cpt_inhi_CLV  <- function() {
     fdepot   <- exp(lfdepot)
 
     kel <- cl/vc
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot-kel*central
     d/dt(precursor)  <- kpin -(kin + kpout)*(1-imax*Cc/(Cc + IC50))*precursor
     d/dt(effect)   <- kin*(1-imax*Cc/(Cc + IC50))*precursor-kout*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }       
diff --git a/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_inhi_r0rmaxcrmax.R b/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_inhi_r0rmaxcrmax.R
@@ -27,14 +27,14 @@ indirect_prec_1cpt_inhi_r0rmaxcrmax  <- function() {
     imax <- (r0-rmax)/r0
     kin <- (kout*(kin+kpout)*r0)/kpin
     IC50 <- crmax*(rmax-(1-imax)*r0)/(r0-rmax)
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot-kel*central
     d/dt(precursor)  <- kpin -(kin + kpout)*(1-imax*Cc/(Cc + IC50))*precursor
     d/dt(effect)   <- kin*(1-imax*Cc/(Cc + IC50))*precursor-kout*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_stim_CLV.R b/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_stim_CLV.R
@@ -26,14 +26,14 @@ indirect_prec_1cpt_stim_CLV  <- function() {
     fdepot   <- exp(lfdepot)
 
     kel <- cl/vc
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot-kel*central
     d/dt(precursor)  <- kpin -(kin + kpout)*(1+emax*Cc/(Cc + EC50))*precursor
     d/dt(effect)   <- kin*(1+emax*Cc/(Cc + EC50))*precursor-kout*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }
diff --git a/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_stim_r0rmaxcrmax.R b/inst/modeldb/pharmacodynamics/indirect_prec_1cpt_stim_r0rmaxcrmax.R
@@ -27,14 +27,14 @@ indirect_prec_1cpt_stim_r0rmaxcrmax <- function() {
     emax <- (rmax-r0)/rmax
     kin <- (kout*(kin+kpout)*r0)/kpin
     EC50 <- crmax*(r0*(1+emax)-rmax)/(rmax-r0)
+    Cc <-  central/vc
 
     d/dt(depot)      <- -ka*depot
     f(depot)         <- fdepot
     d/dt(central)    <- ka*depot-kel*central
     d/dt(precursor)  <- kpin -(kin + kpout)*(1+emax*Cc/(Cc + EC50))*precursor
     d/dt(effect)   <- kin*(1+emax*Cc/(Cc + EC50))*precursor-kout*effect
 
-    Cc <-  central/vc
     Cc ~ prop(propSd)
   })
 }