PBPK Model for Mab with Shedding Error #1041

Ravua1992 · 2023-01-17T22:14:54Z

Ravua1992
Jan 17, 2023

Hi I am trying to run a a minimal PBPK model for a mAB in mrgsolve without any success.


$PROB
- Date: `r Sys.Date()`
- Version: `r packageVersion("mrgsolve")`
$PLUGIN Rcpp
$PARAM @annotated
Q : 1 :
L :1:
VV :1:
VE :1:
VL : 1:
KRCEX :1:
FUEX : 1:
KUPEX :1 :
sigmav :1:
sigmai :1:
KEXRC :1:
KUPiEX :1:
KONM :1:
KONS :1:
KOFF :1:
alpha :1:
KSYNM :1:
KDEGM :1:
KSHP :1:
KINTM :1: 
CLCATEX :1:
KSYNS :1:
KDEGS :1:
KONP :1:
KOFFP :1:
KINTP :1:
lambda :1:
R0 :1:
VI :1:
VP :1:
FR :1:
KSYNP:1:
KDEGP:1:

$CMT  

CVEX:
CTEEX:
CLEX:
CPEX:
CIEX:
RM:
RS:
RMCIEX:
RSCIEX:
RP:
RPCPEX:

$ODE 

dxdt_CVEX=(Q*CPEX+FR*KRCEX*(1-FUEX)*CTEEX*VE-KUPEX*CVEX*VV-(1-sigmav)*L*CVEX-(Q-L)*CVEX)/VV;

dxdt_CTEEX=(KUPEX*CVEX*VV+alpha*KUPEX*CIEX*VV-FUEX*CLCATEX*CTEEX-KRCEX*(1-FUEX)*CTEEX*VE)/VE;

dxdt_CLEX=((1-sigmai)*L*CIEX-L*CLEX)/VL;

dxdt_RM=KSYNM-KDEGM*RM-KSHP*RM -KONM*CIEX*RM+KOFFM*RMCIEX;
dxdt_RMCIEX=KONM*CIEX*RM-KOFFM*RMCIEX-KINTM*RMCIEX-KSHP*RMCIEX;

dxdt_RS=KSYNS-KDEGS*RS+KSHP*RM -KONS*CIEX*RS+KOFFS*RSCIEX;
dxdt_RSCIEX=KONS*CIEX*RS-KOFFS*RSCIEX-KINTS*RSCIEX;

dxdt_CIEX=((1-sigmav)*L*CVEX-(1-sigmai)*L*CIEX+  KEXRC*(1-FUEX)*CTEEX*VE-  KUPiEX*CIEX*VI-  KONM*CIEX*RM*VI-KONS*CIEX*VI+KOFF*RSCIEX*VI)/VI;

dxdt_RP=KSYNP-KDEGP*RP+lambda*RS*(VI/VP)-KONP*CPEX*RP+KOFFP*RPCPEX;
dxdt_RPCPEX=KONP*CPEX*RP-KOFFP*RPCPEX-KINTP*RPCPEX;

dxdt_CPEX=(ln(t)+R0+(Q-L)*CVEX+L*CLEX-Q*CPEX-KONP*CPEX*VP+VOFFP*RPCPEX*VP)/VP;

$TABLE 

capture TV = CPEX + CVEX + CTEEX + CIEX + CLEX;
capture TS = RS + RSCIEX + RP + RPCPEX;
capture TM = RM + RMCIEX;
capture TB = RMCIEX + RSCIEX + RPCPEX;
capture TOCCS = RSCIEX/(RS + RSCIEX);
capture TOCCM = RMCIEX/(RM + RMCIEX);

I get an error when trying to read the .cpp file```
; Error in names(object) <- nm :
'names' attribute [33] must be the same length as the vector [0]


Any suggestion how to fix this ?

Thanks

Answered by kylebaron

Jan 17, 2023

@Ravua1992 Is that supposed to be log(SOVLERTIME)?

View full answer

kylebaron · 2023-01-17T22:48:10Z

kylebaron
Jan 17, 2023
Maintainer

Hi @Ravua1992 -

First: missing @annotated flag in the $CMT block. You can add that or just stick with the standard syntax.

When I fix that, I'm not getting the same error. Not sure why that is; I'll put my sessionInfo() below. If I put the @annotated flag on $CMT I get the following

