コード例 #1
0
class AbstractPublicationBiasWizard(QtGui.QWizard):
    def __init__(self, model, parent=None):
        super(AbstractPublicationBiasWizard, self).__init__(parent)
    
        self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True)
    
        self.model = model
        self.last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type

        # Initialize pages that we will need to access later
        self.data_location_page = DataLocationPage(model=model)
        self.setPage(Page_DataLocation, self.data_location_page)
        
        self.refine_studies_page = RefineStudiesPage(model=model)
        self.setPage(Page_RefineStudies, self.refine_studies_page)
        
        self.summary_page = SummaryPage()
        self.setPage(Page_Summary, self.summary_page)

        self.setWizardStyle(QWizard.ClassicStyle)

        QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size)
    
    def _change_size(self, pageid):
        print("changing size")
        self.adjustSize()
        
    def nextId(self):   
        raise NotImplementedError("Not implemented")
        
    #### Getters
    
    # Data location
    def get_data_location(self):
        return self.data_location_page.get_data_locations()
    
    # 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
    
    def save_selections(self): # returns a bool
        # Should the selections be saved? 
        return self.summary_page.save_selections()
コード例 #2
0
ファイル: permutation_wizard.py プロジェクト: gdietz/OpenMEE
    def setup_pages(self, model, last_analysis):
        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)
        
        self.data_location_page = DataLocationPage(model=model)
        self.setPage(Page_DataLocation, self.data_location_page)
        
        self.refine_studies_page = RefineStudiesPage(model=model)
        self.setPage(Page_RefineStudies, self.refine_studies_page)
        
        self.meta_reg_details_page = MetaRegDetailsPage(
                fixed_effects=last_analysis['fixed_effects'], 
                random_effects_method=last_analysis['random_effects_method'],
                analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
                conf_level=last_analysis['conf_level'],
                phylogen=last_analysis['phylogen'],
                disable_analysis_type_groupbox=True,
                disable_output_type_groupbox=True)
        self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
        
        self.ma_details_page = MADetailsPage()
        self.setPage(Page_MADetails, self.ma_details_page)

        self.perm_pg = PermuationPage()
        self.setPage(Page_Permutation, self.perm_pg)

        self.select_covariates_page = SelectCovariatesPage(
                model=model,
                previously_included_covs=last_analysis['included_covariates'],
                disable_require_categorical=True)
        self.setPage(Page_SelectCovariates, self.select_covariates_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)
        
        self.summary_page = SummaryPage()
        self.setPage(Page_Summary, self.summary_page)
コード例 #3
0
    def __init__(self, model, parent=None):
        super(AbstractPublicationBiasWizard, self).__init__(parent)
    
        self.setOption(QWizard.HaveFinishButtonOnEarlyPages,True)
    
        self.model = model
        self.last_analysis = model.get_last_analysis_selections() # selections from last analysis of whatever type

        # Initialize pages that we will need to access later
        self.data_location_page = DataLocationPage(model=model)
        self.setPage(Page_DataLocation, self.data_location_page)
        
        self.refine_studies_page = RefineStudiesPage(model=model)
        self.setPage(Page_RefineStudies, self.refine_studies_page)
        
        self.summary_page = SummaryPage()
        self.setPage(Page_Summary, self.summary_page)

        self.setWizardStyle(QWizard.ClassicStyle)

        QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size)
コード例 #4
0
ファイル: dynamic_wizard.py プロジェクト: gdietz/OpenMEE
    def _create_wizard_pages(self):
        '''
        Initialize wizard pages specified by wizard parameters
        '''

        print "wizard parameters: %s" % str(self.wizard_parameters)

        for page_key, page_parameters in self.wizard_parameters['WIZARD.PAGES'].items():
            page_arguments = {}
            print "page key: %s, page parameters: %s" % (page_key, str(page_parameters))
            if page_key == 'DATALOCATION':
                if 'SHOW.RAW.DATA' in page_parameters:
                    page_arguments['show_raw_data'] = page_parameters['SHOW.RAW.DATA']
                    print "Page arguments: %s" % str(page_arguments)
                self.data_location_page = DataLocationPage(model=self.model, **page_arguments)
                self.setPage(Page_DataLocation, self.data_location_page)
            elif page_key == 'REFINESTUDIES':
                self.refine_studies_page = RefineStudiesPage(model=self.model)
                self.setPage(Page_RefineStudies, self.refine_studies_page)
            elif page_key == 'SUMMARY':
                self.summary_page = SummaryPage()
                self.setPage(Page_Summary, self.summary_page)
コード例 #5
0
class MetaRegressionWizard(QtGui.QWizard):
    def __init__(self, model, parent=None):
        super(MetaRegressionWizard, self).__init__(parent)
        
        self.model = model
        last_analysis=model.get_last_analysis_selections()
        
