def __init__(self, model, parent=None): super(MiMaWizard, self).__init__(parent) self.analysis_label = "Multiply-Imputed Meta Analysis/Regression" self.model = model self.imp_results = None last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type # Initialize pages that we will need to access later self.parameters_page = MetaAnalysisParametersPage(method="FE" if last_analysis['fixed_effects'] else last_analysis['random_effects_method'], level=model.get_conf_level(), digits=model.get_precision(), knha=last_analysis['knha']) self.setPage(Page_Parameters, self.parameters_page) # choose effect size self.choose_effect_size_page = ChooseEffectSizePage(add_generic_effect=True, data_type=last_analysis['data_type'], metric=last_analysis['metric'], var_groups = model.get_variable_groups()) self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page) # data location page self.data_location_page = DataLocationPage(model=model) self.setPage(Page_DataLocation, self.data_location_page) # refine studies page self.refine_studies_page = RefineStudiesPage(model=model) self.setPage(Page_RefineStudies, self.refine_studies_page) # summary page self.summary_page = SummaryPage() self.setPage(Page_Summary, self.summary_page) # Mice Parameters Page self.mice_params_page = MiceParametersPage() self.setPage(Page_MiceParameters, self.mice_params_page) # Covariate Select Page (for choosing covariates to impute with) self.cov_select_page = CovariateSelectPage(model = self.model) self.setPage(Page_CovariateSelect, self.cov_select_page) # Select Covariates page (for choosing covariates to do with regression with) self.select_covariates_page = SelectCovariatesPage( model=model, previously_included_covs=last_analysis['included_covariates'], min_covariates=0, allow_covs_with_missing_data=True) self.setPage(Page_SelectCovariates, self.select_covariates_page) # Reference Value Page self.reference_value_page = ReferenceValuePage( model=model, prev_cov_to_ref_level=last_analysis['cov_2_ref_values']) self.setPage(Page_ReferenceValues, self.reference_value_page) # Mice Output page self.mice_output_page = MiceOutputPage() self.setPage(Page_MiceOutput, self.mice_output_page) self.setWizardStyle(QWizard.ClassicStyle) self.setStartId(Page_ChooseEffectSize) self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True) QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size) self.setWindowTitle("Multiply-Imputed Meta-Analysis")
class MiMaWizard(QtGui.QWizard): def __init__(self, model, parent=None): super(MiMaWizard, self).__init__(parent) self.analysis_label = "Multiply-Imputed Meta Analysis/Regression" self.model = model self.imp_results = None last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type # Initialize pages that we will need to access later self.parameters_page = MetaAnalysisParametersPage(method="FE" if last_analysis['fixed_effects'] else last_analysis['random_effects_method'], level=model.get_conf_level(), digits=model.get_precision(), knha=last_analysis['knha']) self.setPage(Page_Parameters, self.parameters_page) # choose effect size self.choose_effect_size_page = ChooseEffectSizePage(add_generic_effect=True, data_type=last_analysis['data_type'], metric=last_analysis['metric'], var_groups = model.get_variable_groups()) self.setPage(Page_ChooseEffectSize, self.choose_effect_size_page) # data location page self.data_location_page = DataLocationPage(model=model) self.setPage(Page_DataLocation, self.data_location_page) # refine studies page self.refine_studies_page = RefineStudiesPage(model=model) self.setPage(Page_RefineStudies, self.refine_studies_page) # summary page self.summary_page = SummaryPage() self.setPage(Page_Summary, self.summary_page) # Mice Parameters Page self.mice_params_page = MiceParametersPage() self.setPage(Page_MiceParameters, self.mice_params_page) # Covariate Select Page (for choosing covariates to impute with) self.cov_select_page = CovariateSelectPage(model = self.model) self.setPage(Page_CovariateSelect, self.cov_select_page) # Select Covariates page (for choosing covariates to do with regression with) self.select_covariates_page = SelectCovariatesPage( model=model, previously_included_covs=last_analysis['included_covariates'], min_covariates=0, allow_covs_with_missing_data=True) self.setPage(Page_SelectCovariates, self.select_covariates_page) # Reference Value Page self.reference_value_page = ReferenceValuePage( model=model, prev_cov_to_ref_level=last_analysis['cov_2_ref_values']) self.setPage(Page_ReferenceValues, self.reference_value_page) # Mice