Allow to store configuration of variables
that are not pre-defined in NMdata. This should only be needed
in cases where say another package wants to use the NMdata
configuration system for variables unknown to NMdata.
args.fread Arguments passed to fread when reading _input_
data files (fread options for reading Nonmem output tables cannot
be configured at this point). If you change this, you are starting
from scratch, except from file. This means that existing default
argument values are all disregarded.
args.fwrite Arguments passed to fwrite when writing csv
files (NMwriteData). If you use this, you have to supply all
arguments you want to use with fwrite, except for x (the data) and
file.
as.fun A function that will be applied to data returned by various
data reading functions (NMscanData, NMreadTab, NMreadCsv, NMscanInput,
NMscanTables). Also, data processing functions like mergeCheck, findCovs,
findVars, flagsAssign, flagsCount take this into account, but slightly
differently. For these functions that take data as arguments, the as.fun
configuration is only taken into account if a the data passed to the
functions are not of class data.table. The argument as.fun to these
functions is always adhered to. Pass an actual function, say
as.fun=tibble::as_tibble. If you want data.table, use as.fun="data.table"
(not a function).
check.time Logical, applies to NMscanData only. NMscanData by
defaults checks if output control stream is newer than input control stream
and input data. Set this to FALSE if you are in an environment where time
stamps cannot be relied on.
col.flagc The name of the column containing the character
flag values for data row omission. Default value is flag. Used
by flagsAssign, flagsCount.
col.flagn The name of the column containing numerical flag
values for data row omission. Default value is FLAG. Used by
flagsAssign, flagsCount, NMcheckData.
col.model The name of the column that will hold the name of
the model. See modelname too (which defines the values that the
column will hold).
col.nmout A column of this name will be a logical
representing whether row was in output table or not.
col.nomtime The name of the column holding nominal
time. This is only used for sorting columns by NMorderColumns.
col.row The name of the column containing a unique row
identifier. This is used by NMscanData when merge.by.row=TRUE, and
by NMorderColumns (row counter will be first column in data).
col.id The name of the column holding the numeric subject
ID. As of 'NMdata' 0.1.5 this is only used for sorting columns by
NMorderColumns.
col.time The name of the column holding actual time. As of
'NMdata' 0.1.5 this is only used for sorting columns by
NMorderColumns.
dir.psn The directory in which to find psn executables like
'execute' and 'update_inits'. Default is "" meaning that
executables must be in the system search path. Not used by NMdata.
dir.res Directory in which 'NMsim' will store simulation
results files. Not used by NMdata. See dir.sims too.
dir.sims Directory in which 'NMsim' will store Nonmem
simulations. Not used by NMdata. See dir.res too.
file.cov A function that will derive the path to the
covariance (.cov) output file stream based on the path to the
output control stream. Technically, it can be a string too, but
when using NMdataConf, this would make little sense because it
would direct all output control streams to the same input control
streams.
file.ext A function that will derive the path to the
parameter (.ext) output file stream based on the path to the
output control stream. Technically, it can be a string too, but
when using NMdataConf, this would make little sense because it
would direct all output control streams to the same input control
streams.
file.mod A function that will derive the path to the input
control stream based on the path to the output control
stream. Technically, it can be a string too, but when using
NMdataConf, this would make little sense because it would direct
all output control streams to the same input control streams.
file.phi A function that will derive the path to the Nonmem
output (.phi) file containing individual ETA, ETC, and/or PHI
values stream based on the path to the output control
stream. Technically, it can be a string too, but when using
NMdataConf, this would make little sense because it would direct
all output control streams to the same input control streams.
file.data A function that will derive the path to the input
data based on the path to the output control stream. Technically,
it can be a string too, but when using NMdataConf, this would make
little sense because it would direct all output control streams to
the same input control streams.
formats.read Prioritized input data file formats to look
for and use if found. Default is c("rds","csv") which means
rds will be used if found, and csv if
not. fst is possible too.
formats.write character vector of formats.write. Default is
c("csv","rds"). "fst" is possible too.
merge.by.row Adjust the default combine method in
NMscanData.
modelname A function that will translate the output control stream
path to a model name. Default is to strip .lst, so /path/to/run1.lst will
become run1. Technically, it can be a string too, but when using NMdataConf,
this would make little sense because it would translate all output control
streams model name.
path.nonmem Path (a character string) to a nonmem
executable. Not used by NMdata. Default is NULL.
quiet For non-interactive scripts, you can switch off the
chatty behavior once and for all using this setting.
recover.rows In NMscanData, Include rows from input data
files that do not exist in output tables? This will be added
to the $row dataset only, and $run, $id, and $occ datasets are
created before this is taken into account. A column called
nmout will be TRUE when the row was found in output tables,
and FALSE when not. Default is FALSE.
use.input In NMscanData, merge with columns in input data?
Using this, you don't have to worry about remembering including
all relevant variables in the output tables. Default is TRUE.
use.rds Deprecated, use formats.read and
formats.write instead. Affects NMscanData(),
NMscanInput(), NMwriteData().