Description Usage Arguments Details
Parse parameter labels from the model object. Currently this parses labels from comments in the control stream, However it will be extended to parse labels from the model YAML file as well. The syntax for the labeling is described in "Details" below.
1 2 3 4 5 6 7 | param_labels(.mod, ...)
## S3 method for class 'bbi_nonmem_model'
param_labels(.mod, ...)
## S3 method for class 'character'
param_labels(.mod, ...)
|
.mod |
Character scaler of the raw control stream with newline character separating lines |
... |
arguments passed through (currently to nowhere) |
This function will *not* return indices for the parameters, though they can be added with param_labels() %>% apply_indices()
.
See the apply_indices
documentation for more details.
The syntax for parsing labels from comments is inherited from the "Census" specification that was also used in the 'tidynm' and 'mrgtable' packages. The syntax is as follows, with everything after the comment character ';' parsed into the label.
<nonmem_inits> ; [directive] <Parameter name <LOGD>>
Inits are the NONMEM initial values, following NONMEM specs
Directives include:
For fixed effects the directives are translated to units, i.e., L/h
For variance components (and only variance components) the directive is parsed into the 'type' column and can be used for post-processing transformations. Some common types include:
[A] is the assumed directive and it yields standard deviation / correlation. Typically used when the random component has a linear relationship to the typical value.
[P] yields Coefficient of Variation. Commonly transformed with CV_lognormal = sqrt( exp(omega^2)-1 ) \times 100 for omegas, and the value of omega from the correlation matrix (i.e., the SD) for sigmas. Typically used with exponentiated random effects or proportional residual error.
[R] indicates that this is an item that should be read from the correlation matrix as opposed to the covariance matrix. I.e., standard deviation and correlation of the parameter on the raw scale will be reported.
[C] indicates that this item should be read from the covariance matrix, i.e., variance and covariance of the parameter on the raw scale will be reported.
Paramemter name is parsed into the 'label' column, and is commonly formatted to be run through a LaTex parser downstream.
LOGD is a flag to indicate that the parameter is modeled on the log scale (i.e., e^θ) and should be exponentiated for reporting. If so, the standard error for the parameter should adjusted via the delta method. NOTE: this is only a convention, such that downstream code can look for "LOGD" in the 'label' column and transform the estimates accordingly. None of that processing is done automatically by this function.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.