Parse NONMEM model files in R format
Run number to be used to generate model file name. Used in combination with
Prefix to be used to generate model file name. Used in combination with
Extension to be used to generate model file name.Should be one of '.lst' (default), '.out', '.res', '.mod' or '.ctl' for NONMEM.
Model file name (preferably a '.lst' file) containing the file extension. Alternative to
Location of the model files.
A NONMEM model output file (i.e. .lst, .out or .res) should preferably be provided to
read_nm_model to allow for a more extensive xpose
summary. However in some cases these output files may not contain the model code, thus preventing xpose from identifying the associated output
tables names. In such cases xpose will attempt to read the associated model file (i.e. .mod or .ctl) instead to find the model code. Note: it
is important that between the naming convention between the NONMEM output and the model file remains consistent e.g. run001.lst should be
associated with run001.mod.
tibble of class
model containing the following columns:
problem: a numeric identifier for the $PROBLEM associated with the code.
level: a unique numeric identifier to each subroutine block associated with the code.
subroutine: a character identifier named after the 3 first letters of the subroutine name e.g. '$THETA' and '$TABLE' will become 'the' and 'tab' respectively. In addition all output from the .lst is labeled 'lst', the general nonmem output e.g. NM-TRAN messages are labelled 'oth'. With priors thp, tpv, omp, opd, sip, spd abbreviations are given to the THETAP, THETAPV, OMEGAP, etc.
code: the code without comments or subroutine names e.g. '$THETA 0.5 ; TVCL' will return '0.5'.
comment: the last comment of a record e.g. '0.5 ; Clearance (L/h) ; TVCL' will return 'TVCL'.
The rules for model file names generation are as follow:
runno: the full path is generated as
<dir>/<prefix><runno>.<ext> e.g. with
dir = 'model/pk',
prefix = 'run',
runno = '001',
ext = '.lst' the resulting path would be
file: the full path is generated as
<dir>/<file> e.g. with
dir = 'model/pk',
file = 'run001.lst' the resulting path
would also be
model/pk/run001.lst. Note: in this case the file extension should be provided as part of the 'file' argument.
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