Load example from model library
First import the campsismod package. This step is not
required if you have already loaded the campsis
package.
Load 2-compartment PK model from built-in model library and show content.
model <- model_suite$pk$`2cpt_fo`
show(model)## [MAIN]
## TVBIO=THETA_BIO
## TVKA=THETA_KA
## TVVC=THETA_VC
## TVVP=THETA_VP
## TVQ=THETA_Q
## TVCL=THETA_CL
##
## BIO=TVBIO
## KA=TVKA * exp(ETA_KA)
## VC=TVVC * exp(ETA_VC)
## VP=TVVP * exp(ETA_VP)
## Q=TVQ * exp(ETA_Q)
## CL=TVCL * exp(ETA_CL)
##
## [ODE]
## d/dt(A_ABS)=-KA*A_ABS
## d/dt(A_CENTRAL)=KA*A_ABS + Q/VP*A_PERIPHERAL - Q/VC*A_CENTRAL - CL/VC*A_CENTRAL
## d/dt(A_PERIPHERAL)=Q/VC*A_CENTRAL - Q/VP*A_PERIPHERAL
##
## [F]
## A_ABS=BIO
##
## [ERROR]
## CONC=A_CENTRAL/VC
## if (CONC <= 0.001) CONC=0.001
## CONC_ERR=CONC*(1 + EPS_PROP_RUV)
##
##
## THETA's:
## name index value fix label unit
## 1 BIO 1 1 FALSE Bioavailability <NA>
## 2 KA 2 1 FALSE Absorption rate 1/h
## 3 VC 3 10 FALSE Volume of central compartment L
## 4 VP 4 40 FALSE Volume of peripheral compartment L
## 5 Q 5 20 FALSE Inter-compartment flow L/h
## 6 CL 6 3 FALSE Clearance L/h
## OMEGA's:
## name index index2 value fix type
## 1 KA 1 1 25 FALSE cv%
## 2 VC 2 2 25 FALSE cv%
## 3 VP 3 3 25 FALSE cv%
## 4 Q 4 4 25 FALSE cv%
## 5 CL 5 5 25 FALSE cv%
## SIGMA's:
## name index index2 value fix type
## 1 PROP_RUV 1 1 0.1 FALSE sd
## No variance-covariance matrix
##
## Compartments:
## A_ABS (CMT=1)
## A_CENTRAL (CMT=2)
## A_PERIPHERAL (CMT=3)Write Campsis model
A Campsis model can be persisted on your local drive as follows:
## [1] TRUE
list.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).
Read Campsis model
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]
## TVBIO=THETA_BIO
## TVKA=THETA_KA
## TVVC=THETA_VC
## TVVP=THETA_VP
## TVQ=THETA_Q
## TVCL=THETA_CL
##
## BIO=TVBIO
## KA=TVKA * exp(ETA_KA)
## VC=TVVC * exp(ETA_VC)
## VP=TVVP * exp(ETA_VP)
## Q=TVQ * exp(ETA_Q)
## CL=TVCL * exp(ETA_CL)
##
## [ODE]
## d/dt(A_ABS)=-KA*A_ABS
## d/dt(A_CENTRAL)=KA*A_ABS + Q/VP*A_PERIPHERAL - Q/VC*A_CENTRAL - CL/VC*A_CENTRAL
## d/dt(A_PERIPHERAL)=Q/VC*A_CENTRAL - Q/VP*A_PERIPHERAL
##
## [F]
## A_ABS=BIO
##
## [ERROR]
## CONC=A_CENTRAL/VC
## if (CONC <= 0.001) CONC=0.001
## CONC_ERR=CONC*(1 + EPS_PROP_RUV)
##
##
## THETA's:
## name index value fix label unit
## 1 BIO 1 1 FALSE Bioavailability <NA>
## 2 KA 2 1 FALSE Absorption rate 1/h
## 3 VC 3 10 FALSE Volume of central compartment L
## 4 VP 4 40 FALSE Volume of peripheral compartment L
## 5 Q 5 20 FALSE Inter-compartment flow L/h
## 6 CL 6 3 FALSE Clearance L/h
## OMEGA's:
## name index index2 value fix type
## 1 KA 1 1 25 FALSE cv%
## 2 VC 2 2 25 FALSE cv%
## 3 VP 3 3 25 FALSE cv%
## 4 Q 4 4 25 FALSE cv%
## 5 CL 5 5 25 FALSE cv%
## SIGMA's:
## name index index2 value fix type
## 1 PROP_RUV 1 1 0.1 FALSE sd
## No variance-covariance matrix
##
## Compartments:
## A_ABS (CMT=1)
## A_CENTRAL (CMT=2)
## A_PERIPHERAL (CMT=3)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.
Export Campsis model to rxode2
campsismod has powerful export capabilities to
rxode2 and mrgsolve, the 2 simulation engines
supported by campsis. The following code exports the model
to rxode2. Please note that this step is implicit in
Campsis when you call the simulate method with your
preferred simulation engine.