        self.analysis_label = "Meta-Regression"
        self.setWindowTitle(self.analysis_label)
    
        self.setup_pages(model=model, last_analysis=last_analysis)
        
        self.setWizardStyle(QWizard.ClassicStyle)
        # Automatically resize wizard on each page flip
        self.currentIdChanged.connect(self._change_size)
        
    
    def _change_size(self, pageid):
        print("changing size")
        self.adjustSize()
        
    def setup_pages(self, model, last_analysis):
        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)
        
        self.data_location_page = DataLocationPage(model=model)
        self.setPage(Page_DataLocation, self.data_location_page)
        
        self.refine_studies_page = RefineStudiesPage(model=model)
        self.setPage(Page_RefineStudies, self.refine_studies_page)
        
        self.meta_reg_details_page = MetaRegDetailsPage(
                fixed_effects=last_analysis['fixed_effects'], 
                random_effects_method = last_analysis['random_effects_method'],
                analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
                conf_level=last_analysis['conf_level'],
                phylogen=last_analysis['phylogen'])
        self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
        
        self.select_covariates_page = SelectCovariatesPage(
                model=model,
                previously_included_covs=last_analysis['included_covariates'])
        self.setPage(Page_SelectCovariates, self.select_covariates_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)
        
        self.summary_page = SummaryPage()
        self.setPage(Page_Summary, self.summary_page)
        
        # weird stuff
        self.cond_means_pg = CondMeansPage(model=model)
        self.setPage(Page_CondMeans, self.cond_means_pg)
        
        self.bootstrap_page = BootstrapPage(model=model)
        self.setPage(Page_Bootstrap, self.bootstrap_page)
        
    def _require_categorical(self):
        return self.meta_reg_details_page.get_output_type() == CONDITIONAL_MEANS
        
    def nextId(self):
        current_id = self.currentId()
        
        return self.nextId_helper(current_id)
        
    def nextId_helper(self, page_id):        
        if page_id in [Page_MetaRegDetails, Page_Bootstrap, Page_ReferenceValues]:
            analysis_type = self.get_analysis_type() # PARAMETRIC or BOOTSTRAP
            output_type = self.get_output_type()     # NORMAL or CONDITIONAL_MEANS
        
        if page_id == Page_ChooseEffectSize:
            return Page_DataLocation
        elif page_id == Page_DataLocation:
            return Page_RefineStudies
        elif page_id == Page_RefineStudies:
            return Page_SelectCovariates
        elif page_id == Page_SelectCovariates:
            return Page_MetaRegDetails
        elif page_id == Page_MetaRegDetails:
            if self._categorical_covariates_selected():
                return Page_ReferenceValues
            else:
                if analysis_type == BOOTSTRAP:
                    return Page_Bootstrap
                elif output_type == CONDITIONAL_MEANS:
                    return Page_CondMeans
                else:
                    return Page_Summary
        elif page_id == Page_Bootstrap:
            if output_type == CONDITIONAL_MEANS:
                return Page_CondMeans
            else:
                return Page_Summary 
        elif page_id == Page_CondMeans:
            return Page_Summary
        elif page_id == Page_ReferenceValues:
            if analysis_type == BOOTSTRAP:
                return Page_Bootstrap
            elif output_type == CONDITIONAL_MEANS:
                return Page_CondMeans
            else:
                return Page_Summary
        elif page_id == Page_Summary:
            return -1
        

    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
    
    ################ Getters to get data from wizard #########################
    
    # 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()
    
    # Data location page
    def get_data_location(self):
        return self.data_location_page.get_data_locations()
    
    # 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
    
    # Select covariates Page
    def get_included_covariates(self):
        return self.select_covariates_page.get_included_covariates()
    def get_included_interactions(self):
        return self.select_covariates_page.get_interactions()
    
    # Meta regression details page
    def using_fixed_effects(self):
        return self.meta_reg_details_page.get_using_fixed_effects()
    def get_conf_level(self):
        return self.meta_reg_details_page.get_confidence_level()
    def get_random_effects_method(self):
        return self.meta_reg_details_page.get_random_effects_method()
    def get_phylogen(self):
        return self.meta_reg_details_page.get_phylogen()
    def get_analysis_type(self): # NORMAL or BOOTSTRAP
        return self.meta_reg_details_page.get_analysis_type()
    def get_output_type(self): # PARAMETRIC or CONDITIONAL_MEANS
        return self.meta_reg_details_page.get_output_type()
    def get_btt(self): # (a var or interaction, None, 'covariate', 'interaction' i.e. the type)
        return self.meta_reg_details_page.get_btt()
        
    # Reference Values page
    def get_covariate_reference_levels(self):
        return self.reference_value_page.get_covariate_reference_levels()
    