Output page self.mice_output_page = MiceOutputPage() self.setPage(Page_MiceOutput, self.mice_output_page) self.setWizardStyle(QWizard.ClassicStyle) self.setStartId(Page_ChooseEffectSize) self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True) QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size) self.setWindowTitle("Multiply-Imputed Meta-Analysis") # Meta analysis nextID def nextId_helper(self, page_id): if page_id == Page_ChooseEffectSize: return Page_DataLocation elif page_id == Page_DataLocation: return Page_RefineStudies elif page_id == Page_RefineStudies: return Page_Parameters elif page_id == Page_Parameters: # meta analysis parameters return Page_MiceParameters elif page_id == Page_MiceParameters: # mice parameters return Page_CovariateSelect elif page_id == Page_CovariateSelect: return Page_MiceOutput elif page_id == Page_MiceOutput: return Page_SelectCovariates elif page_id == Page_SelectCovariates: if self._categorical_covariates_selected(): return Page_ReferenceValues else: return Page_Summary elif page_id == Page_ReferenceValues: return Page_Summary elif page_id == Page_Summary: return -1 def nextId(self): next_id = self.nextId_helper(self.currentId()) return next_id def _change_size(self, pageid): print("changing size") self.adjustSize() def _require_categorical(self): # just to make select covariates page happy return False def _categorical_covariates_selected(self): '''are categorical variables selected?''' included_covariates = self.get_included_covariates() categorical_covariates = [cov for cov in included_covariates if cov.get_type()==CATEGORICAL] return len(categorical_covariates) > 0 # My details page def get_analysis_parameters(self): return self.parameters_page.get_parameters() # refine studies page def get_included_studies_in_proper_order(self): all_studies = self.model.get_studies_in_current_order() included_studies = self.refine_studies_page.get_included_studies() included_studies_in_order = [study for study in all_studies if study in included_studies] return included_studies_in_order # data location page def get_data_location(self): return self.data_location_page.get_data_locations() # choose effect size page def get_data_type_and_metric(self): ''' returns tuple (data_type, metric) ''' return self.choose_effect_size_page.get_data_type_and_metric() def _run_imputation(self): imp_results = python_to_R.impute(model=self.model, studies=self.get_included_studies_in_proper_order(), covariates=self.get_covariates_for_imputation(), m=self.get_m(), maxit=self.get_maxit(), defaultMethod_rstring=self.get_defaultMethod_rstring()) self.imp_results = imp_results return imp_results def get_imputation_summary(self): return self.imp_results['summary'] # def get_imputation_choices(self): # covariates = self.get_included_covariates() # covariates in original order # # imputation_choices = python_to_R.imputation_dataframes_to_pylist_of_ordered_dicts( # self.imp_results['imputations'], # covariates) # return imputation_choices def get_source_data(self): # an ordered dict mapping covariates --> values to see which ones are # none return self.imp_results['source_data'] def get_imputations(self): return self.imp_results['imputations'] # R list of imputations ######## getters ########### ### Covariate Select Page def get_covariates_for_imputation(self): return self.cov_select_page.get_included_covariates() ### Mice Parameters Page def get_m(self): # number of multiple imputations return self.mice_params_page.get_m() def get_maxit(self): # number of iterations return self.mice_params_page.get_maxit() def get_defaultMethod_rstring(self): return self.mice_params_page.get_defaultMethod_rstring() ### Reference values page def get_covariate_reference_levels(self): return self.reference_value_page.get_covariate_reference_levels() # Select covariates Page def get_included_covariates(self): # covariates for regression (not imputation) return self.select_covariates_page.get_included_covariates() def get_included_interactions(self): return self.select_covariates_page.get_interactions() # Summary page def save_selections(self): return self.summary_page.save_selections() # Summary Page def get_summary(self): ''' Make a summary string to show the user at the end of the wizard summarizing most of the user selections ''' return wizard_summary(wizard=self, next_id_helper=self.nextId_helper, summary_page_id=Page_Summary, analysis_label=self.analysis_label)