R/NMreadParsText.R
NMreadParsText.RdWhen interpreting parameter estimates, it is often needed to recover information about the meaning of the different parameters from control stream. `NMreadParsText` provides a flexible way to organize the comments in the parameter sections into a `data.frame`. This can subsequently easily be merged with parameter values as obtained with `NMreadExt`.
NMreadParsText(
file,
lines,
format,
format.omega = format,
format.sigma = format.omega,
spaces.split = FALSE,
field.idx = "idx",
use.theta.idx = FALSE,
modelname,
col.model,
as.fun,
fields,
fields.omega = fields,
fields.sigma = fields.omega
)Path to the control stream to read.
As an alternative to `file`, the control stream or selected lines of the control stream can be provided as a vector of lines.
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.
Like `fields`, applied to `$OMEGA` section. Default is to reuse `fields`.
Like `fields`, applied to `$SIGMA` section. Default is to reuse `fields.omega`.
Is a blank in `fields` to be treated as a field seperator? Default is not to (i.e. neglect spaces in `fields`).
If an index field is manually provided in the control stream comments, define the name of that field in `format` and tell `NMreadParsTab()` 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 varible 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.
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.
See ?NMscanData
See ?NMscanData
See ?NMscanData
Deprecated. Use `format`.
Deprecated. Use `format.omega`.
Deprecated. Use `format.sigma`.
data.frame with parameter names and fields read from comments
Off-diagonal omega and sigma elements will only be correctly treated if their num field specifies say 1-2 to specify it is covariance between 1 and 2.
SAME elements in $OMEGA will be skipped altogether.
## notice, examples on explicitly stated lines. Most often in
## practice, one would use the file argument to automatically
## extract the $THETA, $OMEGA and $SIGMA sections from a control
## stream.
text <- c("
$THETA (.1) ;[1]; LTVKA (mL/h)
$OMEGA BLOCK(3)
0.126303 ; IIV.CL ; 1 ;IIV ;Between-subject variability on CL;-
0.024 ; IIV.CL.V2.cov ; 1-2 ;IIV ;Covariance of BSV on CL and V2;-
0.127 ; IIV.V2 ; 2 ;IIV ;Between-subject variability on V2;-
0.2 ; IIV.CL.V3.cov ; 1-3 ;IIV ;Covariance of BSV on CL and V3;-
0.2 ; IIV.V2.V3.cov ; 2-3 ;IIV ;Covariance of BSV on V2 and V3;-
0.38 ; IIV.V3 ; 3 ;IIV ;Between-subject variability on V3;-
$OMEGA 0 FIX ; IIV.KA ; 4 ;IIV ;Between-subject variability on KA;-
$SIGMA 1
")
lines <- strsplit(text,split="\n")[[1]]
res <- NMreadParsText(lines=lines,
format="%init;[%num];%symbol",
format.omega="%init; %symbol ; %num ; %type ; %label ; %unit",
field.idx="num")
## BLOCK() SAME are skipped
text <- c("
$THETA
(0,0.1) ; THE1 - 1) 1st theta
(0,4.2) ; THE2 - 2) 2nd theta
$OMEGA 0.08 ; IIV.TH1 ; 1 ;IIV
$OMEGA BLOCK(1)
0.547465 ; IOV.TH1 ; 2 ;IOV
$OMEGA BLOCK(1) SAME
$OMEGA BLOCK(1) SAME")
lines <- strsplit(text,split="\n")[[1]]
res <- NMreadParsText(lines=lines,
format="%init;%symbol - %idx) %label",
format.omega="%init; %symbol ; %idx ; %label "
)