Documentation Center

  • Trial Software
  • Product Updates

EstimatedInfo object

Object containing information about estimated model quantities

Description

The estimatedInfo object contains information about estimated model quantities (species, parameters, or compartments). Use this object to specify which quantities in a SimBiology® model are estimated, what parameter transforms are used, and optionally, the initial estimates for these quantities. Use this object to specify what quantities in a SimBiology model are estimated when using sbiofit or sbiofitmixed.

Construction

estimInfo = estimatedInfo creates an empty estimatedInfo object.

estimInfoArray = estimatedInfo(transformedNames) creates an array of estimatedInfo objects for quantities specified in transformedNames. The initial values for these quantities are obtained from the SimBiology model when you run sbiofit or sbiofitmixed.

estimInfoArray = estimatedInfo(transformedNames,'InitialTransformedValue',itValues) defines the initial transformed values of model quantities specified by itValues.

estimInfoArray = estimatedInfo(transformedNames,'InitialValue',iValues) defines the transformed values of model quantities specified by iValues.

Input Arguments

expand all

transformedNames — Names of estimated model quantitiesstring | cell array of strings

Names of estimated model quantities, specified as a string or cell array of strings. Each string must be in one of these formats:

  • Name or qualified name of a model quantity, such as 'Cl', 'Reaction1.k','[c 1].[r 1]'

  • Name of a supported parameter transform (log, logit, or probit) followed by a quantity name in parenthesis, such as 'log(Cl)', 'logit(Reaction1.k)', 'probit([c 1].[r 1])'

itValues — Initial transformed values of model quantitiesvector | cell array

Initial transformed values of model quantities, specified as a vector or cell array. It must have the same length as transformedNames. If it is a cell array, each element of the cell must be a scalar or the empty matrix [].

iValues — Initial values of model quantitiesvector | cell array

Initial values of model quantities, specified as a vector or cell array. It must have the same length as transformedNames. If it is a cell array, each element of the cell must be a scalar or the empty matrix [].

Output Arguments

expand all

estimInfo — Estimated model quantityestimatedInfo object

Estimated model quantity, returned as an estimatedInfo object.

estimInfoArray — Estimated model quantitiesestimatedInfo object | vector

Estimated model quantities, returned as an estimatedInfo object or vector of estimatedInfo objects. If transformedNames is a single string, estimInfoArray is a scalar estimatedInfo object. Otherwise, estimInfoArray is a vector of estimatedInfo objects with the same length as the input argument transformedNames.

Properties

NameA string indicating the name of an estimated model quantity. Changing this property also updates the TransformedName property.
TransformA string indicating whether the quantity value is transformed during estimation. Valid names are '', 'log', 'logit', and 'probit'. An empty string '' indicates that no transform is applied.

The probit function is the inverse cumulative distribution function associated with the standard normal distribution. For the probit transform, SimBiology uses the norminv function. Hence Statistics Toolbox™ is required for the transform.

The logit function, which is the inverse of sigmoid function, is defined as logit(x) = log(x) – log(1 – x).

TransformedNameA read-only string that combines the transform name (such as 'log') and the quantity name (such as 'Central') into an expression (such as 'log(Central)').
InitialValueA matrix or scalar value specifying the initial values of model quantities used for estimation. If neither InitialValue nor InitialTransformedValue is specified when you created the object, the initial values for estimation are obtained from the relevant quantity property (Value for parameters, InitialAmount for species, and Capacity for compartments).

Changing this property automatically updates the InitialTransformedValue property of corresponding model quantities.

InitialTransformedValueA matrix or scalar value specifying the initial transformed values of model quantities used for estimation. If neither InitialValue nor InitialTransformedValue is specified when you created the object, the initial transformed values for estimation are obtained by transforming the relevant quantity property (Value for parameters, InitialAmount for species, and Capacity for compartments).

Changing this property automatically updates the InitialValue property of corresponding model quantities.

Examples

expand all

Specify Estimated Parameters Using an EstimatedInfo Object

Create a one-compartment PK model with bolus dosing and linear clearance.

pkmd = PKModelDesign;
pkmd.addCompartment('Central','DosingType','Bolus','EliminationType','linear-clearance','HasResponseVariable',true,'HasLag',false);
[model, map] = pkmd.construct;

Suppose you want to estimate two model quantities: the volume of the central compartment (Central) and clearance rate (Cl_Central). You can specify such estimated model quantities as well as appropriate parameter transforms (log transform in this example) and initial values using the estimatedInfo object.

estimatedParams = estimatedInfo({'log(Central)','log(Cl_Central)'},'InitialValue',[1 1])
estimatedParams = 

  1x2 estimatedInfo array with properties:

                 Name        Transform     TransformedName     InitialValue    InitialTransformedValue
             ____________    _________    _________________    ____________    _______________________

    (1,1)    'Central'       'log'        'log(Central)'       [1]             [0]                    
    (1,2)    'Cl_Central'    'log'        'log(Cl_Central)'    [1]             [0] 

For more examples, see sbiofit or sbiofitmixed reference pages.

See Also

| | |

Was this topic helpful?