pmxploit
parses the text inside control streams to extract informations of the NONMEM job related to the model, the estimation steps or the output tables.
To be able to take the most benefit from pmxploit
parsing capacity, one should be careful about how to write NONMEM control streams.
The following coding conventions should be respected for an optimal use of pmxploit
.
$PROBLEM
recordOnly one $PROBLEM record is accepted per run.
$INPUT
recordID
DV=CONC
)IDEN=DROP
)$DATA
recordIGNORE
option is not recommanded (although it may be supported, pmxploit
import of such cases must be carefully verified)$MODEL
recordIt is advised to declare each compartment on a separate line:
$MODEL NCOMP=4 COMP=(Depot) COMP=(Central) COMP=(Peripheral) COMP=(Out)
$ABBR
recordParsing of this record only support the REPLACE
option for ETA
parameters when declared like:
$ABBR REPLACE ETA(OCC_CL)=ETA(3,4,5)
and then used like:
$PK TVCL=THETA(2) ETCL=ETA(2) ETOCC1=ETA(3) ETOCC2=ETA(4) ETOCC3=ETA(5) MU_2=THETA(2) CL=DEXP(MU_2+ETACL)*EXP(ETA(OCC_CL))
$PK
, $PRED
and $ERROR
recordsXXX = THETA(n)
where XXX
is the parameter name and n
is its index in the fixed effects vectorXXX = ETA(n)
where XXX
is the parameter name and n
is its index in the random effects matrix diagonalHence, here is an adequate declaration of parameters:
; THETAs TVCL = THETA(1) ALLOCL = THETA(2) ; ETAs ETACL = ETA(1) ; Individual parameter CL = TVCL * (WT/65)**ALLOCL * EXP(ETACL)
Whereas the following is not advised:
CL = THETA(1) * (WT/65)**THETA(2) * EXP(ETA(1))
$TABLE
record(s)xpose4
conventions regarding tables output should be used (see: http://xpose.sourceforge.net/docs_faq.php)catab
, cotab
and patab
definitions are used to guess the role of each column (respectively categorical covariates, continuous covariates and parameters)pmxploit
merges the dataset and the output tables into one entity called pmxploitab
(a tibble
)FIRSTONLY
option should not be used$SIMULATION
is not supported$MIX
record) has not been fully tested yetAdd the following code to your website.
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