    # Conditional Means page
    def get_meta_reg_cond_means_info(self):
        # returns a tuple (cat. cov to stratify over, the values for the other covariates)
        return self.cond_means_pg.get_meta_reg_cond_means_data()
    
    # Bootstrap page
    def get_bootstrap_params(self):
        return self.bootstrap_page.get_bootstrap_params()

    # Summary page
    def save_selections(self):
        return self.summary_page.save_selections()
    
    ######################### end of getters #################################

    # 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 '''
        summary = wizard_summary(
            wizard=self,
            next_id_helper=self.nextId_helper,
            summary_page_id=Page_Summary,
            analysis_label=self.analysis_label
        )
        return summary
コード例 #6
0
ファイル: dynamic_wizard.py プロジェクト: gdietz/OpenMEE
class DynamicWizard(QtGui.QWizard):
    def __init__(self, model, wizard_parameters, parent=None):
        super(DynamicWizard, self).__init__(parent)

        self.model = model
        self.wizard_parameters = wizard_parameters

        self.setWindowTitle(self.wizard_parameters['WIZARD.WINDOW.TITLE'])
        self.setWizardStyle(QWizard.ClassicStyle)

        self._create_wizard_pages()
        QObject.connect(self, SIGNAL("currentIdChanged(int)"), self._change_size)
    
    def _change_size(self, pageid):
        print("changing size")
        self.adjustSize()

    def _create_wizard_pages(self):
        '''
        Initialize wizard pages specified by wizard parameters
        '''

        print "wizard parameters: %s" % str(self.wizard_parameters)

        for page_key, page_parameters in self.wizard_parameters['WIZARD.PAGES'].items():
            page_arguments = {}
            print "page key: %s, page parameters: %s" % (page_key, str(page_parameters))
            if page_key == 'DATALOCATION':
                if 'SHOW.RAW.DATA' in page_parameters:
                    page_arguments['show_raw_data'] = page_parameters['SHOW.RAW.DATA']
                    print "Page arguments: %s" % str(page_arguments)
                self.data_location_page = DataLocationPage(model=self.model, **page_arguments)
                self.setPage(Page_DataLocation, self.data_location_page)
            elif page_key == 'REFINESTUDIES':
                self.refine_studies_page = RefineStudiesPage(model=self.model)
                self.setPage(Page_RefineStudies, self.refine_studies_page)
            elif page_key == 'SUMMARY':
                self.summary_page = SummaryPage()
                self.setPage(Page_Summary, self.summary_page)

    def nextId(self):
        page_id = self.currentId()
        
        return self.next_id_helper(page_id)
        
    def next_id_helper(self, page_id):
        pages = self.wizard_parameters['WIZARD.PAGES'].keys() # pages in order
        pageids = [pageid[pagekey] for pagekey in pages]

        currentpageindex = pageids.index(page_id)

        if currentpageindex == len(pageids) - 1:
            # End wizard if on last page
            return -1

        # go to next page
        return pageids[currentpageindex+1]

    #### Getters
    
    # Data location
    def get_data_location(self):
        return self.data_location_page.get_data_locations()
    
    # 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

    # 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.next_id_helper,
                              summary_page_id=Page_Summary,
                              analysis_label="Failsafe Analysis")

    def save_selections(self): # returns a bool
        # Should the selections be saved? 
        return self.summary_page.save_selections()
コード例 #7
0
ファイル: permutation_wizard.py プロジェクト: gdietz/OpenMEE
class PermutationWizard(QtGui.QWizard):
    # if meta_reg mode is True, the wizard will do a permutation
    # test for a meta-regression, otherwise it does a standard 
    # meta-analysis
    def __init__(self, model, meta_reg_mode=False, parent=None):
        super(PermutationWizard, self).__init__(parent)
        
        self.model = model
        last_analysis = model.get_last_analysis_selections()
        self.meta_reg_mode = meta_reg_mode

        # Set window title
        if meta_reg_mode:
            self.analysis_label = "Permuted Meta-Regression"
        else:
            self.analysis_label = "Permuted Meta-Analysis"
        self.setWindowTitle(self.analysis_label)

        self.setup_pages(model=model, last_analysis=last_analysis)
        
        self.setWizardStyle(QWizard.ClassicStyle)
        # Automatically resize wizard on each page flip
        self.currentIdChanged.connect(self.adjustSize)

    def setup_pages(self, model, last_analysis):
        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)
        
        self.data_location_page = DataLocationPage(model=model)
        self.setPage(Page_DataLocation, self.data_location_page)
        
        self.refine_studies_page = RefineStudiesPage(model=model)
        self.setPage(Page_RefineStudies, self.refine_studies_page)
        
