- file
Path to the control stream to read.
- lines
As an alternative to `file`, the control stream or
selected lines of the control stream can be provided as a
vector of lines.
- format
Defines naming and splitting of contents of lines in
parameter sections. Default is
"%init;%idx;%symbol;%label;%unit". Be careful to
remember percentage symbols in front of any variable names.
- format.omega
Like `format`, applied to `$OMEGA`
section. Default is to reuse `format`.
- format.sigma
Like `format`, applied to `$SIGMA`
section. Default is to reuse `format.omega`.
- spaces.split
Is a blank in `fields` to be treated as a
field separator? Default is not to (i.e. neglect spaces in
`fields`).
- unique.matches
If TRUE, each line in the control stream is
assigned to one parameter, at most. This means, if two
parameters are listed in one line, the comments will only be
used for one of the parameters, and only that parameter will
be kept in output. Where this will typically happen is in
`$OMEGA` and `$SIGMA` sections where off-diagonal may be put
on the same line as diagonal elements. Since the off-diagonal
elements are covariances of variables that have already been
identified by the diagonals, the off-diagonal elements can be
automatically described. For example, if `OMEGA(1,1)` is
between-subject variability (BSV) on CL and `OMEGA(2,2) is BSV
on V, then we know that `OMEGA(2,1)` is covariance of (BSV on)
CL and V.
- field.idx
If an index field is manually provided in the
control stream comments, define the name of that field in
`format` and tell `NMreadParsText()` to use this idx to
organize especially OMEGA and SIGMA elements by pointing to it
with `field.idx`. The default is to look for a variable called
`idx`. If the index has values like 1-2 on an OMEGA or SIGMA
row, the row is interpreted as the covariance between
OMEGA/SIGMA 1 and 2.
- use.idx
The default method is to automatically identify
element numbering (`i` for THETAs, `i` and `j` for OMEGAs and
SIGMAs). The automated method is based on identification of
`BLOCK()` structures and numbers of initial values. Should
this fail, or should you want to control this manually, you
can include a parameter counter in the comments and have
`NMreadParsText()` use that to assign the
numbering. `use.idx=FALSE` is default and means all blocks are
handled automatically, `use.idx=TRUE` assumes you have a
counter in all sections, and a character vector like
`use.idx="omega"` can be used to denote which sections use
such a counter from the control stream. When using a counter
on OMEGA and SIGMA, off-diagonal elements MUST be denoted by
`i-j`, like `2-1` for OMEGA(2,1). See `field.idx` too.
- add.init
If `TRUE` (default), a field will automatically be
added to the formats for the initial value string. This will
be called "initstr". It will only happen if the first field is
not called either "initstr" or "init". The only situation
where one would use `add.init=FALSE` is if a different name
for the initial value field is already included in formats.
- modelname
See ?NMscanData
- col.model
See ?NMscanData
- as.fun
See ?NMscanData
- use.theta.idx
If an index field in comments should be used
to number thetas. The index field is used to organize
`$OMEGA`s and `$SIGMA`s because they are matrices but I do not
see where this is advantageous to do for `$THETA`s. Default
`use.theta.idx=FALSE` which means `$THETA`s are simply
counted.
- fields
Deprecated. Use `format`.
- fields.omega
Deprecated. Use `format.omega`.
- fields.sigma
Deprecated. Use `format.sigma`.