public class StepwiseAdditiveModelFitterPlugin
extends AbstractPlugin
public StepwiseAdditiveModelFitterPlugin()
public StepwiseAdditiveModelFitterPlugin(java.awt.Frame parentFrame,
boolean isInteractive)
public java.lang.String pluginDescription()
protected void preProcessParameters(DataSet input)
protected void postProcessParameters()
public javax.swing.ImageIcon getIcon()
public java.lang.String getButtonName()
public java.lang.String getToolTipText()
public net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION modelCriterion()
The model selection criterion used to determine which terms enter the model and how many. Value must be one of pval, bic, mbic, or aic
public StepwiseAdditiveModelFitterPlugin modelCriterion(net.maizegenetics.analysis.modelfitter.AdditiveSite.CRITERION value)
Set Model selection criterion. The model selection criterion used to determine which terms enter the model and how many. Value must be one of pval, bic, mbic, or aic
value - Model selection criterionpublic java.lang.Boolean useResiduals()
Should the each new term be tested using residuals from the previous model instead of fitting a complete model each time?
public StepwiseAdditiveModelFitterPlugin useResiduals(java.lang.Boolean value)
Set Fit using residuals. Should the each new term be tested using residuals from the previous model instead of fitting a complete model each time?
value - Fit using residualspublic java.lang.Boolean usePermutations()
Should permutations be used to set the enter and exit limits for stepwise regression? A permutation test will be used to determine the enter limit. The exit limit will be set to 2 times the enter limit.
public StepwiseAdditiveModelFitterPlugin usePermutations(java.lang.Boolean value)
Set Use permutations. Should permutations be used to set the enter and exit limits for stepwise regression? A permutation test will be used to determine the enter limit. The exit limit will be set to 2 times the enter limit.
value - Use permutationspublic java.lang.Integer numberOfPermutations()
The number of permutations used to determine the enter limit.
public StepwiseAdditiveModelFitterPlugin numberOfPermutations(java.lang.Integer value)
Set Number of permutations. The number of permutations used to determine the enter limit.
value - Number of permutationspublic java.lang.Double permutationAlpha()
Type I errors will be controlled at this level.
public StepwiseAdditiveModelFitterPlugin permutationAlpha(java.lang.Double value)
Set Alpha for permutations. Type I errors will be controlled at this level.
value - Alpha for permutationspublic java.lang.Double enterLimit()
When p-value is the model selection criteria, model fitting will stop when the next term chosen has a p-value greater than the enterLimit. This value will be over-ridden the permutation test, if used.
public StepwiseAdditiveModelFitterPlugin enterLimit(java.lang.Double value)
Set enterLimit. When p-value is the model selection criteria, model fitting will stop when the next term chosen has a p-value greater than the enterLimit. This value will be over-ridden the permutation test, if used.
value - enterLimitpublic java.lang.Double exitLimit()
During the backward step of model fitting if p-value has been chosen as the selection criterion, if the term in model with the highest p-value has a p-value > exitLimit, it will be removed from the model.
public StepwiseAdditiveModelFitterPlugin exitLimit(java.lang.Double value)
Set exitLimit. During the backward step of model fitting if p-value has been chosen as the selection criterion, if the term in model with the highest p-value has a p-value > exitLimit, it will be removed from the model.
value - exitLimitpublic java.lang.Integer maxTerms()
The maximum number of SNPs/markers that will be fit. If the model selection criterion is met first, then the fitting process will stop at that point.
public StepwiseAdditiveModelFitterPlugin maxTerms(java.lang.Integer value)
Set Max SNPs/markers. The maximum number of SNPs/markers that will be fit. If the model selection criterion is met first, then the fitting process will stop at that point.
value - Max SNPs/markerspublic java.lang.Boolean isNested()
Should SNPs/markers be nested within a factor, such as family?
public StepwiseAdditiveModelFitterPlugin isNested(java.lang.Boolean value)
Set Is Nested. Should SNPs/markers be nested within a factor, such as family?
value - Is Nestedpublic java.lang.String nestingFactor()
Nest markers within this factor. This parameter cannot be set from the command line. Instead, the first factor in the data set will be used.