---:: stderr ::---------------------------------------------
18:46: error: use of undeclared identifier 'KOFFM'
dxdt_RM=KSYNM-KDEGM*RM-KSHP*RM -KONM*CIEX*RM+KOFFM*RMCIEX;
                                             ^
19:26: error: use of undeclared identifier 'KOFFM'
dxdt_RMCIEX=KONM*CIEX*RM-KOFFM*RMCIEX-KINTM*RMCIEX-KSHP*RMCIEX;
                         ^
20:46: error: use of undeclared identifier 'KOFFS'
dxdt_RS=KSYNS-KDEGS*RS+KSHP*RM -KONS*CIEX*RS+KOFFS*RSCIEX;
                                             ^
21:26: error: use of undeclared identifier 'KOFFS'
dxdt_RSCIEX=KONS*CIEX*RS-KOFFS*RSCIEX-KINTS*RSCIEX;
                         ^
21:39: error: use of undeclared identifier 'KINTS'
dxdt_RSCIEX=KONS*CIEX*RS-KOFFS*RSCIEX-KINTS*RSCIEX;
                                      ^
25:15: error: use of undeclared identifier 't'
dxdt_CPEX=(ln(t)+R0+(Q-L)*CVEX+L*CLEX-Q*CPEX-KONP*CPEX*VP+VOFFP*RPCPEX*VP)/VP;
              ^
25:59: error: use of undeclared identifier 'VOFFP'
dxdt_CPEX=(ln(t)+R0+(Q-L)*CVEX+L*CLEX-Q*CPEX-KONP*CPEX*VP+VOFFP*RPCPEX*VP)/VP;
                                                          ^
7 errors generated.
make: *** [foo-mread-source.o] Error 1

Replace t with SOLVERTIME maybe?
Then define the missing parameters

R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 13.0.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] mrgsolve_1.0.6.9000

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.9       fansi_1.0.3      assertthat_0.2.1 utf8_1.2.2      
 [5] dplyr_1.0.10     R6_2.5.1         DBI_1.1.3        lifecycle_1.0.3 
 [9] magrittr_2.0.3   pillar_1.8.1     rlang_1.0.6      cli_3.4.1       
[13] rstudioapi_0.14  vctrs_0.5.1      generics_0.1.3   tools_4.1.2     
[17] glue_1.6.2       compiler_4.1.2   pkgconfig_2.0.3  tidyselect_1.2.0
[21] tibble_3.1.8

0 replies

Ravua1992 · 2023-01-17T22:53:25Z

Ravua1992
Jan 17, 2023
Author

I was able to fix the error, thanks for your response @kylebaron

However, I am unable to solve the error for solvertime. Code and below

- Date: `r Sys.Date()`
- Version: `r packageVersion("mrgsolve")`
$PLUGIN Rcpp
$PARAM @annotated
Q : 1 : flow 
L :1: flow 
VV :1:
VE :1:
VL : 1:
KRCEX :1:
FUEX : 1:
KUPEX :1 :
sigmav :1:
sigmai :1:
KEXRC :1:
KUPiEX :1:
KONM :1:
KONS :1:
KOFFM :1:
KOFFS :1:
alpha :1:
KSYNM :1:
KDEGM :1:
KSHP :1:
KINTM :1: 
CLCATEX :1:
KSYNS :1:
KDEGS :1:
KONP :1:
KOFFP :1:
KINTP :1:
lambda :1:
R0 :1:
VI :1:
VP :1:
FR :1:
KSYNP:1:
KDEGP:1:
KINTS:1:

$CMT  @annotated 

CVEX :
CTEEX :
CLEX :
CPEX :
CIEX :
RM :
RS :
RSCIEX :
RP :
RPCPEX :
RMCIEX:
  
$ODE 
dxdt_CVEX=(Q*CPEX+FR*KRCEX*(1-FUEX)*CTEEX*VE-KUPEX*CVEX*VV-(1-sigmav)*L*CVEX-(Q-L)*CVEX)/VV;
dxdt_CTEEX=(KUPEX*CVEX*VV+alpha*KUPEX*CIEX*VV-FUEX*CLCATEX*CTEEX-KRCEX*(1-FUEX)*CTEEX*VE)/VE;
dxdt_CLEX=((1-sigmai)*L*CIEX-L*CLEX)/VL;
dxdt_RM=KSYNM-KDEGM*RM-KSHP*RM -KONM*CIEX*RM+KOFFM*RMCIEX;
dxdt_RMCIEX=KONM*CIEX*RM-KOFFM*RMCIEX-KINTM*RMCIEX-KSHP*RMCIEX;
dxdt_RS=KSYNS-KDEGS*RS+KSHP*RM -KONS*CIEX*RS+KOFFS*RSCIEX;
dxdt_RSCIEX=KONS*CIEX*RS-KOFFS*RSCIEX-KINTS*RSCIEX;
dxdt_CIEX=((1-sigmav)*L*CVEX-(1-sigmai)*L*CIEX+  KEXRC*(1-FUEX)*CTEEX*VE-  KUPiEX*CIEX*VI-  KONM*CIEX*RM*VI-KONS*CIEX*VI+KOFFS*RSCIEX*VI)/VI;
dxdt_RP=KSYNP-KDEGP*RP+lambda*RS*(VI/VP)-KONP*CPEX*RP+KOFFP*RPCPEX;
dxdt_RPCPEX=KONP*CPEX*RP-KOFFP*RPCPEX-KINTP*RPCPEX;
dxdt_CPEX=(ln(SOLVERTIME)+R0+(Q-L)*CVEX+L*CLEX-Q*CPEX-KONP*CPEX*VP+KOFFP*RPCPEX*VP)/VP;

