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Get started with CAMPSIS model

Load example from model library

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_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:

model %>% write(file="path_to_model_folder")
## [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 RxODE

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] "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         0.01

Export CAMPSIS model to mrgsolve

The 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_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)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.