public StepwiseAdditiveModelFitterPlugin nestingFactor(java.util.List<java.lang.String> value)
Set Nesting factor. Nest markers within this factor. This parameter cannot be set from the command line. Instead, the first factor in the data set will be used.
value - Nesting factorpublic net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT genotypeTable()
If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
public StepwiseAdditiveModelFitterPlugin genotypeTable(net.maizegenetics.dna.snp.GenotypeTable.GENOTYPE_TABLE_COMPONENT value)
Set Genotype Component. If the genotype table contains more than one type of genotype data, choose the type to use for the analysis.
value - Genotype Componentpublic java.lang.Boolean createAnova()
Create pre- and post-scan anova reports.
public StepwiseAdditiveModelFitterPlugin createAnova(java.lang.Boolean value)
Set Create anova reports. Create pre- and post-scan anova reports.
value - Create anova reportspublic java.lang.Boolean createEffects()
Create a report of marker effects based on the scan results.
public StepwiseAdditiveModelFitterPlugin createEffects(java.lang.Boolean value)
Set Create effects report. Create a report of marker effects based on the scan results.
value - Create effects reportpublic java.lang.Boolean createEffectsPrescan()
Create a report of marker effects based on the results pre-scan.
public StepwiseAdditiveModelFitterPlugin createEffectsPrescan(java.lang.Boolean value)
Set Create prescan effects. Create a report of marker effects based on the results pre-scan.
value - Create prescan effectspublic java.lang.Boolean createStep()
Create a report of the which markers enter and leave the model as it is being fit.
public StepwiseAdditiveModelFitterPlugin createStep(java.lang.Boolean value)
Set Create step report. Create a report of the which markers enter and leave the model as it is being fit.
value - Create step reportpublic java.lang.Boolean createResiduals()
Create a phenotype dataset of model residuals for each chromosome. For each chromosome, the residuals will be calculated from a model with all terms EXCEPT the markers on that chromosome.
public StepwiseAdditiveModelFitterPlugin createResiduals(java.lang.Boolean value)
Set Create residuals. Create a phenotype dataset of model residuals for each chromosome. For each chromosome, the residuals will be calculated from a model with all terms EXCEPT the markers on that chromosome.
value - Create residualspublic java.lang.Boolean writeFiles()
Should the requested output be written to files?
public StepwiseAdditiveModelFitterPlugin writeFiles(java.lang.Boolean value)
Set Write to files. Should the requested output be written to files?
value - Write to filespublic java.lang.String outputName()
The base file path for the save files. Each file saved will add a descriptive name to the base name.
public StepwiseAdditiveModelFitterPlugin outputName(java.lang.String value)
Set Base file path. The base file path for the save files. Each file saved will add a descriptive name to the base name.
value - Base file pathpublic java.lang.Boolean fitAddDom()
Should the plugin fit an additive plus dominance model? If false, an additive only model will be fit. Note this option does not implement a nested model. The isNested parameter will be ignored.
public StepwiseAdditiveModelFitterPlugin fitAddDom(java.lang.Boolean value)
Set Fit AddDom Model. Should the plugin fit an additive plus dominance model? If false, an additive only model will be fit. Note this option does not implement a nested model. The isNested parameter will be ignored.
value - Fit AddDom Modelpublic java.lang.Integer minHets()
The minimum number of individuals that are heterozygous at a site for the dominance term to be included. If the number of hets is less than minHets at a site, an additive only model will be fit for that site.
public StepwiseAdditiveModelFitterPlugin minHets(java.lang.Integer value)
Set Minimum number of heterozygotes. The minimum number of individuals that are heterozygous at a site for the dominance term to be included. If the number of hets is less than minHets at a site, an additive only model will be fit for that site.
value - Minimum number of heterozygotespublic java.lang.Boolean imputedDominance()
Should the plugin impute a value for dominance if data is missing. If false, the dominance score in the design matrix will be 0 for missing genotypes.
public StepwiseAdditiveModelFitterPlugin imputedDominance(java.lang.Boolean value)
Set Impute Dominance Score. Should the plugin impute a value for dominance if data is missing. If false, the dominance score in the design matrix will be 0 for missing genotypes.
value - Impute Dominance Score