        self.meta_reg_details_page = MetaRegDetailsPage(
                fixed_effects=last_analysis['fixed_effects'], 
                random_effects_method=last_analysis['random_effects_method'],
                analysis_type=last_analysis['analysis_type'], # PARAMETRIC or BOOTSTRAP
                conf_level=last_analysis['conf_level'],
                phylogen=last_analysis['phylogen'],
                disable_analysis_type_groupbox=True,
                disable_output_type_groupbox=True)
        self.setPage(Page_MetaRegDetails, self.meta_reg_details_page)
        
        self.ma_details_page = MADetailsPage()
        self.setPage(Page_MADetails, self.ma_details_page)

        self.perm_pg = PermuationPage()
        self.setPage(Page_Permutation, self.perm_pg)

        self.select_covariates_page = SelectCovariatesPage(
                model=model,
                previously_included_covs=last_analysis['included_covariates'],
                disable_require_categorical=True)
        self.setPage(Page_SelectCovariates, self.select_covariates_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)
        
        self.summary_page = SummaryPage()
        self.setPage(Page_Summary, self.summary_page)
        
    def nextId(self):
        current_id = self.currentId()
        return self.nextId_helper(current_id)
        
    def nextId_helper(self, page_id):

        if self.meta_reg_mode:
            if page_id == Page_ChooseEffectSize:
                return Page_DataLocation
            elif page_id == Page_DataLocation:
                return Page_RefineStudies
            elif page_id == Page_RefineStudies:
                return Page_SelectCovariates
            elif page_id == Page_SelectCovariates:
                return Page_MetaRegDetails
            elif page_id == Page_MetaRegDetails:
                if self._categorical_covariates_selected():
                    return Page_ReferenceValues
                else:
                    return Page_Permutation
            elif page_id == Page_ReferenceValues:
                return Page_Permutation
            elif page_id == Page_Permutation:
                return Page_Summary
            elif page_id == Page_Summary:
                return -1
        else: # non-meta regression mode (no moderators)
            if page_id == Page_ChooseEffectSize:
                return Page_DataLocation
            elif page_id == Page_DataLocation:
                return Page_RefineStudies
            elif page_id == Page_RefineStudies:
                return Page_MADetails
            elif page_id == Page_MADetails:
                return Page_Permutation
            elif page_id == Page_ReferenceValues:
                return Page_Permutation
            elif page_id == Page_Permutation:
                return Page_Summary
            elif page_id == Page_Summary:
                return -1

    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
        
    ################# getters #########################
    def get_parameters(self):
        data_type_and_metric = self.choose_effect_size_page.get_data_type_and_metric()
        data_location = self.data_location_page.get_data_locations()
        studies = self.refine_studies_page.get_included_studies_in_proper_order()

        parameters = {
            'data_type_and_metric': data_type_and_metric,
            'data_location': data_location,
            'studies': studies,
        }
        
        parameters.update(self.perm_pg.get_choices())

        # meta-regression specific
        if self.meta_reg_mode:
            covariates = self.select_covariates_page.get_included_covariates()
            interactions = self.select_covariates_page.get_interactions()
            _fixed_effects = self.meta_reg_details_page.get_using_fixed_effects()
            level = self.meta_reg_details_page.get_confidence_level()
            _random_effects_method = self.meta_reg_details_page.get_random_effects_method()
            method = _random_effects_method if not _fixed_effects else FIXED_EFFECTS_METHOD_STR
            phylogen = self.meta_reg_details_page.get_phylogen()
            btt = self.meta_reg_details_page.get_btt()
            reference_values = self.reference_value_page.get_covariate_reference_levels()

            parameters.update({
                'covariates': covariates,
                'interactions': interactions,
                'level': level,
                'method': method,
                'phylogen': phylogen,
                'btt': btt,
                'reference_values': reference_values,
            })
        else:
            # ma specific (no moderators)
            method = self.ma_details_page.get_method()
            intercept = self.ma_details_page.get_intercept()
            weighted = self.ma_details_page.get_weighted_least_squares()
            knha = self.ma_details_page.get_knha()
            level = self.ma_details_page.get_confidence_level()
            digits = self.ma_details_page.get_digits()

            parameters.update({
                'method':method,
                'intercept':intercept,
                'weighted':weighted,
                'knha':knha,
                'level':level,
                'digits':digits,
            })
        return parameters

    # Summary page
    def save_selections(self):
        return self.summary_page.save_selections()
    
    # 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()
    
    # Data location page
    def get_data_location(self):
        return self.data_location_page.get_data_locations()
    
    # 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
    
    # Select covariates Page
    def get_included_covariates(self):
        return self.select_covariates_page.get_included_covariates()
    def get_included_interactions(self):
        return self.select_covariates_page.get_interactions()
    
    ######################### end of getters #################################

    # 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 '''
        summary = wizard_summary(
            wizard=self,
            next_id_helper=self.nextId_helper,
            summary_page_id=Page_Summary,
            analysis_label=self.analysis_label
        )
        return summary
コード例 #8
0
 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")
コード例 #9
0
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)