First import the campsismod package. This step is not
required if you have already loaded the campsis
package.
library(campsismod)Load 2-compartment PK model from built-in model library and show content.
model <- model_library$advan4_trans4
show(model)## [MAIN]
## KA=THETA_KA*exp(ETA_KA)
## CL=THETA_CL*exp(ETA_CL)
## V2=THETA_V2*exp(ETA_V2)
## V3=THETA_V3*exp(ETA_V3)
## Q=THETA_Q*exp(ETA_Q)
## S2=V2
##
## [ODE]
## d/dt(A_DEPOT)=-KA*A_DEPOT
## d/dt(A_CENTRAL)=KA*A_DEPOT + Q*A_PERIPHERAL/V3 + (-CL/V2 - Q/V2)*A_CENTRAL
## d/dt(A_PERIPHERAL)=-Q*A_PERIPHERAL/V3 + Q*A_CENTRAL/V2
## d/dt(A_OUTPUT)=CL*A_CENTRAL/V2
## F=A_CENTRAL/S2
##
## [ERROR]
## CP=F
## OBS_CP=CP*(EPS_PROP + 1)
## Y=OBS_CP
##
##
## THETA's:
## name index value fix
## 1 KA 1 1 FALSE
## 2 CL 2 5 FALSE
## 3 V2 3 80 FALSE
## 4 V3 4 20 FALSE
## 5 Q 5 4 FALSE
## OMEGA's:
## name index index2 value fix type same
## 1 KA 1 1 0.025 FALSE var NA
## 2 CL 2 2 0.025 FALSE var NA
## 3 V2 3 3 0.025 FALSE var NA
## 4 V3 4 4 0.025 FALSE var NA
## 5 Q 5 5 0.025 FALSE var NA
## SIGMA's:
## name index index2 value fix type
## 1 PROP 1 1 0.025 FALSE var
## No variance-covariance matrix
##
## Compartments:
## A_DEPOT (CMT=1)
## A_CENTRAL (CMT=2)
## A_PERIPHERAL (CMT=3)
## A_OUTPUT (CMT=4)A CAMPSIS model can be persisted on your local drive as follows:
model %>% write(file="path_to_model_folder")## [1] TRUElist.files("path_to_model_folder")## [1] "model.campsis" "omega.csv" "sigma.csv" "theta.csv"As shown, the output directory will contain the model (all code
records) and 1 csv file per type of parameter (THETA, OMEGA
and SIGMA).
To read a CAMPSIS model from your local drive, use the
read.campsis function. The exact same model should be
retrieved.
model <- read.campsis(file="path_to_model_folder")
show(model)## [MAIN]
## KA=THETA_KA*exp(ETA_KA)
## CL=THETA_CL*exp(ETA_CL)
## V2=THETA_V2*exp(ETA_V2)
## V3=THETA_V3*exp(ETA_V3)
## Q=THETA_Q*exp(ETA_Q)
## S2=V2
##
## [ODE]
## d/dt(A_DEPOT)=-KA*A_DEPOT
## d/dt(A_CENTRAL)=KA*A_DEPOT + Q*A_PERIPHERAL/V3 + (-CL/V2 - Q/V2)*A_CENTRAL
## d/dt(A_PERIPHERAL)=-Q*A_PERIPHERAL/V3 + Q*A_CENTRAL/V2
## d/dt(A_OUTPUT)=CL*A_CENTRAL/V2
## F=A_CENTRAL/S2
##
## [ERROR]
## CP=F
## OBS_CP=CP*(EPS_PROP + 1)
## Y=OBS_CP
##
##
## THETA's:
## name index value fix
## 1 KA 1 1 FALSE
## 2 CL 2 5 FALSE
## 3 V2 3 80 FALSE
## 4 V3 4 20 FALSE
## 5 Q 5 4 FALSE
## OMEGA's:
## name index index2 value fix type same
## 1 KA 1 1 0.025 FALSE var NA
## 2 CL 2 2 0.025 FALSE var NA
## 3 V2 3 3 0.025 FALSE var NA
## 4 V3 4 4 0.025 FALSE var NA
## 5 Q 5 5 0.025 FALSE var NA
## SIGMA's:
## name index index2 value fix type
## 1 PROP 1 1 0.025 FALSE var
## No variance-covariance matrix
##
## Compartments:
## A_DEPOT (CMT=1)
## A_CENTRAL (CMT=2)
## A_PERIPHERAL (CMT=3)
## A_OUTPUT (CMT=4)The MAIN record is the part of the model where your
model parameters are defined. The ODE record is where your
ordinary differential equations (ODE) go, as well as any equation
depending on the simulation time. The ERROR record is the
place where the error model is defined. The model parameters are then
shown, followed by the all the compartments.
