Estimate nonlinear mixed effects using SimBiology models (requires Statistics and Machine Learning Toolbox software)
sbionlmefit
will be removed in a future
release. Use sbiofitmixed
instead.
results
= sbionlmefit(modelObj
, pkModelMapObject
, pkDataObject
, InitEstimates
)
results
= sbionlmefit(modelObj
, pkModelMapObject
, pkDataObject
, CovModelObj
)
results
= sbionlmefit(..., Name,Value
)
results
= sbionlmefit(..., optionStruct
)
[results
, SimDataI
, SimDataP
]
= sbionlmefit(...)
performs
nonlinear mixedeffects estimation using the SimBiology^{®} model, results
= sbionlmefit(modelObj
, pkModelMapObject
, pkDataObject
, InitEstimates
)modelObj
,
and returns estimated results in the results
structure.
specifies
the relationship between parameters and covariates using results
= sbionlmefit(modelObj
, pkModelMapObject
, pkDataObject
, CovModelObj
)CovModelObj
,
a CovariateModel
object. The CovariateModel
object
also provides the parameter transformation.
performs
nonlinear mixedeffects estimation, with additional options specified
by one or more results
= sbionlmefit(..., Name,Value
)Name,Value
pair arguments.
Following is an alternative to the previous syntax:
specifies results
= sbionlmefit(..., optionStruct
)optionStruct
,
a structure containing fields and values, that are the namevalue
pair arguments accepted by nlmefit
. The defaults
for optionStruct
are the same as the defaults
for the arguments used by nlmefit
, with the exceptions
explained in Input Arguments.
[
returns simulation data of the SimBiology model, results
, SimDataI
, SimDataP
]
= sbionlmefit(...)modelObj
,
using the estimated values of the parameters.

SimBiology model object used to fit observed data. 

NoteIf using a 

NoteFor each subset of data belonging to a single group (as defined
in the data column specified by the


Vector of initial estimates for the fixed effects. The first 

TipTo simultaneously fit data from multiple dose levels, omit the
random effect ( 

Structure containing fields and values that are the namevalue
pairs accepted by the If you have Parallel
Computing Toolbox™, you can enable parallel
computing for faster data fitting by setting the namevalue pair argument parpool; % Open a parpool for parallel computing opt = statset(...,'UseParallel',true); % Enable parallel computing results = sbionlmefit(...,'Options',opt); % Perform data fitting TipSimBiology software includes the TipTo simultaneously fit data from multiple dose levels, use the 
Specify optional
commaseparated pairs of Name,Value
arguments. Name
is
the argument name and Value
is the corresponding value.
Name
must appear inside single quotes (' '
). You can
specify several name and value pair arguments in any order as
Name1,Value1,...,NameN,ValueN
.
The sbionlmefit
function uses the namevalue
pair arguments supported by the nlmefit
function.
These nlmefit
namevalue pairs are hardcoded
in sbionlmefit
, and therefore, you cannot set
them:
FEParamsSelect
FEConstDesign
FEGroupDesign
FEObsDesign
REConstDesign
REGroupDesign
REObsDesign
Vectorization
If you provide a CovariateModel
object as
input to sbionlmefit
, then these nlmefit
namevalue
pairs are computed from the covariate model, and therefore, you cannot
set them:
FEGroupDesign
ParamTransform
REParamsSelect
You can set all other nlmefit
namevalue
pairs. For details, see the nlmefit
reference
page.
Be aware that the defaults for these nlmefit
namevalue
pairs differ when used by sbionlmefit
:

Numeric array specifying the design matrix for each group. For details, see Specify a Nonlinear, MixedEffects Model. Default: 

Vector of integers specifying how the parameters are distributed. For details, see Specify Parameter Transformations. NoteDo not use the Default: Vector of ones, which specifies all parameters are log transformed. 

Character vector specifying the optimization function used in maximizing the likelihood. Default: 

Structure containing multiple fields, including Default: The default for 
SimBiology software includes the sbiofitstatusplot
function,
which you can specify in the OutputFcn
field of
the Options
namevalue pair input argument. This
function lets you monitor the status of fitting.
To simultaneously fit data from multiple dose levels, use the InitEstimates
input
argument and set the REParamsSelect
namevalue
pair input argument to a 1byn logical vector,
with all entries set to false
, where n equals
the number of fixed effects.

Structure containing these fields:





Model object
 PKData object
 PKModelDesign
object
 PKModelMap
object
 SimData object
 nlmefit
 sbiofitstatusplot
 sbionlinfit
 sbionlmefitsa