def fit_alternative_model(self): ibd_model = MixedModel(self.pedigrees, outcome=self.outcome, fixed_effects=self.fixed_effects) ibd_model.add_genetic_effect() ranef = RandomEffect(self.analysis_individuals, 'IBD', incidence_matrix='eye', covariance_matrix=self.ibd_matrix) ibd_model.add_random_effect(ranef) ibd_model.fit_model() ibd_model.maximize(verbose=self.verbose, method=self.maximization) return ibd_model
def vc_linkage(locus): ibd_model = MixedModel( peds, outcome=args.outcome, fixed_effects=args.fixefs) add_relat_mat = null_model.covariance_matrices[0] additive = RandomEffect(analysis_individuals, 'additive', incidence_matrix='eye', covariance_matrix=add_relat_mat) ibdmat = sgs.ibd_matrix(analysis_individuals, locus, location_type='index', onlywithin=args.onlywithin) ranef = RandomEffect(analysis_individuals, 'IBD', incidence_matrix='eye', covariance_matrix=ibdmat) ibd_model.add_random_effect(additive) ibd_model.add_random_effect(ranef) ibd_model.fit_model() ibd_model.maximize( verbose=args.verbose, method=args.maxmethod, starts=args.starts) return ibd_model