campsismod has powerful export capabilities to
RxODE and mrgsolve, the 2 simulation engines
supported by campsis. The following code exports the model
to RxODE. Please note that this step is implicit in CAMPSIS
when you call the simulate method with your preferred
simulation engine.
rxmod <- model %>% export(dest="RxODE")
rxmod## An object of class "rxode_model"
## Slot "code":
## [1] "KA=THETA_KA*exp(ETA_KA)"
## [2] "CL=THETA_CL*exp(ETA_CL)"
## [3] "V2=THETA_V2*exp(ETA_V2)"
## [4] "V3=THETA_V3*exp(ETA_V3)"
## [5] "Q=THETA_Q*exp(ETA_Q)"
## [6] "S2=V2"
## [7] "d/dt(A_DEPOT)=-KA*A_DEPOT"
## [8] "d/dt(A_CENTRAL)=KA*A_DEPOT + Q*A_PERIPHERAL/V3 + (-CL/V2 - Q/V2)*A_CENTRAL"
## [9] "d/dt(A_PERIPHERAL)=-Q*A_PERIPHERAL/V3 + Q*A_CENTRAL/V2"
## [10] "d/dt(A_OUTPUT)=CL*A_CENTRAL/V2"
## [11] "F=A_CENTRAL/S2"
## [12] "CP=F"
## [13] "OBS_CP=CP*(EPS_PROP + 1)"
## [14] "Y=OBS_CP"
##
## Slot "theta":
## THETA_KA THETA_CL THETA_V2 THETA_V3 THETA_Q
## 1 5 80 20 4
##
## Slot "omega":
## ETA_KA ETA_CL ETA_V2 ETA_V3 ETA_Q
## ETA_KA 0.025 0.000 0.000 0.000 0.000
## ETA_CL 0.000 0.025 0.000 0.000 0.000
## ETA_V2 0.000 0.000 0.025 0.000 0.000
## ETA_V3 0.000 0.000 0.000 0.025 0.000
## ETA_Q 0.000 0.000 0.000 0.000 0.025
##
## Slot "sigma":
## EPS_PROP
## EPS_PROP 0.025The following code exports the model to mrgsolve (text
form).
mrgmod <- model %>% export(dest="mrgsolve")
mrgmod## An object of class "mrgsolve_model"
## Slot "param":
## [1] "[PARAM] @annotated" "THETA_KA : 1 : THETA_KA"
## [3] "THETA_CL : 5 : THETA_CL" "THETA_V2 : 80 : THETA_V2"
## [5] "THETA_V3 : 20 : THETA_V3" "THETA_Q : 4 : THETA_Q"
##
## Slot "cmt":
## [1] "[CMT] @annotated" "A_DEPOT : DEPOT"
## [3] "A_CENTRAL : CENTRAL" "A_PERIPHERAL : PERIPHERAL"
## [5] "A_OUTPUT : OUTPUT"
##
## Slot "main":
## [1] "[MAIN]" "double KA=THETA_KA*exp(ETA_KA);"
## [3] "double CL=THETA_CL*exp(ETA_CL);" "double V2=THETA_V2*exp(ETA_V2);"
## [5] "double V3=THETA_V3*exp(ETA_V3);" "double Q=THETA_Q*exp(ETA_Q);"
## [7] "double S2=V2;"
##
## Slot "ode":
## [1] "[ODE]"
## [2] "dxdt_A_DEPOT=-KA*A_DEPOT;"
## [3] "dxdt_A_CENTRAL=KA*A_DEPOT + Q*A_PERIPHERAL/V3 + (-CL/V2 - Q/V2)*A_CENTRAL;"
## [4] "dxdt_A_PERIPHERAL=-Q*A_PERIPHERAL/V3 + Q*A_CENTRAL/V2;"
## [5] "dxdt_A_OUTPUT=CL*A_CENTRAL/V2;"
## [6] "double F=A_CENTRAL/S2;"
##
## Slot "omega":
## [1] "[OMEGA] @annotated @block" "ETA_KA : 0.025 : ETA_KA"
## [3] "ETA_CL : 0 0.025 : ETA_CL" "ETA_V2 : 0 0 0.025 : ETA_V2"
## [5] "ETA_V3 : 0 0 0 0.025 : ETA_V3" "ETA_Q : 0 0 0 0 0.025 : ETA_Q"
##
## Slot "sigma":
## [1] "[SIGMA] @annotated @block" "EPS_PROP : 0.025 : EPS_PROP"
##
## Slot "table":
## [1] "[TABLE]" "capture CP=F;"
## [3] "capture OBS_CP=CP*(EPS_PROP + 1);" "capture Y=OBS_CP;"
##
## Slot "capture":
## character(0)