$TABLE 

capture TV = CPEX + CVEX + CTEEX + CIEX + CLEX;
capture TS = RS + RSCIEX + RP + RPCPEX;
capture TM = RM + RMCIEX;
capture TB = RMCIEX + RSCIEX + RPCPEX;
capture TOCCS = RSCIEX/(RS + RSCIEX);
capture TOCCM = RMCIEX/(RM + RMCIEX);

Error

25:12: error: ‘ln’ was not declared in this scope; did you mean ‘yn’?
   25 | dxdt_CPEX=(ln(SOLVERTIME)+R0+(Q-L)*CVEX+L*CLEX-Q*CPEX-KONP*CPEX*VP+KOFFP*RPCPEX*VP)/VP;
      |            ^~
      |            yn
make: *** [/opt/R/4.2.2/lib/R/etc/Makeconf:178: pbpk1_cpp-mread-source.o] Error 1
------------------------------------------------------------
Error: the model build step failed.

In(t) is the infusion rate and R0 is the mass flux produced by intravenous bolus or subcutaneous administration.

0 replies

Ravua1992 · 2023-01-17T22:57:27Z

Ravua1992
Jan 17, 2023
Author

- Date: `r Sys.Date()`
- Version: `r packageVersion("mrgsolve")`
$PLUGIN Rcpp
$PARAM @annotated
Q : 1 : flow 
L :1: flow 
VV :1:
VE :1:
VL : 1:
KRCEX :1:
FUEX : 1:
KUPEX :1 :
sigmav :1:
sigmai :1:
KEXRC :1:
KUPiEX :1:
KONM :1:
KONS :1:
KOFFM :1:
KOFFS :1:
alpha :1:
KSYNM :1:
KDEGM :1:
KSHP :1:
KINTM :1: 
CLCATEX :1:
KSYNS :1:
KDEGS :1:
KONP :1:
KOFFP :1:
KINTP :1:
lambda :1:
R0 :1:
VI :1:
VP :1:
FR :1:
KSYNP:1:
KDEGP:1:
KINTS:1:

$CMT  @annotated 

CVEX :
CTEEX :
CLEX :
CPEX :
CIEX :
RM :
RS :
RSCIEX :
RP :
RPCPEX :
RMCIEX:
  
$ODE 
dxdt_CVEX=(Q*CPEX+FR*KRCEX*(1-FUEX)*CTEEX*VE-KUPEX*CVEX*VV-(1-sigmav)*L*CVEX-(Q-L)*CVEX)/VV;
dxdt_CTEEX=(KUPEX*CVEX*VV+alpha*KUPEX*CIEX*VV-FUEX*CLCATEX*CTEEX-KRCEX*(1-FUEX)*CTEEX*VE)/VE;
dxdt_CLEX=((1-sigmai)*L*CIEX-L*CLEX)/VL;
dxdt_RM=KSYNM-KDEGM*RM-KSHP*RM -KONM*CIEX*RM+KOFFM*RMCIEX;
dxdt_RMCIEX=KONM*CIEX*RM-KOFFM*RMCIEX-KINTM*RMCIEX-KSHP*RMCIEX;
dxdt_RS=KSYNS-KDEGS*RS+KSHP*RM -KONS*CIEX*RS+KOFFS*RSCIEX;
dxdt_RSCIEX=KONS*CIEX*RS-KOFFS*RSCIEX-KINTS*RSCIEX;
dxdt_CIEX=((1-sigmav)*L*CVEX-(1-sigmai)*L*CIEX+  KEXRC*(1-FUEX)*CTEEX*VE-  KUPiEX*CIEX*VI-  KONM*CIEX*RM*VI-KONS*CIEX*VI+KOFFS*RSCIEX*VI)/VI;
dxdt_RP=KSYNP-KDEGP*RP+lambda*RS*(VI/VP)-KONP*CPEX*RP+KOFFP*RPCPEX;
dxdt_RPCPEX=KONP*CPEX*RP-KOFFP*RPCPEX-KINTP*RPCPEX;
dxdt_CPEX=(R0+(Q-L)*CVEX+L*CLEX-Q*CPEX-KONP*CPEX*VP+KOFFP*RPCPEX*VP)/VP;

$TABLE 

capture TV = CPEX + CVEX + CTEEX + CIEX + CLEX;
capture TS = RS + RSCIEX + RP + RPCPEX;
capture TM = RM + RMCIEX;
capture TB = RMCIEX + RSCIEX + RPCPEX;
capture TOCCS = RSCIEX/(RS + RSCIEX);
capture TOCCM = RMCIEX/(RM + RMCIEX);```

This was without error after removing ln(t) term,

0 replies

kylebaron · 2023-01-17T23:00:29Z

kylebaron
Jan 17, 2023
Maintainer

@Ravua1992 Is that supposed to be log(SOVLERTIME)?

2 replies

Ravua1992 Jan 17, 2023
Author

Thank you!

kylebaron Jan 17, 2023
Maintainer

Just be careful; this won't behave well when SOLVERTIME is zero or negative (sometimes happens).

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PBPK Model for Mab with Shedding Error #1041

Ravua1992 Jan 17, 2023

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