## An object of class "rxode_model"
## Slot "code":
## [1] "TVBIO=THETA_BIO"
## [2] "TVKA=THETA_KA"
## [3] "TVVC=THETA_VC"
## [4] "TVVP=THETA_VP"
## [5] "TVQ=THETA_Q"
## [6] "TVCL=THETA_CL"
## [7] ""
## [8] "BIO=TVBIO"
## [9] "KA=TVKA * exp(ETA_KA)"
## [10] "VC=TVVC * exp(ETA_VC)"
## [11] "VP=TVVP * exp(ETA_VP)"
## [12] "Q=TVQ * exp(ETA_Q)"
## [13] "CL=TVCL * exp(ETA_CL)"
## [14] "d/dt(A_ABS)=-KA*A_ABS"
## [15] "d/dt(A_CENTRAL)=KA*A_ABS + Q/VP*A_PERIPHERAL - Q/VC*A_CENTRAL - CL/VC*A_CENTRAL"
## [16] "d/dt(A_PERIPHERAL)=Q/VC*A_CENTRAL - Q/VP*A_PERIPHERAL"
## [17] "f(A_ABS)=BIO"
## [18] "CONC=A_CENTRAL/VC"
## [19] "if (CONC <= 0.001) CONC=0.001"
## [20] "CONC_ERR=CONC*(1 + EPS_PROP_RUV)"
##
## Slot "theta":
## THETA_BIO THETA_KA THETA_VC THETA_VP THETA_Q THETA_CL
## 1 1 10 40 20 3
##
## Slot "omega":
## ETA_KA ETA_VC ETA_VP ETA_Q ETA_CL
## ETA_KA 0.06062462 0.00000000 0.00000000 0.00000000 0.00000000
## ETA_VC 0.00000000 0.06062462 0.00000000 0.00000000 0.00000000
## ETA_VP 0.00000000 0.00000000 0.06062462 0.00000000 0.00000000
## ETA_Q 0.00000000 0.00000000 0.00000000 0.06062462 0.00000000
## ETA_CL 0.00000000 0.00000000 0.00000000 0.00000000 0.06062462
##
## Slot "sigma":
## EPS_PROP_RUV
## EPS_PROP_RUV 0.01Export Campsis model to mrgsolve
The following code exports the model to mrgsolve (text
form).
## An object of class "mrgsolve_model"
## Slot "param":
## [1] "[PARAM] @annotated" "THETA_BIO : 1 : THETA_BIO"
## [3] "THETA_KA : 1 : THETA_KA" "THETA_VC : 10 : THETA_VC"
## [5] "THETA_VP : 40 : THETA_VP" "THETA_Q : 20 : THETA_Q"
## [7] "THETA_CL : 3 : THETA_CL"
##
## Slot "cmt":
## [1] "[CMT] @annotated" "A_ABS : ABS"
## [3] "A_CENTRAL : CENTRAL" "A_PERIPHERAL : PERIPHERAL"
##
## Slot "main":
## [1] "[MAIN]" "double TVBIO=THETA_BIO;"
## [3] "double TVKA=THETA_KA;" "double TVVC=THETA_VC;"
## [5] "double TVVP=THETA_VP;" "double TVQ=THETA_Q;"
## [7] "double TVCL=THETA_CL;" ""
## [9] "double BIO=TVBIO;" "double KA=TVKA * exp(ETA_KA);"
## [11] "double VC=TVVC * exp(ETA_VC);" "double VP=TVVP * exp(ETA_VP);"
## [13] "double Q=TVQ * exp(ETA_Q);" "double CL=TVCL * exp(ETA_CL);"
## [15] "F_A_ABS=BIO;"
##
## Slot "ode":
## [1] "[ODE]"
## [2] "dxdt_A_ABS=-KA*A_ABS;"
## [3] "dxdt_A_CENTRAL=KA*A_ABS + Q/VP*A_PERIPHERAL - Q/VC*A_CENTRAL - CL/VC*A_CENTRAL;"
## [4] "dxdt_A_PERIPHERAL=Q/VC*A_CENTRAL - Q/VP*A_PERIPHERAL;"
##
## Slot "omega":
## [1] "[OMEGA] @annotated @block"
## [2] "ETA_KA : 0.0606246218164348 : ETA_KA"
## [3] "ETA_VC : 0 0.0606246218164348 : ETA_VC"
## [4] "ETA_VP : 0 0 0.0606246218164348 : ETA_VP"
## [5] "ETA_Q : 0 0 0 0.0606246218164348 : ETA_Q"
## [6] "ETA_CL : 0 0 0 0 0.0606246218164348 : ETA_CL"
##
## Slot "sigma":
## [1] "[SIGMA] @annotated @block" "EPS_PROP_RUV : 0.01 : EPS_PROP_RUV"
##
## Slot "table":
## [1] "[TABLE]"
## [2] "capture CONC=A_CENTRAL/VC;"
## [3] "if (CONC <= 0.001) CONC=0.001;"
## [4] "capture CONC_ERR=CONC*(1 + EPS_PROP_RUV);"
##
## Slot "capture":
## character(0)