strum: STRUctural Modeling of Latent Variables for Family Data

In strum: STRUctural Modeling of Latent Variables for General Pedigree

Description

Main function to run strum analysis and return the result as a (list of) strumFittedModel.

Usage

strum(myStrumModel,
      myStrumData,
      step1OptimControl = list(maxit=5500, fnscale=-10),
      startValueControl = list(initPopulation=NULL,
                               nChildren=NULL,
                               nGenerations=NULL,
                               selection1=NULL,
                               selection2=NULL),
      step2OptimControl = list(maxit=5000, reltol=.Machine$double.eps),
      ibdMarkers=NULL)

Arguments

myStrumModel	Object of class strumModel.
myStrumData	Object of class strumData.
step1OptimControl	List of control parameters for optim function in step1.
startValueControl	List of control parameters for strating value generation function in step2.
step2OptimControl	List of control parameters for optim function in step2.
ibdMarkers	Character vector contaning the name of marker(s) for additive genetic variance component a (see Details).

Details

Three parameters of this function provide more flexibility to users to control the strum analysis in different stage.

The step1OptimControl argument is given as a list of several control parameters that is passed directly to the function optim in the step 1 of model fitting.

The step2OptimControl argument is given as a list of several control parameters that is passed directly to the function optim in the step 2 of model fitting.

The startValueControl argument is given as a list of 5 parameters for the function to generate the starting values (using genetic algorithm) of model fitting in step 2. Five different parameters in the list are:

• initPopulation

  The size of initial population. The default value is the number of model parameters * 120.

• nChildren

  The number of children. The default value is the number of model parameters * 2.

• nGenerations

  The number of generation. The default value is 20.

• selection1

  The size of the initial selection. The default value is 15.

• selection2

  The size of the final selection. The default value is 15.

Note that if the analysis model includes an additive genetic variance component a for the random effects, the value of iMarkers is used to determine the name of marker(s) for a from the imported ibd file. If no values are specified for ibdMarkers, then, by default, all imported ibd markers that exist in the myStrumData object are used, analyzing one by one. Therefore, the analysis result includes a list of strumFittedModel.

Value

Returns a (list of) strumFittedModel object.

See Also

createStrumModel, createStrumData

Examples

## Not run: 
# Run strum analysis.
# - myStrumModel is a strumModel object.
# - myStrumData is a strumData object.
#---------------------------------------
fitResult = strum(myStrumModel, myStrumData, ibdMarkers=c("marker1","marker2"))

## End(Not run)

strum documentation built on May 2, 2019, 7:03 a.m.